Starting phenix.real_space_refine on Mon Mar 18 06:03:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oro_20176/03_2024/6oro_20176.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oro_20176/03_2024/6oro_20176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oro_20176/03_2024/6oro_20176.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oro_20176/03_2024/6oro_20176.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oro_20176/03_2024/6oro_20176.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oro_20176/03_2024/6oro_20176.pdb" } resolution = 3.9 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= -0.001 sd= 0.213 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 12543 2.51 5 N 3345 2.21 5 O 4077 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 456": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "E ARG 8": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 308": "NH1" <-> "NH2" Residue "G ARG 327": "NH1" <-> "NH2" Residue "G ARG 456": "NH1" <-> "NH2" Residue "G ARG 469": "NH1" <-> "NH2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "I PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 327": "NH1" <-> "NH2" Residue "I ARG 456": "NH1" <-> "NH2" Residue "I ARG 469": "NH1" <-> "NH2" Residue "J ARG 66": "NH1" <-> "NH2" Residue "K ARG 8": "NH1" <-> "NH2" Residue "K ARG 61": "NH1" <-> "NH2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 8": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20085 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3540 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "C" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "E" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 806 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3540 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "H" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "I" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3540 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "J" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "K" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 806 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 806 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} 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: 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: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: 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: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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: 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: "g" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "F" 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.89, per 1000 atoms: 0.44 Number of scatterers: 20085 At special positions: 0 Unit cell: (143.6, 132.112, 153.652, 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 120 16.00 O 4077 8.00 N 3345 7.00 C 12543 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.02 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.02 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 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=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.04 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.02 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN W 4 " - " MAN W 5 " " MAN W 5 " - " MAN W 6 " " MAN f 4 " - " MAN f 5 " " MAN f 5 " - " MAN f 6 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA W 3 " - " MAN W 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA O 3 " - " MAN O 4 " " BMA X 3 " - " MAN X 4 " " BMA g 3 " - " MAN g 4 " 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 Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG 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 Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG 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 i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 618 " " NAG A 703 " - " ASN A 637 " " NAG B 620 " - " ASN B 88 " " NAG B 625 " - " ASN B 339 " " NAG B 626 " - " ASN B 355 " " NAG B 629 " - " ASN B 276 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 618 " " NAG C 703 " - " ASN C 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 618 " " NAG G 620 " - " ASN G 88 " " NAG G 625 " - " ASN G 339 " " NAG G 626 " - " ASN G 355 " " NAG G 629 " - " ASN G 276 " " NAG I 620 " - " ASN I 88 " " NAG I 625 " - " ASN I 339 " " NAG I 626 " - " ASN I 355 " " NAG I 629 " - " ASN I 276 " " NAG M 1 " - " ASN B 160 " " NAG N 1 " - " ASN B 332 " " NAG O 1 " - " ASN B 262 " " NAG P 1 " - " ASN B 448 " " NAG Q 1 " - " ASN B 295 " " NAG R 1 " - " ASN B 197 " " NAG S 1 " - " ASN B 392 " " NAG T 1 " - " ASN B 386 " " NAG U 1 " - " ASN B 301 " " NAG V 1 " - " ASN G 160 " " NAG W 1 " - " ASN G 332 " " NAG X 1 " - " ASN G 262 " " NAG Y 1 " - " ASN G 448 " " NAG Z 1 " - " ASN G 295 " " NAG a 1 " - " ASN G 197 " " NAG b 1 " - " ASN G 392 " " NAG c 1 " - " ASN G 386 " " NAG d 1 " - " ASN G 301 " " NAG e 1 " - " ASN I 160 " " NAG f 1 " - " ASN I 332 " " NAG g 1 " - " ASN I 262 " " NAG h 1 " - " ASN I 448 " " NAG i 1 " - " ASN I 295 " " NAG j 1 " - " ASN I 197 " " NAG k 1 " - " ASN I 392 " " NAG l 1 " - " ASN I 386 " " NAG m 1 " - " ASN I 301 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.64 Conformation dependent library (CDL) restraints added in 3.3 seconds 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 42 sheets defined 15.0% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.724A pdb=" N SER A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 removed outlier: 3.774A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 595 removed outlier: 3.527A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.730A pdb=" N TRP A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 619 through 624' Processing helix chain 'A' and resid 627 through 635 removed outlier: 4.437A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 649 removed outlier: 4.356A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 3.526A pdb=" N LYS A 655 " --> pdb=" O ASN A 651 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.740A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP B 113 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 117 removed outlier: 3.536A pdb=" N LYS B 117 " --> pdb=" O GLN B 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 114 through 117' Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 334 through 349 removed outlier: 3.670A pdb=" N GLU B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 353 removed outlier: 3.571A pdb=" N PHE B 353 " --> pdb=" O ARG B 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 350 through 353' Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.617A pdb=" N THR B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 474 through 480 removed outlier: 3.711A pdb=" N ASP B 477 " --> pdb=" O ASP B 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 removed outlier: 3.725A pdb=" N SER C 534 " --> pdb=" O MET C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 removed outlier: 3.776A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 595 removed outlier: 3.528A pdb=" N ALA C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR C 586 " --> pdb=" O ALA C 582 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.731A pdb=" N TRP C 623 " --> pdb=" O LEU C 619 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP C 624 " --> pdb=" O SER C 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 619 through 624' Processing helix chain 'C' and resid 627 through 635 removed outlier: 4.437A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU C 634 " --> pdb=" O GLN C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 649 removed outlier: 4.356A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 659 removed outlier: 3.527A pdb=" N LYS C 655 " --> pdb=" O ASN C 651 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN C 656 " --> pdb=" O GLN C 