Starting phenix.real_space_refine on Fri Feb 23 00:03:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ll1_23411/02_2024/7ll1_23411.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ll1_23411/02_2024/7ll1_23411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ll1_23411/02_2024/7ll1_23411.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ll1_23411/02_2024/7ll1_23411.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ll1_23411/02_2024/7ll1_23411.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ll1_23411/02_2024/7ll1_23411.pdb" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.135 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10164 atoms to isotropic. 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 147 5.16 5 C 16131 2.51 5 N 4329 2.21 5 O 5166 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 32": "OE1" <-> "OE2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "B GLU 584": "OE1" <-> "OE2" Residue "B ASP 632": "OD1" <-> "OD2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C GLU 381": "OE1" <-> "OE2" Residue "C TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 560": "OE1" <-> "OE2" Residue "D GLU 584": "OE1" <-> "OE2" Residue "D TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 632": "OD1" <-> "OD2" Residue "D GLU 657": "OE1" <-> "OE2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G GLU 190": "OE1" <-> "OE2" Residue "G GLU 211": "OE1" <-> "OE2" Residue "G TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 267": "OE1" <-> "OE2" Residue "G GLU 269": "OE1" <-> "OE2" Residue "G PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 340": "OE1" <-> "OE2" Residue "G GLU 370": "OE1" <-> "OE2" Residue "G GLU 381": "OE1" <-> "OE2" Residue "G ASP 412": "OD1" <-> "OD2" Residue "G TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 476": "NH1" <-> "NH2" Residue "G TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 560": "OE1" <-> "OE2" Residue "I GLU 584": "OE1" <-> "OE2" Residue "I TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 632": "OD1" <-> "OD2" Residue "H ARG 50": "NH1" <-> "NH2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 70": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "H ARG 83": "NH1" <-> "NH2" Residue "H ARG 94": "NH1" <-> "NH2" Residue "H PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 101": "OE1" <-> "OE2" Residue "H TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 149": "OE1" <-> "OE2" Residue "H PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 209": "OD1" <-> "OD2" Residue "H GLU 213": "OE1" <-> "OE2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L ASP 60": "OD1" <-> "OD2" Residue "L ARG 69": "NH1" <-> "NH2" Residue "L ARG 76": "NH1" <-> "NH2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 103": "NH1" <-> "NH2" Residue "L ASP 105": "OD1" <-> "OD2" Residue "L ARG 108": "NH1" <-> "NH2" Residue "L GLU 123": "OE1" <-> "OE2" Residue "L GLU 161": "OE1" <-> "OE2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "L GLU 213": "OE1" <-> "OE2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "E TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 70": "NH1" <-> "NH2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E ARG 94": "NH1" <-> "NH2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 209": "OD1" <-> "OD2" Residue "E GLU 213": "OE1" <-> "OE2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "F ARG 31": "NH1" <-> "NH2" Residue "F TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 42": "NH1" <-> "NH2" Residue "F ASP 60": "OD1" <-> "OD2" Residue "F ARG 69": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 103": "NH1" <-> "NH2" Residue "F ASP 105": "OD1" <-> "OD2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 122": "OD1" <-> "OD2" Residue "F GLU 123": "OE1" <-> "OE2" Residue "F GLU 161": "OE1" <-> "OE2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "F PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 213": "OE1" <-> "OE2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "J PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 70": "NH1" <-> "NH2" Residue "J ARG 71": "NH1" <-> "NH2" Residue "J ARG 71": "NH1" <-> "NH2" Residue "J ARG 82": "NH1" <-> "NH2" Residue "J ARG 83": "NH1" <-> "NH2" Residue "J ARG 94": "NH1" <-> "NH2" Residue "J PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 101": "OE1" <-> "OE2" Residue "J TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 149": "OE1" <-> "OE2" Residue "J PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 209": "OD1" <-> "OD2" Residue "J GLU 213": "OE1" <-> "OE2" Residue "K ARG 24": "NH1" <-> "NH2" Residue "K ARG 31": "NH1" <-> "NH2" Residue "K TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 42": "NH1" <-> "NH2" Residue "K ASP 60": "OD1" <-> "OD2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 76": "NH1" <-> "NH2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 103": "NH1" <-> "NH2" Residue "K ARG 108": "NH1" <-> "NH2" Residue "K PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 123": "OE1" <-> "OE2" Residue "K PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 213": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25773 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3533 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 22, 'TRANS': 426} Chain breaks: 3 Chain: "B" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1205 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 1, 'TRANS': 151} Chain: "C" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3533 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 22, 'TRANS': 426} Chain breaks: 3 Chain: "D" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1205 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 1, 'TRANS': 151} Chain: "G" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3533 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 22, 'TRANS': 426} Chain breaks: 3 Chain: "I" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1205 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 1, 'TRANS': 151} Chain: "H" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1729 