Starting phenix.real_space_refine on Fri Feb 23 19:42:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ct5_30460/02_2024/7ct5_30460.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ct5_30460/02_2024/7ct5_30460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ct5_30460/02_2024/7ct5_30460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ct5_30460/02_2024/7ct5_30460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ct5_30460/02_2024/7ct5_30460.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ct5_30460/02_2024/7ct5_30460.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 195 5.16 5 C 25220 2.51 5 N 6443 2.21 5 O 7768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 214": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 408": "NH1" <-> "NH2" 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 TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 918": "OE1" <-> "OE2" 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 214": "NH1" <-> "NH2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D GLU 232": "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 433": "OE1" <-> "OE2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E GLU 232": "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 433": "OE1" <-> "OE2" Residue "E GLU 435": "OE1" <-> "OE2" Residue "E ARG 518": "NH1" <-> "NH2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F GLU 35": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F GLU 232": "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 433": "OE1" <-> "OE2" Residue "F GLU 435": "OE1" <-> "OE2" Residue "F 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: 39626 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7870 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 49, 'TRANS': 957} Chain breaks: 8 Chain: "C" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7866 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "E" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "F" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 19.56, per 1000 atoms: 0.49 Number of scatterers: 39626 At special positions: 0 Unit cell: (182.616, 194.573, 241.314, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 195 16.00 O 7768 8.00 N 6443 7.00 C 25220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.57 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.40 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.19 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.82 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.20 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=1.86 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.25 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.05 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.04 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.05 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.04 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.05 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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 B1406 " - " NAG B1407 " " NAG B1411 " - " NAG B1412 " " NAG C1406 " - " NAG C1407 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 331 " " NAG B1408 " - " ASN B 603 " " NAG B1409 " - " ASN B 616 " " NAG B1410 " - " ASN B 657 " " NAG B1411 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 331 " " NAG C1408 " - " ASN C 603 " " NAG C1409 " - " ASN C 616 " " NAG C1410 " - " ASN C 657 " " NAG D 901 " - " ASN D 322 " " NAG E 901 " - " ASN E 322 " " NAG F 901 " - " ASN F 322 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 343 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 343 " " NAG O 1 " - " ASN B 709 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 343 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " " NAG a 1 " - " ASN D 53 " " NAG b 1 " - " ASN D 90 " " NAG c 1 " - " ASN D 103 " " NAG d 1 " - " ASN D 432 " " NAG e 1 " - " ASN D 546 " " NAG f 1 " - " ASN E 53 " " NAG g 1 " - " ASN E 90 " " NAG h 1 " - " ASN E 103 " " NAG i 1 " - " ASN E 432 " " NAG j 1 " - " ASN E 546 " " NAG k 1 " - " ASN F 53 " " NAG l 1 " - " ASN F 90 " " NAG m 1 " - " ASN F 103 " " NAG n 1 " - " ASN F 432 " " NAG o 1 " - " ASN F 546 " Time building additional restraints: 16.77 Conformation dependent library (CDL) restraints added in 7.5 seconds 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9036 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 53 sheets defined 38.9% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.44 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.153A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.543A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.235A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.631A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.770A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.636A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.644A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.573A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.995A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.628A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.879A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 993 through 1033 removed outlier: 3.687A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.543A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.235A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.963A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.602A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.011A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.372A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.261A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.543A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.236A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.718A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.603A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.591A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.356A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.220A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'D' and resid 22 through 36 removed outlier: 3.520A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP D 30 " --> pdb=" O LYS D 26 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 53 removed outlier: 3.914A pdb=" N GLN D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 78 removed outlier: 3.605A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 82 Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.530A pdb=" N LEU D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.531A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN D 121 " --> pdb=" O ASN D 117 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.629A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 173 removed outlier: 3.746A pdb=" N TRP D 163 " --> pdb=" O ASN D 159 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU D 171 " --> pdb=" O SER D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 4.838A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.698A pdb=" N ARG D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 220 through 252 removed outlier: 3.843A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 4.278A pdb=" N MET D 249 " --> pdb=" O ARG D 245 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.550A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 299 Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.706A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU D 310 " --> pdb=" O ARG D 306 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.791A pdb=" N ASN D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 383 removed outlier: 4.067A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS D 374 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU D 375 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.709A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 411 removed outlier: 3.988A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.557A pdb=" N LEU D 418 " --> pdb=" O THR D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.812A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 465 removed outlier: 3.832A pdb=" N THR D 449 " --> pdb=" O THR D 445 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU D 450 " --> pdb=" O ILE D 446 " (cutoff:3.500A) Proline residue: D 451 - end of helix removed outlier: 3.585A pdb=" N MET D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU D 457 " --> pdb=" O THR D 453 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP D 461 " --> pdb=" O GLU D 457 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 473 removed outlier: 3.616A pdb=" N TRP D 473 " --> pdb=" O LYS D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 484 removed outlier: 3.821A