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.725A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 removed outlier: 3.775A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 595 removed outlier: 3.527A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS F 585 " --> pdb=" O LEU F 581 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR F 586 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 removed outlier: 3.618A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 4.438A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 649 removed outlier: 4.356A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 659 removed outlier: 3.526A pdb=" N LYS F 655 " --> pdb=" O ASN F 651 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 113 removed outlier: 3.739A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU G 111 " --> pdb=" O ASP G 107 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP G 113 " --> pdb=" O ILE G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 117 removed outlier: 3.535A pdb=" N LYS G 117 " --> pdb=" O GLN G 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 114 through 117' Processing helix chain 'G' and resid 139 through 151 removed outlier: 4.134A pdb=" N MET G 150 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG G 151 " --> pdb=" O SER G 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 139 through 151' Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 334 through 349 removed outlier: 3.670A pdb=" N GLU G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN G 348 " --> pdb=" O LYS G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 353 removed outlier: 3.570A pdb=" N PHE G 353 " --> pdb=" O ARG G 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 350 through 353' Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.617A pdb=" N THR G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 368 through 373' Processing helix chain 'G' and resid 474 through 480 removed outlier: 3.711A pdb=" N ASP G 477 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 113 removed outlier: 3.740A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP I 113 " --> pdb=" O ILE I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 117 removed outlier: 3.536A pdb=" N LYS I 117 " --> pdb=" O GLN I 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 114 through 117' Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 334 through 349 removed outlier: 3.670A pdb=" N GLU I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS I 347 " --> pdb=" O GLY I 343 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN I 348 " --> pdb=" O LYS I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 353 removed outlier: 3.571A pdb=" N PHE I 353 " --> pdb=" O ARG I 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 350 through 353' Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.616A pdb=" N THR I 372 " --> pdb=" O ASP I 368 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 368 through 373' Processing helix chain 'I' and resid 474 through 480 removed outlier: 3.711A pdb=" N ASP I 477 " --> pdb=" O ASP I 474 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 3.590A pdb=" N CYS A 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 38 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR A 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL B 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 495 " --> pdb=" O TYR B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.845A pdb=" N LYS B 487 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 93 removed outlier: 4.124A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS B 239 " --> pdb=" O GLU B 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 175 removed outlier: 3.603A pdb=" N PHE B 159 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 259 through 261 removed outlier: 4.281A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 284 through 286 removed outlier: 6.750A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 297 through 298 removed outlier: 3.739A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 304 through 308 removed outlier: 3.510A pdb=" N LYS B 305 " --> pdb=" O TYR B 319 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 307 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 329 through 333 removed outlier: 3.882A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS B 421 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 376 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 603 through 609 removed outlier: 3.573A pdb=" N CYS C 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL G 38 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR C 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL G 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY G 495 " --> pdb=" O TYR G 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.505A pdb=" N THR D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN D 81 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR D 68 " --> pdb=" O GLN D 81 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 46 through 48 removed outlier: 3.901A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 37 " --> pdb=" O TYR D 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 19 through 22 removed outlier: 3.911A pdb=" N SER E 67 " --> pdb=" O THR E 70 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 88 through 91 removed outlier: 3.970A pdb=" N CYS E 88 " --> pdb=" O GLY E 99 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL E 90 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU E 97 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 603 through 609 removed outlier: 3.575A pdb=" N CYS F 604 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL I 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR F 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL I 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY I 495 " --> pdb=" O TYR I 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.845A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'G' and resid 91 through 93 removed outlier: 4.125A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS G 239 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 169 through 175 removed outlier: 3.603A pdb=" N PHE G 159 " --> pdb=" O VAL G 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 259 through 261 removed outlier: 4.280A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 284 through 286 removed outlier: 6.750A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 297 through 298 removed outlier: 3.740A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 304 through 307 removed outlier: 3.511A pdb=" N LYS G 305 " --> pdb=" O TYR G 319 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE G 307 " --> pdb=" O PHE G 317 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 329 through 333 removed outlier: 3.883A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.506A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN H 81 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 46 through 48 removed outlier: 3.901A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.845A pdb=" N LYS I 487 " --> pdb=" O LEU I 226 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AD3, first strand: chain 'I' and resid 91 through 93 removed outlier: 4.125A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS I 239 " --> pdb=" O GLU I 91 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 169 through 175 removed outlier: 3.603A pdb=" N PHE I 159 " --> pdb=" O VAL I 172 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 259 through 261 removed outlier: 4.280A pdb=" N GLY I 451 " --> pdb=" O LEU I 260 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL I 292 " --> pdb=" O ILE I 449 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 284 through 286 removed outlier: 6.750A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 297 through 298 removed outlier: 3.739A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 