Classifications: {'peptide': 229} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 213} Chain: "L" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1659 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 203} Chain: "E" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1729 Classifications: {'peptide': 229} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 213} Chain: "F" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1659 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 203} Chain: "J" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1729 Classifications: {'peptide': 229} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 213} Chain: "K" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1659 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 203} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 12.84, per 1000 atoms: 0.50 Number of scatterers: 25773 At special positions: 0 Unit cell: (176.04, 169.56, 133.92, 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 147 16.00 O 5166 8.00 N 4329 7.00 C 16131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.02 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.04 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS I 605 " distance=2.04 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS H 141 " - pdb=" SG CYS H 197 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 141 " - pdb=" SG CYS E 197 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.02 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 141 " - pdb=" SG CYS J 197 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.02 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 ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN a 4 " - " MAN a 5 " " MAN k 4 " - " MAN k 5 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA a 3 " - " MAN a 4 " " BMA k 3 " - " MAN k 4 " ALPHA1-6 " BMA Q 3 " - " MAN Q 6 " " BMA a 3 " - " MAN a 6 " " BMA k 3 " - " MAN k 6 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 339 " " NAG A 603 " - " ASN A 355 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 339 " " NAG C 603 " - " ASN C 355 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 339 " " NAG G 603 " - " ASN G 355 " " NAG M 1 " - " ASN A 156 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 234 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 276 " " NAG R 1 " - " ASN A 332 " " NAG S 1 " - " ASN A 363 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 392 " " NAG V 1 " - " ASN A 88 " " NAG W 1 " - " ASN C 156 " " NAG X 1 " - " ASN C 160 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 262 " " NAG a 1 " - " ASN C 276 " " NAG b 1 " - " ASN C 332 " " NAG c 1 " - " ASN C 363 " " NAG d 1 " - " ASN C 386 " " NAG e 1 " - " ASN C 392 " " NAG f 1 " - " ASN C 88 " " NAG g 1 " - " ASN G 156 " " NAG h 1 " - " ASN G 160 " " NAG i 1 " - " ASN G 234 " " NAG j 1 " - " ASN G 262 " " NAG k 1 " - " ASN G 276 " " NAG l 1 " - " ASN G 332 " " NAG m 1 " - " ASN G 363 " " NAG n 1 " - " ASN G 386 " " NAG o 1 " - " ASN G 392 " " NAG p 1 " - " ASN G 88 " Time building additional restraints: 11.78 Conformation dependent library (CDL) restraints added in 4.4 seconds 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5826 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 58 sheets defined 21.0% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 353 removed outlier: 4.031A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 483 removed outlier: 4.072A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 521 removed outlier: 4.268A pdb=" N LEU B 520 " --> pdb=" O ALA B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.137A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 547 removed outlier: 5.850A pdb=" N GLY B 547 " --> pdb=" O LEU B 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 544 through 547' Processing helix chain 'B' and resid 548 through 553 Processing helix chain 'B' and resid 566 through 571 Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.558A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.721A pdb=" N TRP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.668A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.684A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 removed outlier: 3.509A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 353 removed outlier: 4.224A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.737A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 removed outlier: 4.243A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 521 removed outlier: 4.539A pdb=" N LEU D 520 " --> pdb=" O ALA D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 547 removed outlier: 3.985A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY D 547 " --> pdb=" O ASN D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 553 Processing helix chain 'D' and resid 566 through 571 Processing helix chain 'D' and resid 572 through 596 removed outlier: 3.556A pdb=" N ARG D 579 " --> pdb=" O GLN D 575 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 removed outlier: 3.653A pdb=" N TRP D 623 " --> pdb=" O LEU D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.971A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 663 removed outlier: 3.577A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS D 655 " --> pdb=" O ASN D 651 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 63 Processing helix chain 'G' and resid 99 through 117 Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 335 through 353 removed outlier: 3.605A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 387 through 390 Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.827A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 483 removed outlier: 4.057A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 517 through 521 removed outlier: 4.426A pdb=" N LEU I 520 " --> pdb=" O ALA I 517 " (cutoff:3.500A) Processing helix chain 'I' and resid 523 through 528 removed outlier: 4.695A pdb=" N GLY I 527 " --> pdb=" O GLY I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 547 