pdb=" N MET D 480 " --> pdb=" O LYS D 476 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 484 " --> pdb=" O MET D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 511 through 514 removed outlier: 4.056A pdb=" N ARG D 514 " --> pdb=" O SER D 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 511 through 514' Processing helix chain 'D' and resid 515 through 533 removed outlier: 4.041A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN D 522 " --> pdb=" O ARG D 518 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA D 528 " --> pdb=" O GLN D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.659A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.839A pdb=" N LEU D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 4.017A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 588 removed outlier: 3.680A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 583 through 588' Processing helix chain 'D' and resid 588 through 596 Processing helix chain 'D' and resid 597 through 600 removed outlier: 3.860A pdb=" N LYS D 600 " --> pdb=" O ASP D 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 597 through 600' Processing helix chain 'E' and resid 22 through 36 removed outlier: 3.520A pdb=" N LYS E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP E 30 " --> pdb=" O LYS E 26 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 53 removed outlier: 3.914A pdb=" N GLN E 42 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER E 47 " --> pdb=" O SER E 43 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN E 51 " --> pdb=" O SER E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 78 removed outlier: 3.605A pdb=" N ASN E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE E 72 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR E 78 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 82 Processing helix chain 'E' and resid 90 through 101 removed outlier: 3.531A pdb=" N LEU E 97 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 removed outlier: 3.532A pdb=" N ASN E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN E 121 " --> pdb=" O ASN E 117 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR E 122 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR E 127 " --> pdb=" O MET E 123 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER E 128 " --> pdb=" O SER E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.629A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 170 removed outlier: 3.746A pdb=" N TRP E 163 " --> pdb=" O ASN E 159 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 4.839A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU E 189 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET E 190 " --> pdb=" O LEU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 removed outlier: 3.697A pdb=" N ARG E 204 " --> pdb=" O GLY E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 207 No H-bonds generated for 'chain 'E' and resid 205 through 207' Processing helix chain 'E' and resid 220 through 252 removed outlier: 3.843A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE E 233 " --> pdb=" O THR E 229 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E 234 " --> pdb=" O PHE E 230 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 4.278A pdb=" N MET E 249 " --> pdb=" O ARG E 245 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.549A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 299 Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.706A pdb=" N ILE E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU E 310 " --> pdb=" O ARG E 306 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE E 315 " --> pdb=" O ALA E 311 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.791A pdb=" N ASN E 330 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 383 removed outlier: 4.068A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS E 374 " --> pdb=" O LEU E 370 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU E 375 " --> pdb=" O THR E 371 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET E 376 " --> pdb=" O ALA E 372 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 removed outlier: 3.709A pdb=" N ARG E 393 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 411 removed outlier: 3.989A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER E 411 " --> pdb=" O ILE E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.558A pdb=" N LEU E 418 " --> pdb=" O THR E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 444 removed outlier: 3.812A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 465 removed outlier: 3.832A pdb=" N THR E 449 " --> pdb=" O THR E 445 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU E 450 " --> pdb=" O ILE E 446 " (cutoff:3.500A) Proline residue: E 451 - end of helix removed outlier: 3.584A pdb=" N MET E 455 " --> pdb=" O PRO E 451 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU E 457 " --> pdb=" O THR E 453 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 473 removed outlier: 3.616A pdb=" N TRP E 473 " --> pdb=" O LYS E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 3.821A pdb=" N MET E 480 " --> pdb=" O LYS E 476 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG E 482 " --> pdb=" O TRP E 478 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE E 484 " --> pdb=" O MET E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 511 through 514 removed outlier: 4.056A pdb=" N ARG E 514 " --> pdb=" O SER E 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 511 through 514' Processing helix chain 'E' and resid 515 through 533 removed outlier: 4.041A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN E 522 " --> pdb=" O ARG E 518 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA E 528 " --> pdb=" O GLN E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 removed outlier: 3.660A pdb=" N CYS E 542 " --> pdb=" O LEU E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 559 removed outlier: 3.839A pdb=" N LEU E 554 " --> pdb=" O ALA E 550 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG E 559 " --> pdb=" O PHE E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 removed outlier: 4.017A pdb=" N GLU E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN E 572 " --> pdb=" O LEU E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 588 removed outlier: 3.680A pdb=" N TYR E 587 " --> pdb=" O PRO E 583 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 583 through 588' Processing helix chain 'E' and resid 588 through 596 Processing helix chain 'F' and resid 22 through 36 removed outlier: 3.521A pdb=" N LYS F 26 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP F 30 " --> pdb=" O LYS F 26 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 53 removed outlier: 3.914A pdb=" N GLN F 42 " --> pdb=" O ASP F 38 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER F 43 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER F 47 " --> pdb=" O SER F 43 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN F 51 " --> pdb=" O SER F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 78 removed outlier: 3.605A pdb=" N ASN F 64 " --> pdb=" O GLN F 60 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE F 72 " --> pdb=" O LYS F 68 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR F 78 " --> pdb=" O LYS F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 82 Processing helix chain 'F' and resid 90 through 101 removed outlier: 3.530A pdb=" N LEU F 97 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 removed outlier: 3.531A pdb=" N ASN F 117 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN F 121 " --> pdb=" O ASN F 117 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR F 122 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR F 127 " --> pdb=" O MET F 123 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER F 128 " --> pdb=" O SER F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 155 removed outlier: 3.628A pdb=" N MET F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 173 removed outlier: 3.745A pdb=" N TRP F 163 " --> pdb=" O ASN F 159 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG F 169 " --> pdb=" O TRP F 165 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 193 removed outlier: 4.837A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU F 189 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET F 190 " --> pdb=" O LEU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 204 removed outlier: 3.698A pdb=" N ARG F 204 " --> pdb=" O GLY F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 207 No H-bonds generated for 'chain 'F' and resid 205 through 207' Processing helix chain 'F' and resid 220 through 252 removed outlier: 3.843A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS F 