304 through 308 removed outlier: 3.511A pdb=" N LYS I 305 " --> pdb=" O TYR I 319 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE I 307 " --> pdb=" O PHE I 317 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 329 through 333 removed outlier: 3.882A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE I 376 " --> pdb=" O PHE I 383 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.505A pdb=" N THR J 77 " --> pdb=" O ASP J 72 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN J 81 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR J 68 " --> pdb=" O GLN J 81 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 46 through 48 removed outlier: 3.902A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL J 37 " --> pdb=" O TYR J 91 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 19 through 22 removed outlier: 3.910A pdb=" N SER K 67 " --> pdb=" O THR K 70 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 88 through 91 removed outlier: 3.969A pdb=" N CYS K 88 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL K 90 " --> pdb=" O LEU K 97 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU K 97 " --> pdb=" O VAL K 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 19 through 22 removed outlier: 3.911A pdb=" N SER L 67 " --> pdb=" O THR L 70 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 88 through 91 removed outlier: 3.968A pdb=" N CYS L 88 " --> pdb=" O GLY L 99 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL L 90 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU L 97 " --> pdb=" O VAL L 90 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 936 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: 5.80 Time building geometry restraints manager: 9.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 3214 1.26 - 1.40: 4782 1.40 - 1.54: 12093 1.54 - 1.68: 230 1.68 - 1.82: 162 Bond restraints: 20481 Sorted by residual: bond pdb=" C ASN F 618 " pdb=" O ASN F 618 " ideal model delta sigma weight residual 1.233 1.118 0.115 1.36e-02 5.41e+03 7.13e+01 bond pdb=" C ASN F 618 " pdb=" N LEU F 619 " ideal model delta sigma weight residual 1.332 1.218 0.114 1.40e-02 5.10e+03 6.62e+01 bond pdb=" C ILE B 309 " pdb=" O ILE B 309 " ideal model delta sigma weight residual 1.236 1.159 0.077 1.19e-02 7.06e+03 4.17e+01 bond pdb=" C ILE G 309 " pdb=" O ILE G 309 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.19e-02 7.06e+03 3.64e+01 bond pdb=" C ALA I 316 " pdb=" O ALA I 316 " ideal model delta sigma weight residual 1.233 1.163 0.071 1.28e-02 6.10e+03 3.05e+01 ... (remaining 20476 not shown) Histogram of bond angle deviations from ideal: 96.11 - 104.53: 343 104.53 - 112.95: 11472 112.95 - 121.36: 10295 121.36 - 129.78: 5476 129.78 - 138.19: 212 Bond angle restraints: 27798 Sorted by residual: angle pdb=" CA PRO G 313 " pdb=" N PRO G 313 " pdb=" CD PRO G 313 " ideal model delta sigma weight residual 111.50 96.11 15.39 1.40e+00 5.10e-01 1.21e+02 angle pdb=" CA PRO B 313 " pdb=" N PRO B 313 " pdb=" CD PRO B 313 " ideal model delta sigma weight residual 111.50 99.17 12.33 1.40e+00 5.10e-01 7.76e+01 angle pdb=" CA PRO I 313 " pdb=" N PRO I 313 " pdb=" CD PRO I 313 " ideal model delta sigma weight residual 111.50 99.85 11.65 1.40e+00 5.10e-01 6.92e+01 angle pdb=" N PRO B 136 " pdb=" CA PRO B 136 " pdb=" C PRO B 136 " ideal model delta sigma weight residual 113.47 101.67 11.80 1.43e+00 4.89e-01 6.81e+01 angle pdb=" N PRO I 136 " pdb=" CA PRO I 136 " pdb=" C PRO I 136 " ideal model delta sigma weight residual 113.47 102.44 11.03 1.43e+00 4.89e-01 5.95e+01 ... (remaining 27793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 12560 21.75 - 43.51: 571 43.51 - 65.26: 182 65.26 - 87.01: 94 87.01 - 108.76: 51 Dihedral angle restraints: 13458 sinusoidal: 6549 harmonic: 6909 Sorted by residual: dihedral pdb=" CA ASN C 637 " pdb=" C ASN C 637 " pdb=" N TYR C 638 " pdb=" CA TYR C 638 " ideal model delta harmonic sigma weight residual 180.00 130.97 49.03 0 5.00e+00 4.00e-02 9.61e+01 dihedral pdb=" CA ASN A 637 " pdb=" C ASN A 637 " pdb=" N TYR A 638 " pdb=" CA TYR A 638 " ideal model delta harmonic sigma weight residual 180.00 130.97 49.03 0 5.00e+00 4.00e-02 9.61e+01 dihedral pdb=" CA ASN F 637 " pdb=" C ASN F 637 " pdb=" N TYR F 638 " pdb=" CA TYR F 638 " ideal model delta harmonic sigma weight residual 180.00 130.99 49.01 0 5.00e+00 4.00e-02 9.61e+01 ... (remaining 13455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.302: 3355 0.302 - 0.604: 15 0.604 - 0.907: 3 0.907 - 1.209: 0 1.209 - 1.511: 2 Chirality restraints: 3375 Sorted by residual: chirality pdb=" C1 NAG C 702 " pdb=" ND2 ASN C 618 " pdb=" C2 NAG C 702 " pdb=" O5 NAG C 702 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-01 2.50e+01 5.71e+01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 618 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-01 2.50e+01 5.70e+01 chirality pdb=" C1 NAG B 629 " pdb=" ND2 ASN B 276 " pdb=" C2 NAG B 629 " pdb=" O5 NAG B 629 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.59e+01 ... (remaining 3372 not shown) Planarity restraints: 3480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 617 " -0.030 2.00e-02 2.50e+03 6.10e-02 3.73e+01 pdb=" C ARG F 617 " 0.106 2.00e-02 2.50e+03 pdb=" O ARG F 617 " -0.039 2.00e-02 2.50e+03 pdb=" N ASN F 618 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 309 " 0.024 2.00e-02 2.50e+03 4.75e-02 2.25e+01 pdb=" C ILE B 309 " -0.082 2.00e-02 2.50e+03 pdb=" O ILE B 309 " 0.029 2.00e-02 2.50e+03 pdb=" N GLY B 312 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 703 " 0.049 2.00e-02 2.50e+03 4.05e-02 2.05e+01 pdb=" C7 NAG F 703 " 0.000 2.00e-02 2.50e+03 pdb=" C8 NAG F 703 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG F 703 " -0.068 2.00e-02 2.50e+03 pdb=" O7 NAG F 703 " -0.012 2.00e-02 2.50e+03 ... (remaining 3477 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 313 2.62 - 3.19: 16485 3.19 - 3.76: 27050 3.76 - 4.33: 35037 4.33 - 4.90: 58333 Nonbonded interactions: 137218 Sorted by model distance: nonbonded pdb=" O4 NAG F 703 " pdb=" O6 NAG F 703 " model vdw 2.048 2.440 nonbonded pdb=" OE2 GLU C 621 " pdb=" C5 NAG C 702 " model vdw 2.220 3.470 nonbonded pdb=" OE2 GLU A 621 " pdb=" C5 NAG A 702 " model vdw 2.220 3.470 nonbonded pdb=" O VAL H 12 " pdb=" OG SER H 112 " model vdw 2.263 2.440 nonbonded pdb=" O VAL J 12 " pdb=" OG SER J 112 " model vdw 2.263 2.440 ... (remaining 137213 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 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'V' selection = chain 'e' } ncs_group { reference = chain 'N' selection = chain 'W' selection = chain 'f' } ncs_group { reference = chain 'O' selection = chain 'X' selection = chain 'g' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' } 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.720 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 49.830 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.115 20481 Z= 0.575 Angle : 1.319 17.483 27798 Z= 0.706 Chirality : 0.087 1.511 3375 Planarity : 0.008 0.084 3432 Dihedral : 16.518 108.762 8919 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.59 % Allowed : 13.05 % Favored : 86.35 % Rotamer: Outliers : 2.93 % Allowed : 2.64 % Favored : 94.44 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.92 % 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: -5.30 (0.13), residues: 2367 helix: -4.63 (0.15), residues: 330 sheet: -3.26 (0.20), residues: 465 loop : -3.56 (0.12), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP H 47 HIS 0.011 0.002 HIS L 95B PHE 0.039 0.003 PHE J 100C TYR 0.043 0.003 TYR I 134 ARG 0.020 0.001 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 580 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.9189 (mttp) cc_final: 0.8867 (mtmm) REVERT: A 640 GLN cc_start: 0.9037 (mm110) cc_final: 0.8825 (mm-40) REVERT: B 92 GLU cc_start: 0.5024 (pt0) cc_final: 0.4754 (pt0) REVERT: B 95 MET cc_start: 0.8690 (ptm) cc_final: 0.8425 (ptt) REVERT: B 114 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8383 (tm-30) REVERT: B 161 MET cc_start: 0.8354 (tpp) cc_final: 0.7879 (tpt) REVERT: B 356 ASN cc_start: 0.9183 (t0) cc_final: 0.8980 (t0) REVERT: B 432 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8479 (tp-100) REVERT: B 466 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: C 625 ASN cc_start: 0.8945 (m-40) cc_final: 0.8728 (m-40) REVERT: C 635 ILE cc_start: 0.9296 (tt) cc_final: 0.9000 (tt) REVERT: C 647 GLU cc_start: 0.9068 (pp20) cc_final: 0.8769 (pp20) REVERT: D 19 LYS cc_start: 0.8877 (tttt) cc_final: 0.8674 (tttm) REVERT: D 38 ARG cc_start: 0.7661 (ptm160) cc_final: 0.7183 (ttp-170) REVERT: E 33 VAL cc_start: 0.8233 (p) cc_final: 0.6967 (p) REVERT: E 66 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8359 (tttp) REVERT: E 97 LEU cc_start: 0.8553 (tp) cc_final: 0.8232 (tp) REVERT: E 106 VAL cc_start: 0.6327 (m) cc_final: 0.6015 (m) REVERT: F 616 ASN cc_start: 0.9345 (t0) cc_final: 0.9089 (t0) REVERT: F 640 GLN cc_start: 0.8997 (mm110) cc_final: 0.8758 (mm-40) REVERT: G 104 MET cc_start: 0.8905 (tpp) cc_final: 0.8264 (tpp) REVERT: G 129 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8341 (pp) REVERT: G 180 ASP cc_start: 0.9203 (m-30) cc_final: 0.8585 (m-30) REVERT: G 189 LYS cc_start: 0.8317 (mmtm) cc_final: 0.8025 (mmmt) REVERT: G 308 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.8100 (ttm170) REVERT: G 356 ASN cc_start: 0.9092 (t0) cc_final: 0.8682 (t0) REVERT: G 427 TRP cc_start: 0.8377 (m-90) cc_final: 0.7590 (m-90) REVERT: G 466 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: H 72 ASP cc_start: 0.8941 (t0) cc_final: 0.8600 (t0) REVERT: H 75 LYS cc_start: 0.8589 (pttt) cc_final: 0.8160 (pttm) REVERT: H 99 GLN cc_start: 0.8899 (tp-100) cc_final: 0.8548 (tp40) REVERT: I 104 MET cc_start: 0.9048 (tpp) cc_final: 0.8698 (tpp) REVERT: I 150 MET cc_start: 0.9364 (mmm) cc_final: 0.9048 (mmm) REVERT: I 466 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: J 19 LYS cc_start: 0.8954 (tttt) cc_final: 0.8638 (tttm) REVERT: K 33 VAL cc_start: 0.8233 (p) cc_final: 0.7624 (p) REVERT: L 33 VAL cc_start: 0.7953 (p) cc_final: 0.6593 (p) REVERT: L 60 ASP cc_start: 0.8750 (p0) cc_final: 0.8511 (t0) REVERT: L 66 LYS cc_start: 0.8664 (ttpt) cc_final: 0.8435 (ttpp) outliers start: 61 outliers final: 18 residues processed: 610 average time/residue: 0.3202 time to fit residues: 291.5142 Evaluate side-chains 417 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 393 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 466 GLU Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 313 PRO Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain I residue 466 GLU Chi-restraints excluded: chain J residue 83 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 119 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 70 optimal weight: 0.0770 chunk 111 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 212 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN B 330 HIS B 428 GLN C 543 ASN C 575 GLN C 591 GLN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN D 81 GLN D 99 GLN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 300 ASN G 330 HIS G 440 GLN H 81 GLN H 99 GLN I 258 GLN I 300 ASN I 330 HIS J 99 GLN ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20481 Z= 0.193 Angle : 0.844 18.983 27798 Z= 0.403 Chirality : 0.053 0.683 3375 Planarity : 0.005 0.049 3432 Dihedral : 14.828 102.379 4606 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.62 % Favored : 88.21 % Rotamer: Outliers : 3.21 % Allowed : 11.22 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.85 (0.14), residues: 2367 helix: -3.84 (0.18), residues: 372 sheet: -2.76 (0.18), residues: 597 loop : -3.38 (0.14), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 69 HIS 0.005 0.001 HIS L 95B PHE 0.036 0.002 PHE J 100C TYR 0.014 0.001 TYR J 100E ARG 0.006 0.001 ARG G 151 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 471 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.9143 (mttp) cc_final: 0.8785 (mtmm) REVERT: B 114 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8326 (tm-30) REVERT: B 134 TYR cc_start: 0.6665 (OUTLIER) cc_final: 0.4516 (m-10) REVERT: B 154 LEU cc_start: 0.8328 (mt) cc_final: 0.7938 (mm) REVERT: B 432 GLN cc_start: 0.8823 (tp-100) cc_final: 0.8072 (mm-40) REVERT: C 607 ASN cc_start: 0.7669 (t0) cc_final: 0.7463 (t0) REVERT: C 635 ILE cc_start: 0.8931 (tt) cc_final: 0.8570 (tt) REVERT: D 82 MET cc_start: 0.7576 (mmt) cc_final: 0.7292 (mmp) REVERT: D 91 TYR cc_start: 0.9202 (m-80) cc_final: 0.8982 (m-80) REVERT: E 66 LYS cc_start: 0.8828 (ttpt) cc_final: 0.8195 (tttm) REVERT: F 635 ILE cc_start: 0.8932 (tt) cc_final: 0.8687 (tt) REVERT: G 104 MET cc_start: 0.8764 (tpp) cc_final: 0.8402 (tpp) REVERT: G 129 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8583 (pp) REVERT: G 180 ASP cc_start: 0.9007 (m-30) cc_final: 0.8416 (m-30) REVERT: G 189 LYS cc_start: 0.8406 (mmtm) cc_final: 0.8172 (mmmt) REVERT: G 308 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8034 (mtt90) REVERT: G 356 ASN cc_start: 0.8973 (t0) cc_final: 0.8762 (t0) REVERT: G 432 GLN cc_start: 0.8739 (tp-100) cc_final: 0.8218 (mp10) REVERT: G 475 MET cc_start: 0.8505 (tpp) cc_final: 0.8222 (tpp) REVERT: H 72 ASP cc_start: 0.8871 (t0) cc_final: 0.8461 (t0) REVERT: H 75 LYS cc_start: 0.8489 (pttt) cc_final: 0.8143 (ptmt) REVERT: H 83 ARG cc_start: 0.7517 (pmt170) cc_final: 0.6692 (ptm160) REVERT: H 99 GLN cc_start: 0.8702 (tp40) cc_final: 0.8328 (tp40) REVERT: I 46 LYS cc_start: 0.5027 (mttm) cc_final: 0.4524 (mmtt) REVERT: I 104 MET cc_start: 0.9113 (tpp) cc_final: 0.8445 (tpp) REVERT: I 150 MET cc_start: 0.9109 (mmm) cc_final: 0.8777 (mmm) REVERT: I 432 GLN cc_start: 0.8657 (tp-100) cc_final: 0.8231 (mm110) REVERT: I 475 MET cc_start: 0.8660 (tpp) cc_final: 0.8383 (tpp) REVERT: J 19 LYS cc_start: 0.8919 (tttt) cc_final: 0.8667 (tttm) REVERT: J 82 MET cc_start: 0.7512 (mmt) cc_final: 0.7221 (mmp) REVERT: J 83 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6701 (ttm-80) REVERT: J 97 TRP cc_start: 0.8906 (m100) cc_final: 0.8519 (m100) REVERT: L 31 GLU cc_start: 0.7835 (tp30) cc_final: 0.7332 (tp30) REVERT: L 33 VAL cc_start: 0.7996 (p) cc_final: 0.6633 (p) REVERT: L 49 TYR cc_start: 0.8252 (p90) cc_final: 0.8051 (p90) REVERT: L 66 LYS cc_start: 0.8714 (ttpt) cc_final: 0.8088 (tttp) outliers start: 67 outliers final: 42 residues processed: 508 average time/residue: 0.2894 time to fit residues: 230.0495 Evaluate side-chains 439 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 392 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 83 ARG Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 chunk 176 optimal weight: 5.9990 chunk 144 optimal weight: 0.0980 chunk 58 optimal weight: 0.0970 chunk 212 optimal weight: 1.9990 chunk 229 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 170 optimal weight: 1.