removed outlier: 3.969A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU I 545 " --> pdb=" O ALA I 541 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY I 547 " --> pdb=" O ASN I 543 " (cutoff:3.500A) Processing helix chain 'I' and resid 548 through 553 Processing helix chain 'I' and resid 566 through 571 Processing helix chain 'I' and resid 572 through 596 removed outlier: 3.590A pdb=" N ASP I 589 " --> pdb=" O ARG I 585 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TRP I 596 " --> pdb=" O LEU I 592 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 625 removed outlier: 3.698A pdb=" N TRP I 623 " --> pdb=" O LEU I 619 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 636 removed outlier: 4.038A pdb=" N LYS I 633 " --> pdb=" O LEU I 629 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU I 634 " --> pdb=" O GLN I 630 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 664 removed outlier: 3.671A pdb=" N GLY I 644 " --> pdb=" O GLN I 640 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS I 655 " --> pdb=" O ASN I 651 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.876A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 129 through 134 Processing helix chain 'H' and resid 157 through 159 No H-bonds generated for 'chain 'H' and resid 157 through 159' Processing helix chain 'H' and resid 188 through 190 No H-bonds generated for 'chain 'H' and resid 188 through 190' Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 189 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.935A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'E' and resid 157 through 159 No H-bonds generated for 'chain 'E' and resid 157 through 159' Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'F' and resid 183 through 189 removed outlier: 3.632A pdb=" N HIS F 189 " --> pdb=" O ASP F 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.953A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'J' and resid 129 through 134 removed outlier: 3.881A pdb=" N GLY J 134 " --> pdb=" O LYS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 159 No H-bonds generated for 'chain 'J' and resid 157 through 159' Processing helix chain 'J' and resid 188 through 192 removed outlier: 4.181A pdb=" N GLY J 191 " --> pdb=" O SER J 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 128 Processing helix chain 'K' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.455A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.923A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.445A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 360 through 361 removed outlier: 6.619A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.777A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.315A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.917A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.922A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.744A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.777A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.315A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.917A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.922A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 315 through 323 removed outlier: 6.547A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.494A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.844A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.341A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 393 through 395 removed outlier: 3.612A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.342A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.909A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.155A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.569A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 259 through 261 removed outlier: 10.546A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.342A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.909A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.155A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.569A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 315 through 323 removed outlier: 6.702A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 494 through 499 removed outlier: 5.553A pdb=" N VAL I 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL G 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N THR I 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N TYR G 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N CYS I 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.732A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AC4, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'G' and resid 201 through 203 removed outlier: 6.351A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.667A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.727A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 12.164A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 11.801A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.797A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.912A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 271 through 273 removed outlier: 10.912A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.797A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.801A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 12.164A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.727A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 301 through 312 removed outlier: 6.713A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.790A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.624A pdb=" N PHE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 121 through 125 removed outlier: 4.621A pdb=" N ALA H 138 " --> pdb=" O VAL H 185 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL H 185 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY H 140 " --> pdb=" O VAL H 183 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL H 183 " --> pdb=" O GLY H 140 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU H 142 " --> pdb=" O SER H 181 