234 " --> pdb=" O PHE F 230 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 4.278A pdb=" N MET F 249 " --> pdb=" O ARG F 245 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 removed outlier: 3.549A pdb=" N TYR F 279 " --> pdb=" O THR F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 299 Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.706A pdb=" N ILE F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU F 310 " --> pdb=" O ARG F 306 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE F 315 " --> pdb=" O ALA F 311 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY F 319 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.790A pdb=" N ASN F 330 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 383 removed outlier: 4.068A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS F 374 " --> pdb=" O LEU F 370 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU F 375 " --> pdb=" O THR F 371 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS F 378 " --> pdb=" O HIS F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.708A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 411 removed outlier: 3.988A pdb=" N GLY F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU F 406 " --> pdb=" O GLU F 402 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE F 407 " --> pdb=" O ALA F 403 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER F 411 " --> pdb=" O ILE F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 removed outlier: 3.557A pdb=" N LEU F 418 " --> pdb=" O THR F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 444 removed outlier: 3.812A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 465 removed outlier: 3.832A pdb=" N THR F 449 " --> pdb=" O THR F 445 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU F 450 " --> pdb=" O ILE F 446 " (cutoff:3.500A) Proline residue: F 451 - end of helix removed outlier: 3.585A pdb=" N MET F 455 " --> pdb=" O PRO F 451 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU F 457 " --> pdb=" O THR F 453 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP F 461 " --> pdb=" O GLU F 457 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET F 462 " --> pdb=" O LYS F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 473 removed outlier: 3.615A pdb=" N TRP F 473 " --> pdb=" O LYS F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 484 removed outlier: 3.821A pdb=" N MET F 480 " --> pdb=" O LYS F 476 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG F 482 " --> pdb=" O TRP F 478 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE F 484 " --> pdb=" O MET F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 511 through 514 removed outlier: 4.056A pdb=" N ARG F 514 " --> pdb=" O SER F 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 511 through 514' Processing helix chain 'F' and resid 515 through 533 removed outlier: 4.041A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN F 522 " --> pdb=" O ARG F 518 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN F 524 " --> pdb=" O LEU F 520 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA F 528 " --> pdb=" O GLN F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 3.660A pdb=" N CYS F 542 " --> pdb=" O LEU F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 559 removed outlier: 3.838A pdb=" N LEU F 554 " --> pdb=" O ALA F 550 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG F 559 " --> pdb=" O PHE F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 572 removed outlier: 4.018A pdb=" N GLU F 571 " --> pdb=" O THR F 567 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN F 572 " --> pdb=" O LEU F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 588 removed outlier: 3.680A pdb=" N TYR F 587 " --> pdb=" O PRO F 583 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE F 588 " --> pdb=" O LEU F 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 583 through 588' Processing helix chain 'F' and resid 588 through 596 Processing helix chain 'F' and resid 597 through 600 removed outlier: 3.860A pdb=" N LYS F 600 " --> pdb=" O ASP F 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 597 through 600' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.059A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.570A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 319 removed outlier: 5.930A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.672A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.338A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 653 through 655 Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.570A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 319 removed outlier: 6.314A pdb=" N LYS B 310 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLY B 601 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.672A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 539 through 543 removed outlier: 5.567A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.220A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.059A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.569A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.671A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 539 through 543 removed outlier: 5.338A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 597 through 598 Processing sheet with id=AE4, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.426A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.566A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AF1, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.651A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.642A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 132 through 133 Processing sheet with id=AF4, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.652A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.642A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AF7, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.651A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.642A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) 1383 hydrogen bonds defined for protein. 3867 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.85 Time building geometry restraints manager: 17.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12228 1.34 - 1.46: 10623 1.46 - 1.59: 17428 1.59 - 1.72: 0 1.72 - 1.84: 285 Bond restraints: 40564 Sorted by residual: bond pdb=" C ASP A 985 " pdb=" N PRO A 986 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.18e-02 7.18e+03 2.43e+01 bond pdb=" C PHE B 329 " pdb=" N PRO B 330 " ideal model delta sigma weight residual 1.332 1.389 -0.057 1.33e-02 5.65e+03 1.85e+01 bond pdb=" N PRO B 589 " pdb=" CD PRO B 589 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.85e+01 bond pdb=" N PRO A 986 " pdb=" CD PRO A 986 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.84e+01 bond pdb=" N PRO A 589 " pdb=" CD PRO A 589 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.83e+01 ... (remaining 40559 not shown) Histogram of bond angle deviations from ideal: 97.57 - 105.76: 848 105.76 - 113.95: 23581 113.95 - 122.14: 23420 122.14 - 130.34: 7102 130.34 - 138.53: 197 Bond angle restraints: 55148 Sorted by residual: angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.87 -11.33 1.91e+00 2.74e-01 3.52e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.83 -11.29 1.91e+00 2.74e-01 3.49e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.79 -11.25 1.91e+00 2.74e-01 3.47e+01 angle pdb=" C ASP A 985 " pdb=" N PRO A 986 " pdb=" CA PRO A 986 " ideal model delta sigma weight residual 120.38 114.37 6.01 1.03e+00 9.43e-01 3.40e+01 angle pdb=" C PHE B 329 " pdb=" N PRO B 330 " pdb=" CA PRO B 330 " ideal model delta sigma weight residual 119.89 114.08 5.81 1.02e+00 9.61e-01 3.25e+01 ... (remaining 55143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 21950 17.92 - 35.83: 2513 35.83 - 53.75: 701 53.75 - 71.67: 211 71.67 - 89.58: 67 Dihedral angle restraints: 25442 sinusoidal: 11416 harmonic: 14026 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -171.93 85.93 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -171.91 85.91 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -171.91 85.91 1 1.00e+01 1.00e-02 8.92e+01 ... (remaining 25439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 6365 0.328 - 0.655: 6 0.655 - 0.983: 4 0.983 - 1.310: 1 1.310 - 1.638: 1 Chirality restraints: 6377 Sorted by residual: chirality pdb=" C1 NAG C1407 " pdb=" O4 NAG C1406 " pdb=" C2 NAG C1407 " pdb=" O5 NAG C1407 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-02 2.50e+03 1.97e+03 chirality pdb=" C1 NAG B1407 " pdb=" O4 NAG B1406 " pdb=" C2 NAG B1407 " pdb=" O5 NAG B1407 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-02 2.50e+03 1.45e+03 chirality pdb=" C1 