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20481 Z= 0.186 Angle : 0.781 17.417 27798 Z= 0.370 Chirality : 0.050 0.355 3375 Planarity : 0.004 0.043 3432 Dihedral : 12.712 102.615 4580 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.96 % Favored : 87.87 % Rotamer: Outliers : 3.84 % Allowed : 14.44 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.15), residues: 2367 helix: -3.07 (0.22), residues: 342 sheet: -2.40 (0.20), residues: 597 loop : -3.20 (0.14), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP G 69 HIS 0.002 0.000 HIS K 95B PHE 0.031 0.002 PHE D 100C TYR 0.014 0.001 TYR K 49 ARG 0.006 0.000 ARG F 617 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 418 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.9131 (mttp) cc_final: 0.8869 (mtmm) REVERT: B 114 GLN cc_start: 0.8534 (tm130) cc_final: 0.8267 (tm-30) REVERT: B 134 TYR cc_start: 0.6488 (OUTLIER) cc_final: 0.4363 (m-10) REVERT: B 154 LEU cc_start: 0.8337 (mt) cc_final: 0.8100 (mm) REVERT: B 356 ASN cc_start: 0.8866 (t0) cc_final: 0.8609 (t0) REVERT: B 432 GLN cc_start: 0.8803 (tp-100) cc_final: 0.8117 (mm-40) REVERT: C 635 ILE cc_start: 0.8878 (tt) cc_final: 0.8594 (tt) REVERT: D 34 MET cc_start: 0.8988 (mmm) cc_final: 0.8765 (mmm) REVERT: D 67 PHE cc_start: 0.6599 (m-80) cc_final: 0.5833 (m-10) REVERT: D 82 MET cc_start: 0.7341 (mmt) cc_final: 0.7005 (mmt) REVERT: D 83 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6565 (ptm160) REVERT: D 99 GLN cc_start: 0.8754 (tp40) cc_final: 0.8523 (tp40) REVERT: E 38 GLN cc_start: 0.7640 (tt0) cc_final: 0.7420 (tt0) REVERT: E 66 LYS cc_start: 0.8846 (ttpt) cc_final: 0.8372 (tttp) REVERT: F 617 ARG cc_start: 0.8663 (mtt-85) cc_final: 0.8413 (mtt-85) REVERT: F 635 ILE cc_start: 0.8847 (tt) cc_final: 0.8593 (tt) REVERT: G 104 MET cc_start: 0.8799 (tpp) cc_final: 0.8370 (tpp) REVERT: G 129 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8517 (pp) REVERT: G 180 ASP cc_start: 0.8959 (m-30) cc_final: 0.8484 (m-30) REVERT: G 189 LYS cc_start: 0.8407 (mmtm) cc_final: 0.8093 (mmmt) REVERT: G 308 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7977 (mtt90) REVERT: G 356 ASN cc_start: 0.9050 (t0) cc_final: 0.8840 (t0) REVERT: G 432 GLN cc_start: 0.8779 (tp-100) cc_final: 0.8165 (mp10) REVERT: H 72 ASP cc_start: 0.8806 (t0) cc_final: 0.8423 (t0) REVERT: I 46 LYS cc_start: 0.4998 (mttm) cc_final: 0.4341 (mmtp) REVERT: I 104 MET cc_start: 0.9111 (tpp) cc_final: 0.8635 (tpp) REVERT: I 432 GLN cc_start: 0.8624 (tp-100) cc_final: 0.8189 (mm110) REVERT: J 47 TRP cc_start: 0.8651 (t60) cc_final: 0.8114 (t60) REVERT: J 67 PHE cc_start: 0.6796 (m-80) cc_final: 0.6148 (m-10) REVERT: J 82 MET cc_start: 0.7649 (mmt) cc_final: 0.7232 (mmt) REVERT: J 83 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6893 (ttm-80) REVERT: J 97 TRP cc_start: 0.8903 (m100) cc_final: 0.8503 (m100) REVERT: K 38 GLN cc_start: 0.7685 (tt0) cc_final: 0.7448 (tt0) REVERT: K 97 LEU cc_start: 0.8652 (tp) cc_final: 0.8198 (tt) REVERT: L 6 GLN cc_start: 0.7438 (pm20) cc_final: 0.7219 (pm20) REVERT: L 31 GLU cc_start: 0.7774 (tp30) cc_final: 0.7510 (tp30) REVERT: L 66 LYS cc_start: 0.8776 (ttpt) cc_final: 0.8117 (tttp) outliers start: 80 outliers final: 56 residues processed: 454 average time/residue: 0.2965 time to fit residues: 208.8590 Evaluate side-chains 450 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 389 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 368 ASP Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 73 ASN Chi-restraints excluded: chain J residue 83 ARG Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 chunk 213 optimal weight: 0.9980 chunk 226 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN C 543 ASN C 640 GLN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 20481 Z= 0.245 Angle : 0.776 16.168 27798 Z= 0.370 Chirality : 0.050 0.362 3375 Planarity : 0.004 0.047 3432 Dihedral : 11.563 101.853 4571 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.13 % Favored : 87.71 % Rotamer: Outliers : 5.37 % Allowed : 13.91 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.15), residues: 2367 helix: -2.26 (0.28), residues: 306 sheet: -2.23 (0.20), residues: 597 loop : -3.02 (0.14), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 69 HIS 0.003 0.001 HIS G 330 PHE 0.030 0.002 PHE D 100C TYR 0.016 0.001 TYR B 134 ARG 0.006 0.001 ARG J 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 403 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.9076 (mttp) cc_final: 0.8668 (mtmm) REVERT: B 103 GLN cc_start: 0.7823 (pt0) cc_final: 0.7353 (tt0) REVERT: B 114 GLN cc_start: 0.8647 (tm130) cc_final: 0.8162 (tm-30) REVERT: B 134 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.4821 (m-10) REVERT: B 432 GLN cc_start: 0.8777 (tp-100) cc_final: 0.8364 (tp-100) REVERT: C 571 TRP cc_start: 0.8198 (m100) cc_final: 0.7857 (m100) REVERT: C 635 ILE cc_start: 0.8995 (tt) cc_final: 0.8644 (tt) REVERT: C 650 GLN cc_start: 0.7405 (mm-40) cc_final: 0.6845 (mm-40) REVERT: D 13 GLN cc_start: 0.8041 (mp10) cc_final: 0.7813 (mp10) REVERT: D 34 MET cc_start: 0.8871 (mmm) cc_final: 0.8620 (mmm) REVERT: D 67 PHE cc_start: 0.7033 (m-80) cc_final: 0.5994 (m-10) REVERT: D 72 ASP cc_start: 0.8740 (t0) cc_final: 0.8515 (t0) REVERT: D 80 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8456 (tt) REVERT: D 99 GLN cc_start: 0.8782 (tp40) cc_final: 0.8384 (tp-100) REVERT: E 66 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8401 (tttp) REVERT: F 616 ASN cc_start: 0.9191 (t0) cc_final: 0.8986 (t0) REVERT: G 80 ASN cc_start: 0.8148 (p0) cc_final: 0.7907 (m-40) REVERT: G 111 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9092 (tt) REVERT: G 129 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8447 (pp) REVERT: G 180 ASP cc_start: 0.8984 (m-30) cc_final: 0.8471 (m-30) REVERT: G 308 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7933 (mtt90) REVERT: G 356 ASN cc_start: 0.9010 (t0) cc_final: 0.8756 (t0) REVERT: G 427 TRP cc_start: 0.8174 (m-90) cc_final: 0.7137 (m-90) REVERT: G 432 GLN cc_start: 0.8809 (tp-100) cc_final: 0.8195 (mp10) REVERT: H 72 ASP cc_start: 0.8765 (t0) cc_final: 0.8434 (t0) REVERT: H 81 GLN cc_start: 0.8865 (tt0) cc_final: 0.8539 (tt0) REVERT: H 99 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8021 (tp40) REVERT: I 46 LYS cc_start: 0.4845 (mttm) cc_final: 0.4469 (mmtt) REVERT: I 104 MET cc_start: 0.9088 (tpp) cc_final: 0.8810 (tpp) REVERT: I 432 GLN cc_start: 0.8660 (tp-100) cc_final: 0.8061 (mp10) REVERT: J 72 ASP cc_start: 0.8935 (t0) cc_final: 0.8662 (t0) REVERT: J 83 ARG cc_start: 0.7288 (pmt-80) cc_final: 0.6959 (ttm-80) REVERT: J 97 TRP cc_start: 0.8924 (m100) cc_final: 0.8619 (m100) REVERT: J 105 GLN cc_start: 0.8408 (pm20) cc_final: 0.8044 (pm20) REVERT: K 38 GLN cc_start: 0.7824 (tt0) cc_final: 0.7393 (tt0) REVERT: K 97 LEU cc_start: 0.8638 (tp) cc_final: 0.8194 (tt) REVERT: L 66 LYS cc_start: 0.8821 (ttpt) cc_final: 0.8052 (tttp) outliers start: 112 outliers final: 88 residues processed: 461 average time/residue: 0.2799 time to fit residues: 204.7954 Evaluate side-chains 486 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 392 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 368 ASP Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain G residue 448 ASN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 99 GLN Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 73 ASN Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 193 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 203 optimal weight: 40.0000 chunk 57 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 258 GLN H 81 GLN H 99 GLN ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 20481 Z= 0.240 Angle : 0.762 15.702 27798 Z= 0.364 Chirality : 0.050 0.357 3375 Planarity : 0.004 0.054 3432 Dihedral : 11.020 98.356 4557 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.51 % Favored : 87.33 % Rotamer: Outliers : 5.61 % Allowed : 15.11 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.15), residues: 2367 helix: -2.14 (0.27), residues: 336 sheet: -2.06 (0.21), residues: 579 loop : -3.04 (0.14), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 69 HIS 0.003 0.001 HIS L 95B PHE 0.025 0.002 PHE H 100C TYR 0.015 0.001 TYR B 134 ARG 0.005 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 390 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.9031 (mttp) cc_final: 0.8645 (mtmm) REVERT: B 103 GLN cc_start: 0.8193 (pt0) cc_final: 0.7745 (tt0) REVERT: B 114 GLN cc_start: 0.8622 (tm130) cc_final: 0.8110 (tm-30) REVERT: B 134 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.4790 (m-10) REVERT: B 432 GLN cc_start: 0.8770 (tp-100) cc_final: 0.8377 (tp-100) REVERT: C 571 TRP cc_start: 0.8123 (m100) cc_final: 0.7906 (m100) REVERT: C 635 ILE cc_start: 0.8991 (tt) cc_final: 0.8652 (tt) REVERT: C 650 GLN cc_start: 0.7351 (mm-40) cc_final: 0.6846 (mm-40) REVERT: D 13 GLN cc_start: 0.8009 (mp10) cc_final: 0.7745 (mp10) REVERT: D 34 MET cc_start: 0.8761 (mmm) cc_final: 0.8515 (mmm) REVERT: D 80 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8492 (tt) REVERT: D 82 MET cc_start: 0.7698 (mmp) cc_final: 0.7418 (mmp) REVERT: D 83 ARG cc_start: 0.7435 (pmt-80) cc_final: 0.7110 (pmt-80) REVERT: D 99 GLN cc_start: 0.8730 (tp40) cc_final: 0.8358 (tp-100) REVERT: E 33 VAL cc_start: 0.7954 (p) cc_final: 0.7372 (p) REVERT: E 66 LYS cc_start: 0.8840 (ttpt) cc_final: 0.8374 (tttp) REVERT: F 660 LEU cc_start: 0.8998 (mt) cc_final: 0.8797 (mt) REVERT: G 111 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9090 (tt) REVERT: G 129 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8437 (pp) REVERT: G 180 ASP cc_start: 0.9055 (m-30) cc_final: 0.8483 (m-30) REVERT: G 308 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7915 (mtt90) REVERT: G 356 ASN cc_start: 0.9018 (t0) cc_final: 0.8755 (t0) REVERT: G 427 TRP cc_start: 0.8183 (m-90) cc_final: 0.7081 (m-90) REVERT: G 432 GLN cc_start: 0.8797 (tp-100) cc_final: 0.8184 (mp10) REVERT: H 72 ASP cc_start: 0.8768 (t0) cc_final: 0.8422 (t0) REVERT: H 99 GLN cc_start: 0.8332 (tp40) cc_final: 0.8043 (tp40) REVERT: I 46 LYS cc_start: 0.4865 (mttm) cc_final: 0.4480 (mmtt) REVERT: I 432 GLN cc_start: 0.8649 (tp-100) cc_final: 0.8071 (mp10) REVERT: J 72 ASP cc_start: 0.8919 (t0) cc_final: 0.8643 (t0) REVERT: J 83 ARG cc_start: 0.7015 (pmt-80) cc_final: 0.6815 (ttm170) REVERT: J 97 TRP cc_start: 0.8904 (m100) cc_final: 0.8505 (m100) REVERT: J 105 GLN cc_start: 0.8461 (pm20) cc_final: 0.8048 (pm20) REVERT: K 38 GLN cc_start: 0.7943 (tt0) cc_final: 0.7357 (tt0) REVERT: K 97 LEU cc_start: 0.8635 (tp) cc_final: 0.8172 (tt) REVERT: L 31 GLU cc_start: 0.8173 (tp30) cc_final: 0.7545 (tp30) REVERT: L 66 LYS cc_start: 0.8844 (ttpt) cc_final: 0.8104 (tttp) REVERT: L 79 GLU cc_start: 0.7619 (tp30) cc_final: 0.7036 (mp0) outliers start: 117 outliers final: 98 residues processed: 451 average time/residue: 0.2931 time to fit residues: 208.4356 Evaluate side-chains 476 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 373 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 368 ASP Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 448 ASN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 97 TRP Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain I residue 424 ILE Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 73 ASN Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 10.0000 chunk 203 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 132 optimal weight: 0.0030 chunk 55 optimal weight: 3.9990 chunk 226 optimal weight: 0.1980 chunk 187 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 18 optimal weight: 0.0670 chunk 74 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 overall best weight: 0.3928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 ASN ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 ASN ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20481 Z= 0.152 Angle : 0.710 15.379 27798 Z= 0.336 Chirality : 0.047 0.337 3375 Planarity : 0.004 0.043 3432 Dihedral : 9.923 67.152 4554 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.07 % Favored : 88.76 % Rotamer: Outliers : 4.46 % Allowed : 16.59 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.16), residues: 2367 helix: -1.91 (0.28), residues: 324 sheet: -2.09 (0.20), residues: 633 loop : -2.87 (0.14), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP G 69 HIS 0.002 0.000 HIS B 374 PHE 0.030 0.001 PHE H 67 TYR 0.015 0.001 TYR B 134 ARG 0.008 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 414 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.8935 (mttp) cc_final: 0.8557 (mtmm) REVERT: B 103 GLN cc_start: 0.8106 (pt0) cc_final: 0.7745 (tt0) REVERT: B 114 GLN cc_start: 0.8581 (tm130) cc_final: 0.8227 (tm-30) REVERT: B 134 TYR cc_start: 0.7117 (OUTLIER) cc_final: 0.4678 (m-10) REVERT: B 328 MET cc_start: 0.8378 (mmm) cc_final: 0.8171 (mmt) REVERT: B 432 GLN cc_start: 0.8719 (tp-100) cc_final: 0.8111 (mm-40) REVERT: C 571 TRP cc_start: 0.7921 (m100) cc_final: 0.7692 (m100) REVERT: C 607 ASN cc_start: 0.8116 (t0) cc_final: 0.7913 (t0) REVERT: C 635 ILE cc_start: 0.8817 (tt) cc_final: 0.8548 (tt) REVERT: C 650 GLN cc_start: 0.7067 (mm-40) cc_final: 0.6654 (mm-40) REVERT: D 13 GLN cc_start: 0.7931 (mp10) cc_final: 0.7670 (mp10) REVERT: D 34 MET cc_start: 0.8620 (mmm) cc_final: 0.8348 (mmm) REVERT: D 80 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8494 (tt) REVERT: D 99 GLN cc_start: 0.8406 (tp40) cc_final: 0.8016 (tp-100) REVERT: E 33 VAL cc_start: 0.7256 (p) cc_final: 0.6747 (p) REVERT: E 66 LYS cc_start: 0.8806 (ttpt) cc_final: 0.8344 (tttp) REVERT: G 80 ASN cc_start: 0.8331 (m-40) cc_final: 0.8087 (p0) REVERT: G 111 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9077 (tt) REVERT: G 129 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8349 (pp) REVERT: G 134 TYR cc_start: 0.7410 (OUTLIER) cc_final: 0.5759 (m-80) REVERT: G 180 ASP cc_start: 0.9053 (m-30) cc_final: 0.8565 (m-30) REVERT: G 308 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7841 (ttp-110) REVERT: G 356 ASN cc_start: 0.9057 (t0) cc_final: 0.8797 (t0) REVERT: G 427 TRP cc_start: 0.8072 (m-90) cc_final: 0.7088 (m-90) REVERT: G 432 GLN cc_start: 0.8758 (tp-100) cc_final: 0.8162 (mp10) REVERT: H 72 ASP cc_start: 0.8809 (t0) cc_final: 0.8465 (t0) REVERT: H 81 GLN cc_start: 0.8822 (tt0) cc_final: 0.8384 (tt0) REVERT: H 82 MET cc_start: 0.8047 (mmp) cc_final: 0.7787 (mmp) REVERT: H 86 ASP cc_start: 0.5980 (m-30) cc_final: 0.5443 (p0) REVERT: H 99 GLN cc_start: 0.8248 (tp40) cc_final: 0.8030 (tp40) REVERT: I 69 TRP cc_start: 0.6297 (p-90) cc_final: 0.5952 (p-90) REVERT: I 432 GLN cc_start: 0.8591 (tp-100) cc_final: 0.8054 (mp10) REVERT: J 72 ASP cc_start: 0.9005 (t0) cc_final: 0.8676 (t0) REVERT: J 86 ASP cc_start: 0.5923 (m-30) cc_final: 0.5275 (p0) REVERT: K 38 GLN cc_start: 0.7743 (tt0) cc_final: 0.7391 (tt0) REVERT: K 97 LEU cc_start: 0.8600 (tp) cc_final: 0.8175 (tt) REVERT: L 31 GLU cc_start: 0.8015 (tp30) cc_final: 0.7329 (tp30) REVERT: L 50 ASP cc_start: 0.7817 (t0) cc_final: 0.7258 (t0) REVERT: L 66 LYS cc_start: 0.8804 (ttpt) cc_final: 0.8073 (tttp) REVERT: L 79 GLU cc_start: 0.7564 (tp30) cc_final: 0.6969 (mp0) outliers start: 93 outliers final: 69 residues processed: 469 average time/residue: 0.2973 time to fit residues: 216.7219 Evaluate side-chains 465 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 390 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 368 ASP Chi-restraints excluded: chain G residue 419 ARG Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 448 ASN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 137 ASN Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 424 ILE Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain J residue 73 ASN Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 128 optimal weight: 0.0980 chunk 165 optimal weight: 4.9990 chunk 190 optimal weight: 0.0270 chunk 126 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 104 optimal weight: 0.0870 chunk 139 optimal weight: 0.5980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 20481 Z= 0.152 Angle : 0.697 15.517 27798 Z= 0.329 Chirality : 0.047 0.331 3375 Planarity : 0.003 0.044 3432 Dihedral : 9.359 59.966 4552 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.77 % Favored : 89.06 % Rotamer: Outliers : 4.56 % Allowed : 17.03 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.16), residues: 2367 helix: -1.70 (0.28), residues: 324 sheet: -1.77 (0.21), residues: 591 loop : -2.82 (0.14), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP G 69 HIS 0.001 0.000 HIS I 374 PHE 0.021 0.001 PHE H 100C TYR 0.013 0.001 TYR B 134 ARG 0.011 0.000 ARG J 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 416 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.8861 (mttp) cc_final: 0.8486 (mtmm) REVERT: B 46 LYS cc_start: 0.6108 (mmtt) cc_final: 0.5298 (mmtp) REVERT: B 103 GLN cc_start: 0.8144 (pt0) cc_final: 0.7810 (tt0) REVERT: B 114 GLN cc_start: 0.8588 (tm130) cc_final: 0.8152 (tm-30) REVERT: B 134 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.4677 (m-10) REVERT: B 432 GLN cc_start: 0.8701 (tp-100) cc_final: 0.8085 (mm-40) REVERT: C 571 TRP cc_start: 0.8172 (m100) cc_final: 0.7923 (m100) REVERT: C 635 ILE cc_start: 0.8755 (tt) cc_final: 0.8513 (tt) REVERT: C 650 GLN cc_start: 0.7029 (mm-40) cc_final: 0.6687 (mm-40) REVERT: D 13 GLN cc_start: 0.7888 (mp10) cc_final: 0.7633 (mp10) REVERT: D 34 MET cc_start: 0.8617 (mmm) cc_final: 0.8377 (mmm) REVERT: D 67 PHE cc_start: 0.7312 (m-10) cc_final: 0.7019 (m-10) REVERT: D 80 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8490 (tt) REVERT: D 99 GLN cc_start: 0.8275 (tp40) cc_final: 0.7915 (tp-100) REVERT: E 66 LYS cc_start: 0.8769 (ttpt) cc_final: 0.8319 (tttp) REVERT: G 129 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8319 (pp) REVERT: G 134 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.5874 (m-80) REVERT: G 180 ASP cc_start: 0.9044 (m-30) cc_final: 0.8583 (m-30) REVERT: G 265 LEU cc_start: 0.9184 (mm) cc_final: 0.8803 (mt) REVERT: G 308 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7827 (mtm-85) REVERT: G 356 ASN cc_start: 0.9026 (t0) cc_final: 0.8778 (t0) REVERT: G 427 TRP cc_start: 0.8066 (m-90) cc_final: 0.7097 (m-90) REVERT: G 432 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8166 (mp10) REVERT: H 72 ASP cc_start: 0.8778 (t0) cc_final: 0.8400 (t0) REVERT: H 81 GLN cc_start: 0.8725 (tt0) cc_final: 0.8272 (tt0) REVERT: H 86 ASP cc_start: 0.6069 (m-30) cc_final: 0.5458 (p0) REVERT: I 69 TRP cc_start: 0.6241 (p-90) cc_final: 0.5887 (p-90) REVERT: I 111 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8924 (tt) REVERT: I 432 GLN cc_start: 0.8583 (tp-100) cc_final: 0.8055 (mp10) REVERT: J 72 ASP cc_start: 0.8985 (t0) cc_final: 0.8658 (t0) REVERT: J 86 ASP cc_start: 0.5852 (m-30) cc_final: 0.5284 (p0) REVERT: K 38 GLN cc_start: 0.7697 (tt0) cc_final: 0.7333 (tt0) REVERT: L 31 GLU cc_start: 0.7933 (tp30) cc_final: 0.7319 (tp30) REVERT: L 50 ASP cc_start: 0.7758 (t0) cc_final: 0.7111 (t0) REVERT: L 66 LYS cc_start: 0.8822 (ttpt) cc_final: 0.8114 (tttp) outliers start: 95 outliers final: 75 residues processed: 474 average time/residue: 0.2911 time to fit residues: 215.6259 Evaluate side-chains 478 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 397 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 368 ASP Chi-restraints excluded: chain G residue 419 ARG Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 448 ASN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 424 ILE Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain J residue 73 ASN Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 478 ASN G 80 ASN ** I 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 428 GLN I 478 ASN ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 20481 Z= 0.390 Angle : 0.846 14.591 27798 Z= 0.409 Chirality : 0.053 0.381 3375 Planarity : 0.004 0.051 3432 Dihedral : 9.887 59.640 4552 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.90 % Favored : 85.93 % Rotamer: Outliers : 5.37 % Allowed : 16.88 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.16), residues: 2367 helix: -1.67 (0.29), residues: 336 sheet: -1.97 (0.20), residues: 645 loop : -2.97 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 103 HIS 0.005 0.001 HIS L 95B PHE 0.021 0.002 PHE H 100C TYR 0.024 0.002 TYR B 134 ARG 0.007 0.001 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 385 time to evaluate : 2.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.8995 (mttp) cc_final: 0.8668 (mtmm) REVERT: A 650 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7312 (mm110) REVERT: B 46 LYS cc_start: 0.5620 (mmtt) cc_final: 0.5223 (mmtt) REVERT: B 134 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.5835 (m-80) REVERT: B 432 GLN cc_start: 0.8793 (tp-100) cc_final: 0.8480 (tp-100) REVERT: C 574 LYS cc_start: 0.8338 (mtpt) cc_final: 0.7785 (mtmt) REVERT: C 635 ILE cc_start: 0.9051 (tt) cc_final: 0.8685 (tt) REVERT: C 650 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7233 (mm-40) REVERT: D 13 GLN cc_start: 0.8039 (mp10) cc_final: 0.7765 (mp10) REVERT: D 18 LEU cc_start: 0.8896 (mt) cc_final: 0.8655 (mt) REVERT: D 67 PHE cc_start: 0.7397 (m-10) cc_final: 0.7160 (m-10) REVERT: D 99 GLN cc_start: 0.8658 (tp40) cc_final: 0.8226 (tp-100) REVERT: E 66 LYS cc_start: 0.8886 (ttpt) cc_final: 0.8228 (tttm) REVERT: G 80 ASN cc_start: 0.7977 (OUTLIER) cc_final: 0.7705 (m-40) REVERT: G 129 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8375 (pp) REVERT: G 134 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.5747 (m-80) REVERT: G 180 ASP cc_start: 0.9070 (m-30) cc_final: 0.8463 (m-30) REVERT: G 308 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7906 (mtt90) REVERT: G 356 ASN cc_start: 0.9067 (t0) cc_final: 0.8736 (t0) REVERT: G 427 TRP cc_start: 0.8237 (m-90) cc_final: 0.7190 (m-90) REVERT: G 432 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8196 (mp10) REVERT: H 28 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8434 (p) REVERT: H 72 ASP cc_start: 0.8776 (t0) cc_final: 0.8438 (t0) REVERT: H 81 GLN cc_start: 0.8866 (tt0) cc_final: 0.8389 (tt0) REVERT: H 82 MET cc_start: 0.8250 (mmp) cc_final: 0.7965 (mmp) REVERT: H 86 ASP cc_start: 0.6057 (m-30) cc_final: 0.5634 (p0) REVERT: I 46 LYS cc_start: 0.5483 (mmtt) cc_final: 0.4925 (mmtt) REVERT: I 432 GLN cc_start: 0.8696 (tp-100) cc_final: 0.8039 (mp10) REVERT: J 72 ASP cc_start: 0.8971 (t0) cc_final: 0.8633 (t0) REVERT: J 105 GLN cc_start: 0.8609 (pt0) cc_final: 0.8065 (pm20) REVERT: K 97 LEU cc_start: 0.8858 (tp) cc_final: 0.8579 (tt) REVERT: L 31 GLU cc_start: 0.8225 (tp30) cc_final: 0.7696 (tp30) REVERT: L 66 LYS cc_start: 0.8944 (ttpt) cc_final: 0.8182 (tttm) REVERT: L 79 GLU cc_start: 0.7725 (tp30) cc_final: 0.7510 (mm-30) REVERT: L 89 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8289 (tm-30) outliers start: 112 outliers final: 88 residues processed: 454 average time/residue: 0.2787 time to fit residues: 198.9105 Evaluate side-chains 466 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 372 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 87 TYR Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 80 ASN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 368 ASP Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 448 ASN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 424 ILE Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 73 ASN Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 95 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 0.0980 chunk 197 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 chunk 209 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS B 80 ASN G 80 ASN ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 ASN ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20481 Z= 0.207 Angle : 0.742 13.353 27798 Z= 0.357 Chirality : 0.049 0.362 3375 Planarity : 0.004 0.041 3432 Dihedral : 9.461 59.993 4552 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.25 % Favored : 87.58 % Rotamer: Outliers : 4.84 % Allowed : 17.31 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.16), residues: 2367 helix: -1.43 (0.31), residues: 318 sheet: -1.79 (0.22), residues: 558 loop : -2.83 (0.14), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 69 HIS 0.004 0.001 HIS A 570 PHE 0.025 0.002 PHE H 100C TYR 0.023 0.001 TYR B 134 ARG 0.007 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 385 time to evaluate : 2.