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N SER H 181 " --> pdb=" O LEU H 142 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LYS H 144 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU H 179 " --> pdb=" O LYS H 144 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 151 through 155 Processing sheet with id=AD6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.408A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYR L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N SER L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.408A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.402A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AE2, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AE3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.505A pdb=" N GLN E 10 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.505A pdb=" N GLN E 10 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 121 through 125 removed outlier: 4.974A pdb=" N ALA E 138 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL E 185 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLY E 140 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL E 183 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU E 142 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER E 181 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYS E 144 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU E 179 " --> pdb=" O LYS E 144 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 121 through 125 removed outlier: 4.974A pdb=" N ALA E 138 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL E 185 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLY E 140 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL E 183 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU E 142 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER E 181 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYS E 144 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU E 179 " --> pdb=" O LYS E 144 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 151 through 155 Processing sheet with id=AE8, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.398A pdb=" N LEU F 11 " --> pdb=" O ASP F 105 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.398A pdb=" N LEU F 11 " --> pdb=" O ASP F 105 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 114 through 118 removed outlier: 5.331A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 153 through 155 removed outlier: 4.579A pdb=" N TRP F 148 " --> pdb=" O GLN F 155 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AF5, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.848A pdb=" N ILE J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.671A pdb=" N PHE J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 121 through 125 removed outlier: 3.645A pdb=" N PHE J 123 " --> pdb=" O LEU J 142 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ALA J 138 " --> pdb=" O VAL J 185 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL J 185 " --> pdb=" O ALA J 138 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLY J 140 " --> pdb=" O VAL J 183 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL J 183 " --> pdb=" O GLY J 140 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU J 142 " --> pdb=" O SER J 181 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER J 181 " --> pdb=" O LEU J 142 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LYS J 144 " --> pdb=" O LEU J 179 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU J 179 " --> pdb=" O LYS J 144 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 151 through 155 Processing sheet with id=AF9, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AG1, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.236A pdb=" N LEU K 11 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ILE K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N TYR K 49 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.236A pdb=" N LEU K 11 " --> pdb=" O ASP K 105 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 114 through 118 removed outlier: 5.455A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 153 through 155 removed outlier: 4.468A pdb=" N TRP K 148 " --> pdb=" O GLN K 155 " (cutoff:3.500A) 979 hydrogen bonds defined for protein. 2565 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: 10.08 Time building geometry restraints manager: 12.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4735 1.32 - 1.44: 6171 1.44 - 1.57: 15189 1.57 - 1.69: 2 1.69 - 1.82: 195 Bond restraints: 26292 Sorted by residual: bond pdb=" CA PRO C 437 " pdb=" C PRO C 437 " ideal model delta sigma weight residual 1.514 1.538 -0.024 5.50e-03 3.31e+04 1.83e+01 bond pdb=" C2 MAN a 4 " pdb=" O2 MAN a 4 " ideal model delta sigma weight residual 1.407 1.490 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C4 NAG e 1 " pdb=" O4 NAG e 1 " ideal model delta sigma weight residual 1.409 1.492 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C4 NAG U 1 " pdb=" O4 NAG U 1 " ideal model delta sigma weight residual 1.409 1.492 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C2 MAN k 4 " pdb=" O2 MAN k 4 " ideal model delta sigma weight residual 1.407 1.489 -0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 26287 not shown) Histogram of bond angle deviations from ideal: 96.97 - 104.68: 463 104.68 - 112.40: 12305 112.40 - 120.11: 12143 120.11 - 127.83: 10510 127.83 - 135.54: 291 Bond angle restraints: 35712 Sorted by residual: angle pdb=" CA VAL C 89 " pdb=" CB VAL C 89 " pdb=" CG1 VAL C 89 " ideal model delta sigma weight residual 110.40 130.56 -20.16 1.70e+00 3.46e-01 1.41e+02 angle pdb=" CA VAL A 89 " pdb=" CB VAL A 89 " pdb=" CG1 VAL A 89 " ideal model delta sigma weight residual 110.40 129.91 -19.51 1.70e+00 3.46e-01 1.32e+02 angle pdb=" CA VAL G 89 " pdb=" CB VAL G 89 " pdb=" CG1 VAL G 89 " ideal model delta sigma weight residual 110.40 129.03 -18.63 1.70e+00 3.46e-01 1.20e+02 angle pdb=" CA ILE G 84 " pdb=" CB ILE G 84 " pdb=" CG1 ILE G 84 " ideal model delta sigma weight residual 110.40 