NAG B1412 " pdb=" O4 NAG B1411 " pdb=" C2 NAG B1412 " pdb=" O5 NAG B1412 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 ... (remaining 6374 not shown) Planarity restraints: 7067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.136 2.00e-02 2.50e+03 1.69e-01 3.58e+02 pdb=" CG ASN C 331 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.290 2.00e-02 2.50e+03 pdb=" C1 NAG C1406 " 0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.073 2.00e-02 2.50e+03 1.23e-01 1.88e+02 pdb=" CG ASN B 331 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.050 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.221 2.00e-02 2.50e+03 pdb=" C1 NAG B1406 " 0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 709 " 0.049 2.00e-02 2.50e+03 5.49e-02 3.77e+01 pdb=" CG ASN C 709 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN C 709 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN C 709 " -0.091 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " 0.063 2.00e-02 2.50e+03 ... (remaining 7064 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 464 2.55 - 3.14: 30316 3.14 - 3.72: 60929 3.72 - 4.31: 86300 4.31 - 4.90: 139306 Nonbonded interactions: 317315 Sorted by model distance: nonbonded pdb=" O ALA C 701 " pdb=" O GLU C 702 " model vdw 1.960 3.040 nonbonded pdb=" O VAL A 524 " pdb=" SG CYS A 525 " model vdw 2.157 3.400 nonbonded pdb=" O VAL A 327 " pdb=" CD ARG A 328 " model vdw 2.177 3.440 nonbonded pdb=" OG SER C 708 " pdb=" N ASN C 709 " model vdw 2.180 2.520 nonbonded pdb=" O SER A 813 " pdb=" OG SER A 813 " model vdw 2.183 2.440 ... (remaining 317310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 620 or resid 640 through 939 or resid 944 throu \ gh 1146 or resid 1401 through 1409)) selection = (chain 'B' and (resid 27 through 620 or resid 640 through 826 or resid 855 throu \ gh 1146 or resid 1401 through 1409)) selection = (chain 'C' and (resid 27 through 620 or resid 640 through 826 or resid 855 throu \ gh 1146 or resid 1401 through 1409)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 7.670 Check model and map are aligned: 0.600 Set scattering table: 0.380 Process input model: 102.000 Find NCS groups from input model: 3.050 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: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.117 40564 Z= 0.617 Angle : 1.025 13.528 55148 Z= 0.578 Chirality : 0.070 1.638 6377 Planarity : 0.007 0.080 7001 Dihedral : 17.084 89.585 16262 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.95 % Allowed : 8.90 % Favored : 90.16 % Rotamer: Outliers : 7.37 % Allowed : 14.68 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.38 (0.10), residues: 4744 helix: -3.31 (0.09), residues: 1554 sheet: -2.19 (0.18), residues: 703 loop : -2.86 (0.10), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 104 HIS 0.009 0.002 HIS A1048 PHE 0.025 0.003 PHE A 898 TYR 0.026 0.003 TYR B1067 ARG 0.012 0.001 ARG F 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 904 time to evaluate : 4.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.7587 (mt) cc_final: 0.7296 (mp) REVERT: A 105 ILE cc_start: 0.8388 (pt) cc_final: 0.7687 (mt) REVERT: A 153 MET cc_start: 0.1425 (mpp) cc_final: 0.1019 (ptm) REVERT: A 360 ASN cc_start: 0.7839 (m110) cc_final: 0.7166 (p0) REVERT: A 492 LEU cc_start: -0.0163 (OUTLIER) cc_final: -0.0374 (mt) REVERT: A 698 SER cc_start: 0.7648 (OUTLIER) cc_final: 0.7364 (t) REVERT: A 736 VAL cc_start: 0.6879 (m) cc_final: 0.6638 (t) REVERT: A 763 LEU cc_start: 0.8375 (mt) cc_final: 0.8050 (mt) REVERT: A 988 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6333 (mp0) REVERT: B 158 ARG cc_start: 0.5631 (OUTLIER) cc_final: 0.5232 (mmm160) REVERT: B 226 LEU cc_start: 0.7845 (tp) cc_final: 0.7541 (tp) REVERT: B 556 ASN cc_start: 0.5868 (OUTLIER) cc_final: 0.5343 (p0) REVERT: B 887 THR cc_start: 0.8369 (p) cc_final: 0.8124 (m) REVERT: C 492 LEU cc_start: 0.4956 (OUTLIER) cc_final: 0.4737 (mm) REVERT: C 529 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6300 (mmtt) REVERT: C 1042 PHE cc_start: 0.7964 (t80) cc_final: 0.7749 (t80) REVERT: C 1136 THR cc_start: 0.7163 (OUTLIER) cc_final: 0.6957 (t) REVERT: D 383 MET cc_start: 0.5806 (mtp) cc_final: 0.4069 (ppp) REVERT: E 133 CYS cc_start: -0.2908 (OUTLIER) cc_final: -0.3532 (p) REVERT: E 455 MET cc_start: -0.0893 (tmm) cc_final: -0.1161 (tmm) REVERT: E 574 VAL cc_start: 0.0831 (t) cc_final: 0.0602 (t) REVERT: F 82 MET cc_start: 0.3023 (ttp) cc_final: 0.2599 (mtt) REVERT: F 133 CYS cc_start: -0.0241 (OUTLIER) cc_final: -0.0833 (p) REVERT: F 240 LEU cc_start: 0.6080 (mp) cc_final: 0.5572 (tp) REVERT: F 312 GLU cc_start: 0.6387 (tt0) cc_final: 0.5702 (pt0) REVERT: F 379 ILE cc_start: 0.7475 (mm) cc_final: 0.7231 (mm) REVERT: F 383 MET cc_start: 0.5957 (mtp) cc_final: 0.5052 (mtp) REVERT: F 479 GLU cc_start: 0.5763 (mt-10) cc_final: 0.5553 (tp30) REVERT: F 496 THR cc_start: 0.6233 (OUTLIER) cc_final: 0.5675 (t) outliers start: 311 outliers final: 66 residues processed: 1146 average time/residue: 0.5061 time to fit residues: 941.8964 Evaluate side-chains 498 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 421 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain F residue 133 CYS Chi-restraints excluded: chain F residue 496 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 402 optimal weight: 7.9990 chunk 361 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 243 optimal weight: 6.9990 chunk 193 optimal weight: 0.9980 chunk 373 optimal weight: 40.0000 chunk 144 optimal weight: 0.9990 chunk 227 optimal weight: 20.0000 chunk 278 optimal weight: 0.8980 chunk 433 optimal weight: 9.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 188 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 460 ASN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 655 HIS A 703 ASN A 755 GLN A 764 ASN A 804 GLN A 901 GLN A 914 ASN A 919 ASN A 955 ASN A 965 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 137 ASN B 188 ASN B 334 ASN B 360 ASN B 450 ASN B 460 ASN B 493 GLN B 519 HIS B 556 ASN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 953 ASN B 992 GLN B1010 GLN B1054 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 188 ASN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 580 GLN C 690 GLN C 703 ASN C 751 ASN C 784 GLN C 787 GLN C 804 GLN C 914 ASN C 935 GLN C 992 GLN C1071 GLN C1101 HIS D 24 GLN D 63 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN D 340 GLN D 374 HIS D 401 HIS D 522 GLN D 580 ASN D 586 ASN E 63 ASN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 GLN E 300 GLN E 330 ASN E 340 GLN E 378 HIS E 401 HIS E 417 HIS E 472 GLN E 522 GLN ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 556 ASN E 586 ASN F 63 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 ASN F 139 GLN F 330 ASN F 340 GLN F 378 HIS F 417 HIS ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 556 ASN F 586 ASN Total number of N/Q/H flips: 81 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 40564 Z= 0.239 Angle : 0.781 15.907 55148 Z= 0.389 Chirality : 0.050 0.485 6377 Planarity : 0.006 0.063 7001 Dihedral : 9.585 61.803 7465 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.75 % Favored : 94.20 % Rotamer: Outliers : 5.52 % Allowed : 19.08 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.98 (0.11), residues: 4744 helix: -1.71 (0.11), residues: 1657 sheet: -1.29 (0.18), residues: 709 loop : -2.39 (0.11), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 165 HIS 0.011 0.001 HIS B 519 PHE 0.025 0.002 PHE C1075 TYR 0.027 0.002 TYR B 200 ARG 0.008 0.001 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 458 time to evaluate : 4.665 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: A 153 MET cc_start: 0.1529 (mpp) cc_final: 0.1128 (ptm) REVERT: A 220 PHE cc_start: 0.6469 (t80) cc_final: 0.6148 (t80) REVERT: A 763 LEU cc_start: 0.8332 (mt) cc_final: 0.8070 (mp) REVERT: A 1050 MET cc_start: 0.7734 (ptp) cc_final: 0.7484 (ptp) REVERT: B 52 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: B 645 THR cc_start: 0.6929 (OUTLIER) cc_final: 0.6648 (p) REVERT: B 704 SER cc_start: 0.8418 (m) cc_final: 0.8174 (t) REVERT: B 770 ILE cc_start: 0.7901 (mt) cc_final: 0.7458 (mt) REVERT: B 1012 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8455 (tp) REVERT: C 367 VAL cc_start: 0.7873 (p) cc_final: 0.7530 (m) REVERT: C 427 ASP cc_start: 0.6147 (m-30) cc_final: 0.5896 (p0) REVERT: C 699 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8220 (mt) REVERT: D 383 MET cc_start: 0.5771 (mtp) cc_final: 0.3969 (ppp) REVERT: D 480 MET cc_start: 0.2181 (ttt) cc_final: 0.1126 (ptm) REVERT: D 573 VAL cc_start: 0.1612 (OUTLIER) cc_final: 0.1248 (m) REVERT: D 579 MET cc_start: -0.1042 (ptp) cc_final: -0.1391 (ptp) REVERT: E 144 LEU cc_start: 0.1811 (tp) cc_final: 