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.8896 (mttp) cc_final: 0.8542 (mtmm) REVERT: B 46 LYS cc_start: 0.5384 (mmtt) cc_final: 0.5108 (mptt) REVERT: B 114 GLN cc_start: 0.8696 (tm130) cc_final: 0.8193 (tm130) REVERT: B 134 TYR cc_start: 0.7416 (OUTLIER) cc_final: 0.5883 (m-80) REVERT: B 432 GLN cc_start: 0.8692 (tp-100) cc_final: 0.8416 (tp-100) REVERT: C 635 ILE cc_start: 0.8944 (tt) cc_final: 0.8616 (tt) REVERT: C 650 GLN cc_start: 0.7318 (mm-40) cc_final: 0.6985 (mm-40) REVERT: D 13 GLN cc_start: 0.7972 (mp10) cc_final: 0.7686 (mp10) REVERT: D 18 LEU cc_start: 0.8838 (mt) cc_final: 0.8589 (mt) REVERT: D 67 PHE cc_start: 0.8031 (m-10) cc_final: 0.7822 (m-10) REVERT: D 99 GLN cc_start: 0.8358 (tp40) cc_final: 0.7960 (tp-100) REVERT: E 66 LYS cc_start: 0.8801 (ttpt) cc_final: 0.8056 (tttm) REVERT: F 650 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7227 (mm110) REVERT: G 129 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8492 (pp) REVERT: G 134 TYR cc_start: 0.7584 (OUTLIER) cc_final: 0.5922 (m-80) REVERT: G 180 ASP cc_start: 0.9075 (m-30) cc_final: 0.8488 (m-30) REVERT: G 308 ARG cc_start: 0.8075 (mtm180) cc_final: 0.7736 (mtt90) REVERT: G 356 ASN cc_start: 0.9042 (t0) cc_final: 0.8769 (t0) REVERT: G 427 TRP cc_start: 0.8156 (m-90) cc_final: 0.7277 (m-90) REVERT: G 432 GLN cc_start: 0.8639 (tp-100) cc_final: 0.8117 (mp10) REVERT: H 28 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8462 (p) REVERT: H 67 PHE cc_start: 0.7509 (m-10) cc_final: 0.7225 (m-10) REVERT: H 72 ASP cc_start: 0.8761 (t0) cc_final: 0.8341 (t0) REVERT: H 81 GLN cc_start: 0.8871 (tt0) cc_final: 0.8413 (tt0) REVERT: H 86 ASP cc_start: 0.5712 (m-30) cc_final: 0.5467 (p0) REVERT: H 99 GLN cc_start: 0.8405 (tp40) cc_final: 0.8049 (tp40) REVERT: I 46 LYS cc_start: 0.5267 (mmtt) cc_final: 0.4321 (mmtp) REVERT: I 69 TRP cc_start: 0.6290 (p-90) cc_final: 0.6008 (p-90) REVERT: I 432 GLN cc_start: 0.8620 (tp-100) cc_final: 0.8049 (mp10) REVERT: J 72 ASP cc_start: 0.8937 (t0) cc_final: 0.8590 (t0) REVERT: J 86 ASP cc_start: 0.5994 (m-30) cc_final: 0.5596 (p0) REVERT: K 97 LEU cc_start: 0.8749 (tp) cc_final: 0.8486 (tt) REVERT: L 31 GLU cc_start: 0.8116 (tp30) cc_final: 0.7545 (tp30) REVERT: L 66 LYS cc_start: 0.8956 (ttpt) cc_final: 0.8253 (tttp) REVERT: L 79 GLU cc_start: 0.7529 (tp30) cc_final: 0.7302 (mm-30) outliers start: 101 outliers final: 85 residues processed: 443 average time/residue: 0.2907 time to fit residues: 202.0758 Evaluate side-chains 468 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 379 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 87 TYR Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 368 ASP Chi-restraints excluded: chain G residue 419 ARG Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 448 ASN Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 137 ASN Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 424 ILE Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 73 ASN Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 233 optimal weight: 0.6980 chunk 214 optimal weight: 6.9990 chunk 185 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 143 optimal weight: 0.0020 chunk 113 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 overall best weight: 1.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS B 80 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 ASN ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20481 Z= 0.221 Angle : 0.741 13.867 27798 Z= 0.356 Chirality : 0.049 0.360 3375 Planarity : 0.004 0.052 3432 Dihedral : 9.255 59.701 4548 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.89 % Favored : 86.95 % Rotamer: Outliers : 4.75 % Allowed : 17.17 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.16), residues: 2367 helix: -1.34 (0.31), residues: 318 sheet: -1.87 (0.20), residues: 624 loop : -2.82 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 69 HIS 0.009 0.001 HIS A 570 PHE 0.022 0.002 PHE H 100C TYR 0.022 0.001 TYR B 134 ARG 0.008 0.000 ARG D 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 386 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.8868 (mttp) cc_final: 0.8497 (mtmm) REVERT: A 650 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7244 (mm110) REVERT: B 46 LYS cc_start: 0.5350 (mmtt) cc_final: 0.4833 (mmtm) REVERT: B 114 GLN cc_start: 0.8702 (tm130) cc_final: 0.8156 (tm130) REVERT: B 134 TYR cc_start: 0.7346 (OUTLIER) cc_final: 0.6009 (m-80) REVERT: B 432 GLN cc_start: 0.8717 (tp-100) cc_final: 0.8435 (tp-100) REVERT: C 635 ILE cc_start: 0.8917 (tt) cc_final: 0.8591 (tt) REVERT: C 650 GLN cc_start: 0.7335 (mm-40) cc_final: 0.6984 (mm-40) REVERT: D 13 GLN cc_start: 0.7953 (mp10) cc_final: 0.7668 (mp10) REVERT: D 18 LEU cc_start: 0.8852 (mt) cc_final: 0.8617 (mt) REVERT: D 99 GLN cc_start: 0.8366 (tp40) cc_final: 0.7977 (tp-100) REVERT: E 60 ASP cc_start: 0.9004 (t0) cc_final: 0.8581 (t0) REVERT: E 66 LYS cc_start: 0.8870 (ttpt) cc_final: 0.8016 (tttm) REVERT: G 129 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8476 (pp) REVERT: G 134 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.6094 (m-80) REVERT: G 180 ASP cc_start: 0.9061 (m-30) cc_final: 0.8518 (m-30) REVERT: G 265 LEU cc_start: 0.9177 (mm) cc_final: 0.8813 (mt) REVERT: G 308 ARG cc_start: 0.8159 (mtm180) cc_final: 0.7933 (mtm180) REVERT: G 356 ASN cc_start: 0.9051 (t0) cc_final: 0.8778 (t0) REVERT: G 432 GLN cc_start: 0.8644 (tp-100) cc_final: 0.8121 (mp10) REVERT: H 28 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8466 (p) REVERT: H 67 PHE cc_start: 0.7625 (m-10) cc_final: 0.7313 (m-10) REVERT: H 72 ASP cc_start: 0.8781 (t0) cc_final: 0.8455 (t0) REVERT: H 81 GLN cc_start: 0.8769 (tt0) cc_final: 0.8302 (tt0) REVERT: H 86 ASP cc_start: 0.5751 (m-30) cc_final: 0.5493 (p0) REVERT: I 46 LYS cc_start: 0.5277 (mmtt) cc_final: 0.4657 (mmtt) REVERT: I 69 TRP cc_start: 0.6316 (p-90) cc_final: 0.5962 (p-90) REVERT: I 432 GLN cc_start: 0.8633 (tp-100) cc_final: 0.8051 (mp10) REVERT: J 47 TRP cc_start: 0.8822 (t60) cc_final: 0.8319 (t60) REVERT: J 72 ASP cc_start: 0.8936 (t0) cc_final: 0.8584 (t0) REVERT: J 86 ASP cc_start: 0.6024 (m-30) cc_final: 0.5611 (p0) REVERT: J 105 GLN cc_start: 0.8581 (pt0) cc_final: 0.8105 (pm20) REVERT: K 97 LEU cc_start: 0.8758 (tp) cc_final: 0.8530 (tt) REVERT: L 31 GLU cc_start: 0.8132 (tp30) cc_final: 0.7557 (tp30) REVERT: L 66 LYS cc_start: 0.8957 (ttpt) cc_final: 0.8253 (tttp) REVERT: L 79 GLU cc_start: 0.7415 (tp30) cc_final: 0.7066 (mm-30) outliers start: 99 outliers final: 87 residues processed: 443 average time/residue: 0.2826 time to fit residues: 197.1047 Evaluate side-chains 472 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 381 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 87 TYR Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 368 ASP Chi-restraints excluded: chain G residue 419 ARG Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 448 ASN Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 137 ASN Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 424 ILE Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 73 ASN Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 190 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 34 optimal weight: 0.0770 chunk 163 optimal weight: 8.9990 overall best weight: 0.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 570 HIS ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN I 137 ASN ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108066 restraints weight = 32418.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111426 restraints weight = 18195.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.113669 restraints weight = 12645.087| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20481 Z= 0.168 Angle : 0.722 14.639 27798 Z= 0.345 Chirality : 0.048 0.349 3375 Planarity : 0.004 0.048 3432 Dihedral : 8.927 59.286 4548 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.79 % Favored : 88.04 % Rotamer: Outliers : 4.27 % Allowed : 17.65 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.16), residues: 2367 helix: -1.29 (0.30), residues: 318 sheet: -1.80 (0.21), residues: 573 loop : -2.76 (0.14), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 69 HIS 0.010 0.001 HIS C 570 PHE 0.021 0.001 PHE H 100C TYR 0.020 0.001 TYR B 134 ARG 0.008 0.000 ARG D 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4362.31 seconds wall clock time: 79 minutes 24.49 seconds (4764.49 seconds total)