127.61 -17.21 1.70e+00 3.46e-01 1.02e+02 angle pdb=" N VAL C 89 " pdb=" CA VAL C 89 " pdb=" C VAL C 89 " ideal model delta sigma weight residual 109.55 122.23 -12.68 1.38e+00 5.25e-01 8.45e+01 ... (remaining 35707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.67: 15706 21.67 - 43.34: 946 43.34 - 65.01: 227 65.01 - 86.68: 206 86.68 - 108.35: 123 Dihedral angle restraints: 17208 sinusoidal: 8169 harmonic: 9039 Sorted by residual: dihedral pdb=" C VAL C 89 " pdb=" N VAL C 89 " pdb=" CA VAL C 89 " pdb=" CB VAL C 89 " ideal model delta harmonic sigma weight residual -122.00 -149.50 27.50 0 2.50e+00 1.60e-01 1.21e+02 dihedral pdb=" C VAL G 89 " pdb=" N VAL G 89 " pdb=" CA VAL G 89 " pdb=" CB VAL G 89 " ideal model delta harmonic sigma weight residual -122.00 -149.26 27.26 0 2.50e+00 1.60e-01 1.19e+02 dihedral pdb=" C VAL A 89 " pdb=" N VAL A 89 " pdb=" CA VAL A 89 " pdb=" CB VAL A 89 " ideal model delta harmonic sigma weight residual -122.00 -148.97 26.97 0 2.50e+00 1.60e-01 1.16e+02 ... (remaining 17205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.300: 4289 0.300 - 0.600: 56 0.600 - 0.900: 0 0.900 - 1.200: 3 1.200 - 1.500: 11 Chirality restraints: 4359 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-02 2.50e+03 4.79e+03 chirality pdb=" C1 BMA c 3 " pdb=" O4 NAG c 2 " pdb=" C2 BMA c 3 " pdb=" O5 BMA c 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-02 2.50e+03 4.77e+03 chirality pdb=" C1 BMA m 3 " pdb=" O4 NAG m 2 " pdb=" C2 BMA m 3 " pdb=" O5 BMA m 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-02 2.50e+03 4.76e+03 ... (remaining 4356 not shown) Planarity restraints: 4446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 88 " -0.139 2.00e-02 2.50e+03 1.48e-01 2.73e+02 pdb=" CG ASN C 88 " 0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN C 88 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 88 " 0.229 2.00e-02 2.50e+03 pdb=" C1 NAG f 1 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 2 " -0.179 2.00e-02 2.50e+03 1.48e-01 2.73e+02 pdb=" C7 NAG Z 2 " 0.058 2.00e-02 2.50e+03 pdb=" C8 NAG Z 2 " -0.133 2.00e-02 2.50e+03 pdb=" N2 NAG Z 2 " 0.236 2.00e-02 2.50e+03 pdb=" O7 NAG Z 2 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 88 " -0.141 2.00e-02 2.50e+03 1.46e-01 2.65e+02 pdb=" CG ASN G 88 " 0.092 2.00e-02 2.50e+03 pdb=" OD1 ASN G 88 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN G 88 " 0.217 2.00e-02 2.50e+03 pdb=" C1 NAG p 1 " -0.175 2.00e-02 2.50e+03 ... (remaining 4443 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 5 2.53 - 3.12: 19183 3.12 - 3.72: 38004 3.72 - 4.31: 55985 4.31 - 4.90: 90917 Nonbonded interactions: 204094 Sorted by model distance: nonbonded pdb=" OE2 GLU A 102 " pdb=" CD1 ILE D 559 " model vdw 1.939 3.460 nonbonded pdb=" CD1 ILE B 559 " pdb=" CG2 THR G 106 " model vdw 2.457 3.880 nonbonded pdb=" N ALA K 50 " pdb=" O ALA K 50 " model vdw 2.521 2.496 nonbonded pdb=" N ALA F 50 " pdb=" O ALA F 50 " model vdw 2.523 2.496 nonbonded pdb=" N ALA L 50 " pdb=" O ALA L 50 " model vdw 2.523 2.496 ... (remaining 204089 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' 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 '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 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'Q' selection = chain 'a' selection = chain 'k' } 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.020 Extract box with map and model: 8.230 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 69.740 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 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 : 0.014 0.083 26292 Z= 0.918 Angle : 1.909 20.162 35712 Z= 1.222 Chirality : 0.133 1.500 4359 Planarity : 0.017 0.203 4407 Dihedral : 19.959 108.354 11247 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.79 % Favored : 92.82 % Rotamer: Outliers : 1.46 % Allowed : 7.61 % Favored : 90.93 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 10.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.14), residues: 3093 helix: -2.09 (0.18), residues: 525 sheet: -0.24 (0.18), residues: 813 loop : -1.24 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.153 0.024 TRP A 96 HIS 0.018 0.005 HIS G 72 PHE 0.065 0.013 PHE K 71 TYR 0.183 0.028 TYR A 217 ARG 0.017 0.001 ARG G 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 108 time to evaluate : 3.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9347 (ttm) cc_final: 0.9084 (tpp) REVERT: A 150 MET cc_start: 0.8722 (mmm) cc_final: 0.8006 (tpt) REVERT: G 150 MET cc_start: 0.8826 (mmm) cc_final: 0.8597 (mmp) outliers start: 40 outliers final: 11 residues processed: 146 average time/residue: 0.4637 time to fit residues: 105.5795 Evaluate side-chains 81 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain H residue 99 PHE Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 175 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 156 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 239 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 chunk 178 optimal weight: 9.9990 chunk 277 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN B 650 GLN D 650 GLN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 ASN ** I 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 616 ASN I 650 GLN L 89 GLN L 137 ASN L 147 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS F 137 ASN F 138 ASN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN K 137 ASN K 138 ASN ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26292 Z= 0.219 Angle : 0.810 10.695 35712 Z= 0.400 Chirality : 0.052 0.319 4359 Planarity : 0.004 0.044 4407 Dihedral : 16.471 78.736 5567 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.49 % Favored : 95.44 % Rotamer: Outliers : 1.79 % Allowed : 9.11 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.15), residues: 3093 helix: -0.42 (0.22), residues: 507 sheet: 0.09 (0.16), residues: 948 loop : -0.86 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 571 HIS 0.008 0.001 HIS B 564 PHE 0.018 0.002 PHE C 53 TYR 0.020 0.002 TYR A 318 ARG 0.004 0.001 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 70 time to evaluate : 3.