0.1069 (tp) REVERT: E 282 THR cc_start: 0.1784 (OUTLIER) cc_final: 0.1354 (p) REVERT: E 293 VAL cc_start: 0.1968 (OUTLIER) cc_final: 0.1178 (m) REVERT: E 366 MET cc_start: -0.1841 (tpt) cc_final: -0.2859 (tmm) REVERT: E 453 THR cc_start: -0.5743 (OUTLIER) cc_final: -0.5989 (m) REVERT: E 455 MET cc_start: -0.0662 (tmm) cc_final: -0.2033 (tmm) REVERT: E 483 GLU cc_start: 0.2483 (mp0) cc_final: 0.2274 (tm-30) REVERT: E 574 VAL cc_start: 0.0782 (t) cc_final: 0.0502 (t) REVERT: F 82 MET cc_start: 0.3250 (ttp) cc_final: 0.2815 (mtt) REVERT: F 123 MET cc_start: 0.2285 (ttp) cc_final: 0.1317 (ptt) REVERT: F 133 CYS cc_start: 0.0911 (OUTLIER) cc_final: -0.0189 (p) REVERT: F 134 ASN cc_start: 0.1114 (OUTLIER) cc_final: 0.0852 (m-40) REVERT: F 137 ASN cc_start: 0.5614 (m110) cc_final: 0.5008 (t0) REVERT: F 224 GLU cc_start: 0.6856 (mp0) cc_final: 0.5995 (pt0) REVERT: F 240 LEU cc_start: 0.5751 (mp) cc_final: 0.5264 (tp) REVERT: F 312 GLU cc_start: 0.6345 (tt0) cc_final: 0.5701 (pt0) REVERT: F 379 ILE cc_start: 0.7493 (mm) cc_final: 0.6776 (pt) REVERT: F 383 MET cc_start: 0.5877 (mtp) cc_final: 0.5303 (mtp) REVERT: F 428 PHE cc_start: 0.1325 (OUTLIER) cc_final: 0.1086 (m-10) REVERT: F 479 GLU cc_start: 0.5372 (mt-10) cc_final: 0.5037 (tp30) outliers start: 233 outliers final: 113 residues processed: 644 average time/residue: 0.4706 time to fit residues: 516.3037 Evaluate side-chains 468 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 344 time to evaluate : 4.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 133 CYS Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 428 PHE Chi-restraints excluded: chain F residue 480 MET Chi-restraints excluded: chain F residue 496 THR Chi-restraints excluded: chain F residue 573 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 240 optimal weight: 0.9990 chunk 134 optimal weight: 30.0000 chunk 360 optimal weight: 20.0000 chunk 294 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 433 optimal weight: 4.9990 chunk 468 optimal weight: 20.0000 chunk 386 optimal weight: 20.0000 chunk 430 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 348 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 134 GLN A 188 ASN A 388 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 493 GLN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 658 ASN A 755 GLN A1106 GLN B 30 ASN B 81 ASN B 422 ASN B 542 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 690 GLN B 762 GLN B 784 GLN B 804 GLN B 872 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN B1005 GLN ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN ** D 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS D 505 HIS D 572 ASN D 586 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 586 ASN E 599 ASN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 ASN F 239 HIS F 373 HIS ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 599 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.161 40564 Z= 0.385 Angle : 0.834 13.283 55148 Z= 0.418 Chirality : 0.051 0.540 6377 Planarity : 0.006 0.080 7001 Dihedral : 8.708 59.636 7374 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.12 % Favored : 92.81 % Rotamer: Outliers : 6.14 % Allowed : 20.27 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.11), residues: 4744 helix: -1.07 (0.12), residues: 1610 sheet: -1.34 (0.18), residues: 707 loop : -2.20 (0.11), residues: 2427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 477 HIS 0.010 0.002 HIS A1048 PHE 0.039 0.003 PHE B1089 TYR 0.022 0.002 TYR D 255 ARG 0.007 0.001 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 320 time to evaluate : 4.989 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 233 ILE cc_start: 0.5490 (OUTLIER) cc_final: 0.5125 (tt) REVERT: A 813 SER cc_start: 0.8740 (t) cc_final: 0.8521 (p) REVERT: A 869 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.6466 (mtt) REVERT: A 987 PRO cc_start: 0.7101 (Cg_exo) cc_final: 0.6567 (Cg_endo) REVERT: A 1108 ASN cc_start: 0.5628 (OUTLIER) cc_final: 0.5353 (t0) REVERT: B 105 ILE cc_start: 0.5684 (OUTLIER) cc_final: 0.5323 (tt) REVERT: B 210 ILE cc_start: 0.6372 (OUTLIER) cc_final: 0.6116 (tp) REVERT: B 692 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7442 (mm) REVERT: B 704 SER cc_start: 0.8319 (m) cc_final: 0.8028 (t) REVERT: B 742 ILE cc_start: 0.8476 (mm) cc_final: 0.8049 (mt) REVERT: B 770 ILE cc_start: 0.8704 (mt) cc_final: 0.8435 (mm) REVERT: B 1088 HIS cc_start: 0.4574 (m90) cc_final: 0.3973 (m90) REVERT: B 1117 THR cc_start: 0.6172 (OUTLIER) cc_final: 0.5814 (t) REVERT: C 231 ILE cc_start: 0.6560 (OUTLIER) cc_final: 0.5995 (mm) REVERT: C 473 TYR cc_start: 0.3558 (t80) cc_final: 0.2932 (t80) REVERT: D 383 MET cc_start: 0.5941 (mtp) cc_final: 0.5647 (mtt) REVERT: D 480 MET cc_start: 0.1510 (ttt) cc_final: 0.0833 (ptm) REVERT: D 573 VAL cc_start: 0.1762 (OUTLIER) cc_final: 0.1416 (m) REVERT: E 282 THR cc_start: 0.2315 (OUTLIER) cc_final: 0.2039 (p) REVERT: E 293 VAL cc_start: 0.2366 (OUTLIER) cc_final: 0.1975 (m) REVERT: E 366 MET cc_start: -0.1443 (tpt) cc_final: -0.2353 (tmm) REVERT: E 455 MET cc_start: -0.1222 (tmm) cc_final: -0.2061 (tmm) REVERT: E 496 THR cc_start: 0.2490 (OUTLIER) cc_final: 0.2271 (m) REVERT: E 574 VAL cc_start: 0.0505 (t) cc_final: 0.0226 (t) REVERT: E 579 MET cc_start: 0.1046 (mpp) cc_final: -0.0134 (mmp) REVERT: F 82 MET cc_start: 0.4380 (ttp) cc_final: 0.3659 (mtm) REVERT: F 123 MET cc_start: 0.2511 (ttp) cc_final: 0.1671 (ptt) REVERT: F 134 ASN cc_start: 0.1094 (OUTLIER) cc_final: 0.0837 (m-40) REVERT: F 312 GLU cc_start: 0.6032 (tt0) cc_final: 0.5353 (pt0) REVERT: F 323 MET cc_start: 0.2390 (tpp) cc_final: 0.2185 (tpp) REVERT: F 366 MET cc_start: 0.4710 (ppp) cc_final: 0.4464 (tmm) REVERT: F 383 MET cc_start: 0.5858 (mtp) cc_final: 0.5288 (mtp) REVERT: F 428 PHE cc_start: 0.0471 (OUTLIER) cc_final: 0.0156 (m-10) REVERT: F 479 GLU cc_start: 0.5709 (mt-10) cc_final: 0.5153 (tp30) outliers start: 259 outliers final: 149 residues processed: 540 average time/residue: 0.4742 time to fit residues: 444.7117 Evaluate side-chains 436 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 273 time to evaluate : 4.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 428 PHE Chi-restraints excluded: chain F residue 573 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 428 optimal weight: 1.9990 chunk 326 optimal weight: 6.9990 chunk 225 optimal weight: 8.9990 chunk 48 optimal weight: 0.3980 chunk 207 optimal weight: 4.9990 chunk 291 optimal weight: 1.9990 chunk 435 optimal weight: 20.0000 chunk 461 optimal weight: 7.9990 chunk 227 optimal weight: 20.0000 chunk 412 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 188 ASN A 394 ASN B 30 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 134 GLN ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 ASN ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 531 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 40564 Z= 0.190 Angle : 0.678 12.269 55148 Z= 0.333 Chirality : 0.047 0.509 6377 Planarity : 0.004 0.075 7001 Dihedral : 8.009 59.990 7359 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.44 % Favored : 94.52 % Rotamer: Outliers : 4.74 % Allowed : 21.86 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.11), residues: 4744 helix: -0.47 (0.12), residues: 1631 sheet: -1.10 (0.18), residues: 713 loop : -2.03 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 48 HIS 0.006 0.001 HIS F 239 PHE 0.022 0.001 PHE A 220 TYR 0.019 0.001 TYR B 28 ARG 0.005 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 304 time to evaluate : 4.817 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 233 ILE cc_start: 0.5504 (OUTLIER) cc_final: 0.5298 (tt) REVERT: A 726 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8085 (pt) REVERT: A 813 SER cc_start: 0.8723 (t) cc_final: 0.8486 (p) REVERT: A 1066 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.7972 (p) REVERT: A 1108 ASN cc_start: 0.5631 (OUTLIER) cc_final: 0.5388 (t0) REVERT: B 52 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: B 105 ILE cc_start: 0.6022 (OUTLIER) cc_final: 0.5599 (tt) REVERT: B 324 GLU cc_start: 0.5136 (OUTLIER) cc_final: 0.4932 (pm20) REVERT: B 704 SER cc_start: 0.8206 (m) cc_final: 0.7910 (t) REVERT: B 731 MET cc_start: 0.7783 (mtm) cc_final: 0.7519 (ptp) REVERT: B 742 ILE cc_start: 0.8467 (mm) cc_final: 0.8160 (mt) REVERT: B 1012 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8620 (tp) REVERT: C 231 ILE cc_start: 0.6661 (OUTLIER) cc_final: 0.6087 (mm) REVERT: C 473 TYR cc_start: 0.3653 (t80) cc_final: 0.3088 (t80) REVERT: C 1115 ILE cc_start: 0.5910 (tp) cc_final: 0.5592 (tt) REVERT: D 568 LEU cc_start: 0.4926 (mp) cc_final: 0.3824 (tt) REVERT: D 573 VAL cc_start: 0.2183 (OUTLIER) cc_final: 0.1772 (m) REVERT: E 114 LYS cc_start: 0.5890 (tptt) cc_final: 0.5137 (mttp) REVERT: E 282 THR cc_start: 0.2138 (OUTLIER) cc_final: 0.1899 (p) REVERT: E 293 VAL cc_start: 0.2519 (OUTLIER) cc_final: 0.2056 (m) REVERT: E 332 MET cc_start: 0.0734 (ppp) cc_final: 0.0529 (ppp) REVERT: E 366 MET cc_start: -0.0975 (tpt) cc_final: -0.1922 (tmm) REVERT: E 455 MET cc_start: -0.1649 (tmm) cc_final: -0.2334 (tmm) REVERT: E 496 THR cc_start: 0.2242 (OUTLIER) cc_final: 0.2006 (m) REVERT: E 574 VAL cc_start: 0.0469 (t) cc_final: 0.0187 (t) REVERT: F 82 MET cc_start: 0.4398 (ttp) cc_final: 0.3744 (mtm) REVERT: F 123 MET cc_start: 0.2722 (ttp) cc_final: 0.1745 (ptt) REVERT: F 224 GLU cc_start: 0.5594 (mp0) cc_final: 0.4801 (pt0) REVERT: F 312 GLU cc_start: 0.5981 (tt0) cc_final: 0.5308 (pt0) REVERT: F 323 MET cc_start: 0.2726 (tpp) cc_final: 0.2472 (tpp) REVERT: F 366 MET cc_start: 0.4940 (ppp) cc_final: 0.4622 (tmm) REVERT: F 383 MET cc_start: 0.5841 (mtp) cc_final: 0.5451 (mtp) REVERT: F 428 PHE cc_start: 0.0531 (OUTLIER) cc_final: 0.0214 (m-10) REVERT: F 479 GLU cc_start: 0.5704 (mt-10) cc_final: 0.4936 (tp30) REVERT: F 589 GLU cc_start: 0.6529 (mm-30) cc_final: 0.5141 (mt-10) outliers start: 200 outliers final: 126 residues processed: 471 average time/residue: 0.4454 time to fit residues: 367.6872 Evaluate side-chains 411 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 271 time to evaluate : 4.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 428 PHE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 573 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 383 optimal weight: 30.0000 chunk 261 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 343 optimal weight: 30.0000 chunk 190 optimal weight: 0.7980 chunk 393 optimal weight: 40.0000 chunk 318 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 235 optimal weight: 9.9990 chunk 413 optimal weight: 20.0000 chunk 116 optimal weight: 0.0370 overall best weight: 2.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B1106 GLN B1108 ASN C 751 ASN ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS E 552 GLN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 531 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 40564 Z= 0.202 Angle : 0.664 12.447 55148 Z= 0.326 Chirality : 0.046 0.485 6377 Planarity : 0.004 0.086 7001 Dihedral : 7.602 59.944 7354 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.20 % Favored : 93.78 % Rotamer: Outliers : 4.74 % Allowed : 22.21 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.68 (0.12), residues: 4744 helix: -0.12 (0.13), residues: 1632 sheet: -0.93 (0.19), residues: 692 loop : -1.90 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 275 HIS 0.006 0.001 HIS D 493 PHE 0.030 0.001 PHE B 135 TYR 0.018 0.001 TYR C1110 ARG 0.006 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 284 time to evaluate : 4.700 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: A 523 THR cc_start: 0.4112 (OUTLIER) cc_final: 0.3830 (m) REVERT: A 726 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8088 (pt) REVERT: A 870 ILE cc_start: 0.8310 (pt) cc_final: 0.7957 (mt) REVERT: B 52 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: B 480 CYS cc_start: 0.4257 (OUTLIER) cc_final: 0.3467 (m) REVERT: B 645 THR cc_start: 0.7206 (OUTLIER) cc_final: 0.6958 (p) REVERT: B 704 SER cc_start: 0.8225 (m) cc_final: 0.7892 (t) REVERT: B 742 ILE cc_start: 0.8500 (mm) cc_final: 0.8261 (mt) REVERT: B 901 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: C 231 ILE cc_start: 0.6609 (OUTLIER) cc_final: 0.6036 (mm) REVERT: D 383 MET cc_start: 0.4599 (mtp) cc_final: 0.2512 (ppp) REVERT: D 568 LEU cc_start: 0.4832 (mp) cc_final: 0.3639 (tt) REVERT: D 573 VAL cc_start: 0.2138 (OUTLIER) cc_final: 0.1698 (m) REVERT: E 114 LYS cc_start: 0.5960 (tptt) cc_final: 0.5248 (mttp) REVERT: E 186 LEU cc_start: 0.0507 (OUTLIER) cc_final: 0.0164 (tp) REVERT: E 282 THR cc_start: 0.2165 (OUTLIER) cc_final: 0.1904 (p) REVERT: E 293 VAL cc_start: 0.2543 (OUTLIER) cc_final: 0.2036 (m) REVERT: E 297 MET cc_start: -0.1331 (mmt) cc_final: -0.1795 (mmt) REVERT: E 332 MET cc_start: 0.0626 (ppp) cc_final: 0.0422 (ppp) REVERT: E 366 MET cc_start: -0.0362 (tpt) cc_final: -0.1584 (tmm) REVERT: E 455 MET cc_start: -0.1638 (tmm) cc_final: -0.2242 (tmm) REVERT: E 574 VAL cc_start: 0.0388 (t) cc_final: 0.0106 (t) REVERT: F 82 MET cc_start: 0.4810 (ttp) cc_final: 0.4106 (mtm) REVERT: F 123 MET cc_start: 0.2837 (ttp) cc_final: 0.1908 (ptt) REVERT: F 224 GLU cc_start: 0.5669 (mp0) cc_final: 0.4841 (pt0) REVERT: F 302 TRP cc_start: 0.2511 (m-10) cc_final: 0.1832 (m100) REVERT: F 312 GLU cc_start: 0.6018 (tt0) cc_final: 0.5336 (pt0) REVERT: F 366 MET cc_start: 0.5319 (ppp) cc_final: 0.4692 (ppp) REVERT: F 383 MET cc_start: 0.5936 (mtp) cc_final: 0.5549 (mtp) REVERT: F 428 PHE cc_start: 0.0467 (OUTLIER) cc_final: 0.0183 (m-10) REVERT: F 479 GLU cc_start: 0.5409 (mt-10) cc_final: 0.4624 (tp30) REVERT: F 549 GLU cc_start: 0.5843 (pm20) cc_final: 0.4027 (tm-30) REVERT: F 589 GLU cc_start: 0.6314 (mm-30) cc_final: 0.5128 (mt-10) outliers start: 200 outliers final: 141 residues processed: 450 average time/residue: 0.4379 time to fit residues: 344.7574 Evaluate side-chains 417 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 264 time to evaluate : 4.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 428 PHE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 573 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 155 optimal weight: 1.9990 chunk 415 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 270 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 461 optimal weight: 20.0000 chunk 383 optimal weight: 20.0000 chunk 213 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 242 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 394 ASN B 30 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 115 GLN ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 GLN ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.6337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 40564 Z= 0.287 Angle : 0.723 12.462 55148 Z= 0.357 Chirality : 0.048 0.500 6377 Planarity : 0.005 0.055 7001 Dihedral : 7.879 59.480 7347 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.94 % Favored : 93.04 % Rotamer: Outliers : 5.33 % Allowed : 22.31 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.67 (0.12), residues: 4744 helix: -0.02 (0.13), residues: 1638 sheet: -1.13 (0.19), residues: 690 loop : -1.89 (0.12), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 353 HIS 0.006 0.001 HIS E 34 PHE 0.031 0.002 PHE B 135 TYR 0.022 0.002 TYR C 204 ARG 0.006 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 268 time to evaluate : 4.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 726 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8120 (pt) REVERT: A 983 ARG cc_start: 0.5522 (OUTLIER) cc_final: 0.5253 (ptt180) REVERT: A 1050 MET cc_start: 0.7820 (ptp) cc_final: 0.7509 (ptt) REVERT: B 480 CYS cc_start: 0.3997 (OUTLIER) cc_final: 0.3105 (m) REVERT: B 901 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7862 (tt0) REVERT: B 985 ASP cc_start: 0.7666 (p0) cc_final: 0.7381 (p0) REVERT: C 231 ILE cc_start: 0.6805 (OUTLIER) cc_final: 0.6204 (mm) REVERT: C 473 TYR cc_start: 0.3641 (t80) cc_final: 0.2989 (t80) REVERT: D 62 MET cc_start: 0.0946 (ppp) cc_final: 0.0274 (ppp) REVERT: D 383 MET cc_start: 0.5353 (mtp) cc_final: 0.2887 (ppp) REVERT: D 480 MET cc_start: 0.0963 (ttt) cc_final: 0.0576 (ppp) REVERT: D 483 GLU cc_start: 0.5917 (OUTLIER) cc_final: 0.5286 (tt0) REVERT: D 568 LEU cc_start: 0.4515 (mp) cc_final: 0.3320 (tt) REVERT: D 573 VAL cc_start: 0.2104 (OUTLIER) cc_final: 0.1636 (m) REVERT: E 114 LYS cc_start: 0.6030 (tptt) cc_final: 0.5333 (mttp) REVERT: E 282 THR cc_start: 0.2310 (OUTLIER) cc_final: 0.2047 (p) REVERT: E 293 VAL cc_start: 0.2969 (OUTLIER) cc_final: 0.2441 (m) REVERT: E 332 MET cc_start: 0.1152 (ppp) cc_final: 0.0830 (ppp) REVERT: E 366 MET cc_start: -0.0516 (tpt) cc_final: -0.1454 (tmm) REVERT: E 455 MET cc_start: -0.1577 (tmm) cc_final: -0.1814 (tmm) REVERT: E 474 MET cc_start: -0.0975 (ttt) cc_final: -0.1341 (ttt) REVERT: E 574 VAL cc_start: 0.0404 (t) cc_final: 0.0111 (t) REVERT: E 579 MET cc_start: 0.0909 (mmt) cc_final: 0.0697 (mmt) REVERT: F 27 THR cc_start: 0.6014 (p) cc_final: 0.5783 (p) REVERT: F 82 MET cc_start: 0.5089 (ttp) cc_final: 0.4336 (mtp) REVERT: F 123 MET cc_start: 0.2789 (ttp) cc_final: 0.1771 (ptt) REVERT: F 332 MET cc_start: 0.1667 (ttm) cc_final: 0.1368 (ttm) REVERT: F 360 MET cc_start: 0.3887 (pmm) cc_final: 0.3397 (ppp) REVERT: F 366 MET cc_start: 0.5535 (ppp) cc_final: 0.5168 (tmm) REVERT: F 383 MET cc_start: 0.5895 (mtp) cc_final: 0.5629 (mtm) REVERT: F 428 PHE cc_start: 0.0647 (OUTLIER) cc_final: 0.0260 (m-10) REVERT: F 455 MET cc_start: -0.2770 (tmm) cc_final: -0.3156 (tmm) REVERT: F 479 GLU cc_start: 0.5155 (mt-10) cc_final: 0.4513 (tp30) REVERT: F 480 MET cc_start: -0.0915 (OUTLIER) cc_final: -0.1589 (ptt) REVERT: F 589 GLU cc_start: 0.6395 (mm-30) cc_final: 0.5183 (mt-10) outliers start: 225 outliers final: 157 residues processed: 460 average time/residue: 0.4569 time to fit residues: 365.8251 Evaluate side-chains 403 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 235 time to evaluate : 4.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 477 TRP Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 428 PHE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 480 MET Chi-restraints excluded: chain F residue 573 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 444 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 262 optimal weight: 4.9990 chunk 337 optimal weight: 30.0000 chunk 261 optimal weight: 0.9980 chunk 388 optimal weight: 5.9990 chunk 257 optimal weight: 10.0000 chunk 459 optimal weight: 10.0000 chunk 287 optimal weight: 2.9990 chunk 280 optimal weight: 0.7980 chunk 212 optimal weight: 30.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN A 804 GLN B 66 HIS B 493 GLN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS B1106 GLN ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN F 472 GLN ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.6515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 40564 Z= 0.181 Angle : 0.660 12.815 55148 Z= 0.320 Chirality : 0.045 0.384 6377 Planarity : 0.004 0.049 7001 Dihedral : 7.517 58.136 7345 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.22 % Favored : 93.76 % Rotamer: Outliers : 4.05 % Allowed : 23.54 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.12), residues: 4744 helix: 0.29 (0.13), residues: 1636 sheet: -0.83 (0.19), residues: 682 loop : -1.84 (0.12), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 353 HIS 0.004 0.001 HIS D 34 PHE 0.035 0.001 PHE A 392 TYR 0.017 0.001 TYR B 423 ARG 0.004 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 258 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: A 449 TYR cc_start: 0.5121 (m-10) cc_final: 0.4891 (m-10) REVERT: A 726 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8115 (pt) REVERT: A 896 ILE cc_start: 0.7203 (tp) cc_final: 0.6941 (tp) REVERT: B 480 CYS cc_start: 0.3882 (OUTLIER) cc_final: 0.2864 (m) REVERT: B 569 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7747 (mt) REVERT: B 901 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: C 231 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6135 (mm) REVERT: C 455 LEU cc_start: 0.5322 (pt) cc_final: 0.4494 (pt) REVERT: D 116 LEU cc_start: -0.0447 (OUTLIER) cc_final: -0.0681 (tt) REVERT: D 383 MET cc_start: 0.5233 (mtp) cc_final: 0.2746 (ppp) REVERT: D 480 MET cc_start: 0.0896 (ttt) cc_final: 0.0255 (ptm) REVERT: D 483 GLU cc_start: 0.5879 (OUTLIER) cc_final: 0.5243 (tt0) REVERT: D 568 LEU cc_start: 0.4453 (mp) cc_final: 0.3273 (tt) REVERT: D 573 VAL cc_start: 0.2131 (OUTLIER) cc_final: 0.1669 (m) REVERT: E 110 GLU cc_start: 0.0220 (mm-30) cc_final: -0.0530 (pm20) REVERT: E 114 LYS cc_start: 0.5999 (tptt) cc_final: 0.5268 (mttp) REVERT: E 239 HIS cc_start: 0.2102 (OUTLIER) cc_final: 0.1894 (t70) REVERT: E 293 VAL cc_start: 0.2745 (OUTLIER) cc_final: 0.2316 (m) REVERT: E 332 MET cc_start: 0.1205 (ppp) cc_final: 0.0851 (ppp) REVERT: E 366 MET cc_start: -0.0318 (tpt) cc_final: -0.1106 (tmm) REVERT: E 455 MET cc_start: -0.1539 (tmm) cc_final: -0.1782 (tmm) REVERT: E 474 MET cc_start: -0.1144 (ttt) cc_final: -0.1457 (ttt) REVERT: E 574 VAL cc_start: 0.0384 (t) cc_final: 0.0104 (t) REVERT: F 82 MET cc_start: 0.5212 (ttp) cc_final: 0.4470 (mtp) REVERT: F 123 MET cc_start: 0.2620 (ttp) cc_final: 0.1621 (ptt) REVERT: F 302 TRP cc_start: 0.2861 (m-10) cc_final: 0.2044 (m100) REVERT: F 366 MET cc_start: 0.5662 (ppp) cc_final: 0.5255 (tmm) REVERT: F 383 MET cc_start: 0.6288 (mtp) cc_final: 0.5690 (mtm) REVERT: F 428 PHE cc_start: 0.0545 (OUTLIER) cc_final: 0.0216 (m-10) REVERT: F 455 MET cc_start: -0.2445 (tmm) cc_final: -0.2788 (tmm) REVERT: F 479 GLU cc_start: 0.5189 (mt-10) cc_final: 0.4447 (tp30) REVERT: F 480 MET cc_start: -0.0279 (ptt) cc_final: -0.0870 (ptt) REVERT: F 589 GLU cc_start: 0.6286 (mm-30) cc_final: 0.5207 (mt-10) outliers start: 171 outliers final: 129 residues processed: 404 average time/residue: 0.4609 time to fit residues: 324.1960 Evaluate side-chains 374 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 234 time to evaluate : 4.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 477 TRP Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 428 PHE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 573 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 284 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 274 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 292 optimal weight: 0.9980 chunk 313 optimal weight: 20.0000 chunk 227 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 361 optimal weight: 40.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 755 GLN B 66 HIS B 370 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.6642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 40564 Z= 0.160 Angle : 0.647 12.260 55148 Z= 0.311 Chirality : 0.045 0.370 6377 Planarity : 0.004 0.047 7001 Dihedral : 7.187 59.833 7344 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.82 % Favored : 94.16 % Rotamer: Outliers : 3.67 % Allowed : 23.78 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.20 (0.12), residues: 4744 helix: 0.49 (0.13), residues: 1641 sheet: -0.63 (0.20), residues: 659 loop : -1.79 (0.12), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 353 HIS 0.008 0.001 HIS F 505 PHE 0.027 0.001 PHE E 525 TYR 0.015 0.001 TYR B 423 ARG 0.002 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 262 time to evaluate : 4.562 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 449 TYR cc_start: 0.5240 (m-10) cc_final: 0.4995 (m-10) REVERT: A 726 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8034 (pt) REVERT: A 896 ILE cc_start: 0.6949 (tp) cc_final: 0.6697 (tp) REVERT: A 983 ARG cc_start: 0.5489 (OUTLIER) cc_final: 0.5228 (ptt-90) REVERT: B 480 CYS cc_start: 0.3718 (OUTLIER) cc_final: 0.2668 (m) REVERT: B 569 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7747 (mt) REVERT: B 746 SER cc_start: 0.8302 (OUTLIER) cc_final: 0.7784 (m) REVERT: B 901 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: B 1126 CYS cc_start: 0.4717 (OUTLIER) cc_final: 0.4181 (p) REVERT: C 231 ILE cc_start: 0.6963 (OUTLIER) cc_final: 0.6428 (mm) REVERT: D 116 LEU cc_start: -0.0455 (OUTLIER) cc_final: -0.0693 (tt) REVERT: D 383 MET cc_start: 0.5267 (mtp) cc_final: 0.3008 (ppp) REVERT: D 480 MET cc_start: 0.1010 (ttt) cc_final: 0.0431 (ptp) REVERT: D 568 LEU cc_start: 0.4509 (mp) cc_final: 0.3298 (tt) REVERT: D 573 VAL cc_start: 0.1860 (OUTLIER) cc_final: 0.1428 (m) REVERT: E 110 GLU cc_start: 0.0128 (mm-30) cc_final: -0.0441 (pm20) REVERT: E 183 TYR cc_start: 0.0962 (t80) cc_final: 0.0419 (t80) REVERT: E 199 TYR cc_start: 0.2681 (t80) cc_final: 0.2477 (t80) REVERT: E 293 VAL cc_start: 0.2805 (OUTLIER) cc_final: 0.2275 (m) REVERT: E 332 MET cc_start: 0.1037 (ppp) cc_final: 0.0671 (ppp) REVERT: E 366 MET cc_start: 0.0176 (tpt) cc_final: -0.0689 (tmm) REVERT: E 455 MET cc_start: -0.1402 (tmm) cc_final: -0.1810 (tmm) REVERT: E 474 MET cc_start: -0.1193 (ttt) cc_final: -0.1520 (ttt) REVERT: E 574 VAL cc_start: 0.0227 (t) cc_final: 0.0014 (m) REVERT: F 82 MET cc_start: 0.5174 (ttp) cc_final: 0.4463 (mtp) REVERT: F 123 MET cc_start: 0.2705 (ttp) cc_final: 0.1697 (ptt) REVERT: F 302 TRP cc_start: 0.2674 (m-10) cc_final: 0.1986 (m100) REVERT: F 366 MET cc_start: 0.5646 (ppp) cc_final: 0.5289 (tmm) REVERT: F 383 MET cc_start: 0.6161 (mtp) cc_final: 0.5600 (mtm) REVERT: F 455 MET cc_start: -0.2704 (tmm) cc_final: -0.3031 (tmm) REVERT: F 479 GLU cc_start: 0.5255 (mt-10) cc_final: 0.4316 (tp30) REVERT: F 480 MET cc_start: -0.0656 (ptt) cc_final: -0.1241 (ptt) outliers start: 155 outliers final: 118 residues processed: 397 average time/residue: 0.4553 time to fit residues: 313.2702 Evaluate side-chains 367 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 238 time to evaluate : 4.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 477 TRP Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 573 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 418 optimal weight: 8.9990 chunk 440 optimal weight: 20.0000 chunk 401 optimal weight: 8.9990 chunk 428 optimal weight: 20.0000 chunk 257 optimal weight: 9.9990 chunk 186 optimal weight: 8.9990 chunk 336 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 387 optimal weight: 30.0000 chunk 405 optimal weight: 6.9990 chunk 426 optimal weight: 0.0670 overall best weight: 3.