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7501 (OUTLIER) cc_final: 0.7072 (p-80) REVERT: A 104 MET cc_start: 0.9342 (ttm) cc_final: 0.9002 (tpp) REVERT: A 150 MET cc_start: 0.8655 (mmm) cc_final: 0.7980 (tpt) REVERT: A 170 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8493 (pm20) REVERT: G 104 MET cc_start: 0.9313 (tpp) cc_final: 0.8972 (tpp) REVERT: G 467 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8463 (p) outliers start: 49 outliers final: 15 residues processed: 113 average time/residue: 0.3601 time to fit residues: 68.0050 Evaluate side-chains 80 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 62 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain L residue 108 ARG Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 109 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 231 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 278 optimal weight: 10.0000 chunk 300 optimal weight: 10.0000 chunk 247 optimal weight: 2.9990 chunk 276 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 170 GLN G 82 GLN G 99 ASN I 554 ASN L 138 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26292 Z= 0.270 Angle : 0.743 8.456 35712 Z= 0.359 Chirality : 0.052 0.347 4359 Planarity : 0.004 0.048 4407 Dihedral : 12.076 66.875 5556 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 1.98 % Allowed : 10.65 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 3093 helix: -0.05 (0.23), residues: 504 sheet: -0.01 (0.16), residues: 1008 loop : -0.85 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 571 HIS 0.017 0.001 HIS G 249 PHE 0.016 0.002 PHE K 98 TYR 0.021 0.002 TYR K 93 ARG 0.004 0.000 ARG I 585 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 64 time to evaluate : 3.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.7430 (p-80) REVERT: A 104 MET cc_start: 0.9323 (ttm) cc_final: 0.9024 (tpp) REVERT: A 150 MET cc_start: 0.8722 (mmm) cc_final: 0.8011 (tpt) REVERT: A 259 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8427 (pp) REVERT: B 530 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7503 (ttm) REVERT: C 259 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8773 (pt) REVERT: D 520 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6445 (mt) REVERT: G 104 MET cc_start: 0.9253 (tpp) cc_final: 0.8934 (tpp) REVERT: G 259 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8577 (pp) REVERT: I 554 ASN cc_start: 0.3068 (OUTLIER) cc_final: 0.2249 (p0) outliers start: 54 outliers final: 19 residues processed: 112 average time/residue: 0.3477 time to fit residues: 66.8422 Evaluate side-chains 85 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 59 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain I residue 554 ASN Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 181 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 132 optimal weight: 0.6980 chunk 186 optimal weight: 8.9990 chunk 279 optimal weight: 8.9990 chunk 295 optimal weight: 20.0000 chunk 145 optimal weight: 2.9990 chunk 264 optimal weight: 0.0770 chunk 79 optimal weight: 5.9990 overall best weight: 3.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 540 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 ASN K 147 GLN ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26292 Z= 0.266 Angle : 0.691 8.651 35712 Z= 0.333 Chirality : 0.049 0.345 4359 Planarity : 0.004 0.043 4407 Dihedral : 10.625 62.238 5554 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.66 % Favored : 95.28 % Rotamer: Outliers : 1.79 % Allowed : 12.40 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 3093 helix: 0.00 (0.23), residues: 522 sheet: 0.11 (0.16), residues: 987 loop : -0.85 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 571 HIS 0.007 0.001 HIS A 72 PHE 0.013 0.002 PHE K 98 TYR 0.018 0.002 TYR J 177 ARG 0.004 0.000 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 62 time to evaluate : 3.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7859 (OUTLIER) cc_final: 0.7456 (p-80) REVERT: A 104 MET cc_start: 0.9337 (ttm) cc_final: 0.9024 (tpp) REVERT: A 150 MET cc_start: 0.8715 (mmm) cc_final: 0.7992 (tpt) REVERT: A 259 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8431 (pp) REVERT: C 396 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8197 (tp) REVERT: D 518 VAL cc_start: 0.5577 (OUTLIER) cc_final: 0.5273 (m) REVERT: G 72 HIS cc_start: 0.7946 (OUTLIER) cc_final: 0.7737 (p90) REVERT: G 259 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8503 (pp) REVERT: I 554 ASN cc_start: 0.3612 (OUTLIER) cc_final: 0.1996 (p0) outliers start: 49 outliers final: 21 residues processed: 107 average time/residue: 0.3554 time to fit residues: 64.6796 Evaluate side-chains 88 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 60 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain I residue 554 ASN Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 181 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 0.6980 chunk 167 optimal weight: 30.0000 chunk 4 optimal weight: 20.0000 chunk 220 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 252 optimal weight: 20.0000 chunk 204 optimal weight: 0.0020 chunk 0 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 265 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 overall best weight: 2.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 26292 Z= 0.244 Angle : 0.666 11.807 35712 Z= 0.321 Chirality : 0.047 0.345 4359 Planarity : 0.004 0.044 4407 Dihedral : 9.989 59.479 5554 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.27 % Favored : 94.67 % Rotamer: Outliers : 1.87 % Allowed : 13.36 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 3093 helix: 0.16 (0.23), residues: 522 sheet: 0.13 (0.16), residues: 987 loop : -0.79 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 112 HIS 0.019 0.001 HIS B 564 PHE 0.013 0.002 PHE G 93 TYR 0.016 0.001 TYR K 93 ARG 0.003 0.000 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 62 time to evaluate : 3.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.7451 (p-80) REVERT: A 74 CYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7309 (t) REVERT: A 104 MET cc_start: 0.9353 (ttm) cc_final: 0.9020 (tpp) REVERT: A 150 MET cc_start: 0.8719 (mmm) cc_final: 0.8166 (tpt) REVERT: A 259 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8392 (pp) REVERT: G 72 HIS cc_start: 0.7850 (OUTLIER) cc_final: 0.7629 (p90) REVERT: G 82 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7343 (pm20) REVERT: G 104 MET cc_start: 0.9257 (tpp) cc_final: 0.8828 (tpp) REVERT: G 259 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8539 (pp) REVERT: G 467 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8381 (p) REVERT: H 57 MET cc_start: 0.8154 (ptt) cc_final: 0.7950 (ptt) outliers start: 51 outliers final: 27 residues processed: 109 average time/residue: 0.3624 time to fit residues: 66.6277 Evaluate side-chains 95 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 61 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 122 ASP Chi-restraints excluded: chain K residue 181 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 10.0000 chunk 266 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 chunk 73 optimal weight: 0.1980 chunk 296 optimal weight: 4.9990 chunk 245 optimal weight: 8.9990 chunk 137 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 82 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 26292 Z= 0.212 Angle : 0.640 8.307 35712 Z= 0.308 Chirality : 0.047 0.347 4359 Planarity : 0.004 0.044 4407 Dihedral : 9.620 59.429 5551 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.88 % Favored : 95.05 % Rotamer: Outliers : 1.65 % Allowed : 14.05 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3093 helix: 0.21 (0.23), residues: 522 sheet: 0.18 (0.16), residues: 981 loop : -0.76 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 571 HIS 0.007 0.001 HIS A 72 PHE 0.011 0.001 PHE C 53 TYR 0.015 0.001 TYR K 93 ARG 0.002 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 64 time to evaluate : 3.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7850 (OUTLIER) cc_final: 0.7479 (p-80) REVERT: A 74 CYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7334 (t) REVERT: A 104 MET cc_start: 0.9367 (OUTLIER) cc_final: 0.9021 (tpp) REVERT: A 150 MET cc_start: 0.8746 (mmm) cc_final: 0.8064 (tpt) REVERT: A 259 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8558 (pp) REVERT: G 104 MET cc_start: 0.9254 (tpp) cc_final: 0.8826 (tpp) REVERT: G 259 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8477 (pp) REVERT: G 475 MET cc_start: 0.7545 (mmt) cc_final: 0.7319 (mmt) outliers start: 45 outliers final: 27 residues processed: 105 average time/residue: 0.3484 time to fit residues: 62.6188 Evaluate side-chains 94 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 62 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 122 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 216 optimal weight: 30.0000 chunk 167 optimal weight: 20.0000 chunk 249 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 294 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 chunk 179 optimal weight: 8.9990 chunk 136 optimal weight: 0.0970 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 551 GLN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 577 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN K 166 GLN ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 26292 Z= 0.389 Angle : 0.717 8.781 35712 Z= 0.348 Chirality : 0.048 0.356 4359 Planarity : 0.005 0.048 4407 Dihedral : 9.979 59.927 5551 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.27 % Favored : 93.66 % Rotamer: Outliers : 2.31 % Allowed : 14.09 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 3093 helix: 0.11 (0.23), residues: 522 sheet: -0.07 (0.16), residues: 1020 loop : -0.87 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 103 HIS 0.008 0.001 HIS A 72 PHE 0.019 0.002 PHE K 98 TYR 0.022 0.002 TYR K 49 ARG 0.005 0.001 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 63 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7896 (OUTLIER) cc_final: 0.7479 (p-80) REVERT: A 74 CYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7380 (t) REVERT: A 104 MET cc_start: 0.9395 (OUTLIER) cc_final: 0.9036 (tpp) REVERT: A 150 MET cc_start: 0.8780 (mmm) cc_final: 0.8108 (tpt) REVERT: A 259 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8719 (pp) REVERT: G 259 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8598 (pp) REVERT: G 475 MET cc_start: 0.7558 (mmt) cc_final: 0.7284 (mmt) outliers start: 63 outliers final: 38 residues processed: 122 average time/residue: 0.3436 time to fit residues: 71.0806 Evaluate side-chains 104 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 61 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 122 ASP Chi-restraints excluded: chain K residue 181 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 200 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 268 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 551 GLN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN G 82 GLN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26292 Z= 0.182 Angle : 0.624 7.558 35712 Z= 0.300 Chirality : 0.046 0.350 4359 Planarity : 0.004 0.047 4407 Dihedral : 9.491 59.976 5551 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.15 % Rotamer: Outliers : 1.72 % Allowed : 14.67 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 3093 helix: 0.34 (0.24), residues: 522 sheet: 0.20 (0.16), residues: 951 loop : -0.82 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 112 HIS 0.008 0.001 HIS G 374 PHE 0.012 0.001 PHE C 53 TYR 0.013 0.001 TYR K 93 ARG 0.002 0.000 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 63 time to evaluate : 2.