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 388 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 784 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 556 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.7007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 40564 Z= 0.251 Angle : 0.709 20.806 55148 Z= 0.344 Chirality : 0.046 0.428 6377 Planarity : 0.004 0.049 7001 Dihedral : 7.536 61.019 7344 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.02 % Favored : 92.94 % Rotamer: Outliers : 4.01 % Allowed : 23.73 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.28 (0.12), residues: 4744 helix: 0.42 (0.13), residues: 1638 sheet: -0.84 (0.19), residues: 693 loop : -1.79 (0.12), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 436 HIS 0.005 0.001 HIS E 34 PHE 0.027 0.002 PHE E 525 TYR 0.017 0.002 TYR B 369 ARG 0.012 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 239 time to evaluate : 4.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ILE cc_start: 0.6154 (OUTLIER) cc_final: 0.5730 (mp) REVERT: A 449 TYR cc_start: 0.5078 (m-10) cc_final: 0.4797 (m-10) REVERT: A 726 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.7950 (pt) REVERT: A 983 ARG cc_start: 0.6129 (OUTLIER) cc_final: 0.5915 (ptt-90) REVERT: B 480 CYS cc_start: 0.4028 (OUTLIER) cc_final: 0.2739 (m) REVERT: B 746 SER cc_start: 0.8389 (OUTLIER) cc_final: 0.7807 (m) REVERT: B 869 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6685 (mtp) REVERT: B 901 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7705 (tt0) REVERT: C 231 ILE cc_start: 0.6908 (OUTLIER) cc_final: 0.6260 (mm) REVERT: C 362 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7815 (t) REVERT: C 869 MET cc_start: 0.7225 (ptt) cc_final: 0.6794 (ptt) REVERT: D 116 LEU cc_start: -0.0473 (OUTLIER) cc_final: -0.0695 (tt) REVERT: D 383 MET cc_start: 0.5240 (mtp) cc_final: 0.3113 (ppp) REVERT: D 480 MET cc_start: 0.0825 (ttt) cc_final: 0.0153 (ptp) REVERT: D 483 GLU cc_start: 0.6024 (pm20) cc_final: 0.5194 (tt0) REVERT: D 568 LEU cc_start: 0.4818 (mp) cc_final: 0.3683 (tt) REVERT: D 573 VAL cc_start: 0.1811 (OUTLIER) cc_final: 0.1334 (m) REVERT: E 110 GLU cc_start: 0.0176 (mm-30) cc_final: -0.0473 (pm20) REVERT: E 114 LYS cc_start: 0.6080 (tptt) cc_final: 0.5370 (mttp) REVERT: E 293 VAL cc_start: 0.2462 (OUTLIER) cc_final: 0.2099 (m) REVERT: E 332 MET cc_start: 0.1372 (ppp) cc_final: 0.0960 (ppp) REVERT: E 366 MET cc_start: 0.0507 (tpt) cc_final: -0.0603 (tmm) REVERT: E 455 MET cc_start: -0.1353 (tmm) cc_final: -0.1733 (tmm) REVERT: E 474 MET cc_start: -0.0830 (ttt) cc_final: -0.1141 (ttt) REVERT: F 82 MET cc_start: 0.5219 (ttp) cc_final: 0.4517 (mtp) REVERT: F 123 MET cc_start: 0.2984 (ttp) cc_final: 0.2030 (ptt) REVERT: F 302 TRP cc_start: 0.3002 (m-10) cc_final: 0.2092 (m100) REVERT: F 366 MET cc_start: 0.5906 (ppp) cc_final: 0.5568 (tmm) REVERT: F 383 MET cc_start: 0.6176 (mtp) cc_final: 0.5450 (mtm) REVERT: F 455 MET cc_start: -0.2800 (tmm) cc_final: -0.3119 (tmm) REVERT: F 479 GLU cc_start: 0.5186 (mt-10) cc_final: 0.4390 (tp30) REVERT: F 480 MET cc_start: -0.0723 (ptt) cc_final: -0.1128 (ptt) outliers start: 169 outliers final: 127 residues processed: 386 average time/residue: 0.4587 time to fit residues: 307.8104 Evaluate side-chains 369 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 230 time to evaluate : 4.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 423 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 428 PHE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 281 optimal weight: 4.9990 chunk 453 optimal weight: 10.0000 chunk 276 optimal weight: 0.9980 chunk 214 optimal weight: 40.0000 chunk 314 optimal weight: 20.0000 chunk 475 optimal weight: 6.9990 chunk 437 optimal weight: 20.0000 chunk 378 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 232 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 GLN ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN F 508 ASN ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.7282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 40564 Z= 0.241 Angle : 0.699 16.758 55148 Z= 0.339 Chirality : 0.046 0.389 6377 Planarity : 0.004 0.050 7001 Dihedral : 7.554 58.230 7344 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.60 % Favored : 93.36 % Rotamer: Outliers : 3.70 % Allowed : 24.09 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 4744 helix: 0.48 (0.13), residues: 1633 sheet: -0.84 (0.20), residues: 687 loop : -1.77 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 353 HIS 0.005 0.001 HIS E 34 PHE 0.024 0.002 PHE E 525 TYR 0.026 0.002 TYR E 199 ARG 0.016 0.001 ARG A 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 239 time to evaluate : 4.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ILE cc_start: 0.5877 (OUTLIER) cc_final: 0.5544 (tp) REVERT: A 324 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: A 358 ILE cc_start: 0.6150 (OUTLIER) cc_final: 0.5786 (mp) REVERT: A 449 TYR cc_start: 0.5251 (m-10) cc_final: 0.4980 (m-10) REVERT: A 726 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8007 (pt) REVERT: A 967 SER cc_start: 0.8029 (OUTLIER) cc_final: 0.7776 (m) REVERT: B 480 CYS cc_start: 0.3693 (OUTLIER) cc_final: 0.2665 (m) REVERT: B 746 SER cc_start: 0.8280 (OUTLIER) cc_final: 0.7665 (m) REVERT: B 901 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: C 231 ILE cc_start: 0.6934 (OUTLIER) cc_final: 0.6286 (mm) REVERT: C 362 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7758 (t) REVERT: D 116 LEU cc_start: -0.0657 (OUTLIER) cc_final: -0.0877 (tt) REVERT: D 383 MET cc_start: 0.5291 (mtp) cc_final: 0.4290 (ptp) REVERT: D 483 GLU cc_start: 0.6021 (pm20) cc_final: 0.5208 (tt0) REVERT: D 568 LEU cc_start: 0.4896 (mp) cc_final: 0.3604 (tt) REVERT: D 573 VAL cc_start: 0.1682 (OUTLIER) cc_final: 0.1194 (m) REVERT: E 110 GLU cc_start: 0.0184 (mm-30) cc_final: -0.0483 (pm20) REVERT: E 114 LYS cc_start: 0.6092 (tptt) cc_final: 0.5338 (mttp) REVERT: E 190 MET cc_start: -0.2096 (mmm) cc_final: -0.2721 (mmp) REVERT: E 293 VAL cc_start: 0.2684 (OUTLIER) cc_final: 0.2376 (m) REVERT: E 366 MET cc_start: 0.0420 (tpt) cc_final: -0.0560 (ppp) REVERT: E 474 MET cc_start: -0.0647 (ttt) cc_final: -0.1059 (ttt) REVERT: F 82 MET cc_start: 0.5208 (ttp) cc_final: 0.4578 (mtp) REVERT: F 123 MET cc_start: 0.2859 (ttp) cc_final: 0.1841 (ptt) REVERT: F 302 TRP cc_start: 0.2894 (m-10) cc_final: 0.1790 (m100) REVERT: F 366 MET cc_start: 0.6096 (ppp) cc_final: 0.5792 (tmm) REVERT: F 383 MET cc_start: 0.6160 (mtp) cc_final: 0.5386 (mtm) REVERT: F 455 MET cc_start: -0.2864 (tmm) cc_final: -0.3159 (tmm) REVERT: F 479 GLU cc_start: 0.5038 (mt-10) cc_final: 0.4247 (tp30) REVERT: F 480 MET cc_start: -0.0633 (ptt) cc_final: -0.0963 (ptt) REVERT: F 508 ASN cc_start: 0.3674 (OUTLIER) cc_final: 0.2932 (m-40) outliers start: 156 outliers final: 130 residues processed: 374 average time/residue: 0.4633 time to fit residues: 299.6545 Evaluate side-chains 371 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 227 time to evaluate : 4.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 423 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 428 PHE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 508 ASN Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 300 optimal weight: 6.9990 chunk 403 optimal weight: 40.0000 chunk 115 optimal weight: 8.9990 chunk 348 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 105 optimal weight: 20.0000 chunk 379 optimal weight: 30.0000 chunk 158 optimal weight: 0.0370 chunk 389 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 overall best weight: 5.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.130777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.109220 restraints weight = 191028.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.107044 restraints weight = 234335.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.107637 restraints weight = 188305.636| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.7304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.218 40564 Z= 0.279 Angle : 0.778 59.064 55148 Z= 0.403 Chirality : 0.048 1.076 6377 Planarity : 0.004 0.049 7001 Dihedral : 7.563 58.227 7344 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.79 % Favored : 93.17 % Rotamer: Outliers : 3.67 % Allowed : 24.13 % Favored : 72.19 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.12), residues: 4744 helix: 0.49 (0.13), residues: 1633 sheet: -0.85 (0.20), residues: 687 loop : -1.77 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 353 HIS 0.010 0.001 HIS E 493 PHE 0.020 0.002 PHE E 525 TYR 0.025 0.001 TYR E 199 ARG 0.009 0.000 ARG A 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8330.33 seconds wall clock time: 154 minutes 58.90 seconds (9298.90 seconds total)