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7866 (OUTLIER) cc_final: 0.7496 (p-80) REVERT: A 74 CYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7403 (t) REVERT: A 104 MET cc_start: 0.9355 (ttm) cc_final: 0.9022 (tpp) REVERT: A 150 MET cc_start: 0.8741 (mmm) cc_final: 0.8526 (tpt) REVERT: A 259 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8564 (pp) REVERT: G 87 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6477 (pp20) REVERT: G 104 MET cc_start: 0.9223 (tpp) cc_final: 0.8804 (tpp) REVERT: G 475 MET cc_start: 0.7560 (mmt) cc_final: 0.7283 (mmt) outliers start: 47 outliers final: 33 residues processed: 106 average time/residue: 0.3527 time to fit residues: 64.1190 Evaluate side-chains 99 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 62 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 122 ASP Chi-restraints excluded: chain K residue 181 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 8.9990 chunk 257 optimal weight: 30.0000 chunk 274 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 215 optimal weight: 0.0770 chunk 84 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 chunk 259 optimal weight: 5.9990 chunk 273 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 overall best weight: 5.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 HIS ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 374 HIS ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 26292 Z= 0.387 Angle : 0.720 10.802 35712 Z= 0.348 Chirality : 0.048 0.355 4359 Planarity : 0.005 0.050 4407 Dihedral : 9.920 59.853 5551 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.50 % Favored : 93.44 % Rotamer: Outliers : 2.12 % Allowed : 14.86 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.15), residues: 3093 helix: 0.32 (0.24), residues: 504 sheet: -0.15 (0.16), residues: 1008 loop : -0.93 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 103 HIS 0.008 0.001 HIS A 72 PHE 0.018 0.002 PHE K 98 TYR 0.022 0.002 TYR K 49 ARG 0.004 0.001 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 62 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7873 (OUTLIER) cc_final: 0.7475 (p-80) REVERT: A 74 CYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7327 (t) REVERT: A 104 MET cc_start: 0.9414 (OUTLIER) cc_final: 0.9086 (tpp) REVERT: A 150 MET cc_start: 0.8777 (mmm) cc_final: 0.8141 (tpt) REVERT: A 259 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8793 (pp) REVERT: G 259 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8587 (pp) REVERT: G 271 MET cc_start: 0.8258 (mmm) cc_final: 0.7971 (tpt) REVERT: G 475 MET cc_start: 0.7649 (mmt) cc_final: 0.7381 (mmt) outliers start: 58 outliers final: 41 residues processed: 113 average time/residue: 0.3541 time to fit residues: 68.2228 Evaluate side-chains 107 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 61 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 626 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 374 HIS Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain I residue 518 VAL Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 122 ASP Chi-restraints excluded: chain K residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 chunk 137 optimal weight: 0.5980 chunk 202 optimal weight: 3.9990 chunk 304 optimal weight: 7.9990 chunk 280 optimal weight: 40.0000 chunk 242 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 HIS ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 374 HIS ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26292 Z= 0.243 Angle : 0.650 9.954 35712 Z= 0.313 Chirality : 0.047 0.351 4359 Planarity : 0.004 0.049 4407 Dihedral : 9.639 59.630 5551 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.56 % Favored : 94.37 % Rotamer: Outliers : 1.87 % Allowed : 15.08 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 3093 helix: 0.31 (0.24), residues: 522 sheet: -0.06 (0.16), residues: 975 loop : -0.86 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 112 HIS 0.007 0.001 HIS G 374 PHE 0.013 0.002 PHE K 98 TYR 0.015 0.001 TYR K 49 ARG 0.005 0.000 ARG G 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 61 time to evaluate : 2.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.7479 (p-80) REVERT: A 74 CYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7341 (t) REVERT: A 104 MET cc_start: 0.9366 (OUTLIER) cc_final: 0.9038 (tpp) REVERT: A 150 MET cc_start: 0.8756 (mmm) cc_final: 0.8141 (tpt) REVERT: A 259 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8731 (pp) REVERT: G 104 MET cc_start: 0.9228 (tpp) cc_final: 0.8804 (tpp) REVERT: G 259 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8611 (pp) REVERT: G 271 MET cc_start: 0.8242 (mmm) cc_final: 0.7994 (tpt) REVERT: G 475 MET cc_start: 0.7555 (mmt) cc_final: 0.7273 (mmt) outliers start: 51 outliers final: 42 residues processed: 106 average time/residue: 0.3343 time to fit residues: 61.2161 Evaluate side-chains 109 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 62 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 626 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 374 HIS Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 122 ASP Chi-restraints excluded: chain K residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 223 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 243 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 249 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 213 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.042937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.031931 restraints weight = 195562.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.032746 restraints weight = 124257.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.033258 restraints weight = 95302.711| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26292 Z= 0.227 Angle : 0.642 9.789 35712 Z= 0.308 Chirality : 0.046 0.350 4359 Planarity : 0.004 0.048 4407 Dihedral : 9.514 58.991 5551 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.69 % Favored : 94.25 % Rotamer: Outliers : 1.87 % Allowed : 15.04 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.15), residues: 3093 helix: 0.52 (0.24), residues: 504 sheet: 0.08 (0.17), residues: 948 loop : -0.88 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 112 HIS 0.022 0.001 HIS G 374 PHE 0.014 0.001 PHE G 376 TYR 0.013 0.001 TYR K 93 ARG 0.003 0.000 ARG G 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3655.43 seconds wall clock time: 69 minutes 51.65 seconds (4191.65 seconds total)