Starting phenix.real_space_refine on Thu Jul 25 17:02:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn2_36430/07_2024/8jn2_36430.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn2_36430/07_2024/8jn2_36430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn2_36430/07_2024/8jn2_36430.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn2_36430/07_2024/8jn2_36430.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn2_36430/07_2024/8jn2_36430.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jn2_36430/07_2024/8jn2_36430.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 204 5.16 5 C 19018 2.51 5 N 5056 2.21 5 O 5710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 13": "OD1" <-> "OD2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B ARG 27": "NH1" <-> "NH2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 10": "OD1" <-> "OD2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C ASP 147": "OD1" <-> "OD2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "C ASP 382": "OD1" <-> "OD2" Residue "C TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 419": "OD1" <-> "OD2" Residue "C TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 49": "OE1" <-> "OE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E ARG 186": "NH1" <-> "NH2" Residue "E PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 309": "OE1" <-> "OE2" Residue "E GLU 323": "OE1" <-> "OE2" Residue "E PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 89": "OD1" <-> "OD2" Residue "L PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 83": "OD1" <-> "OD2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 154": "OE1" <-> "OE2" Residue "O TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 182": "OE1" <-> "OE2" Residue "O ARG 284": "NH1" <-> "NH2" Residue "O GLU 291": "OE1" <-> "OE2" Residue "O GLU 323": "OE1" <-> "OE2" Residue "O PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 361": "OE1" <-> "OE2" Residue "O PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 405": "NH1" <-> "NH2" Residue "O ARG 409": "NH1" <-> "NH2" Residue "O PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 13": "OD1" <-> "OD2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P ARG 27": "NH1" <-> "NH2" Residue "P PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 10": "OD1" <-> "OD2" Residue "Q ASP 71": "OD1" <-> "OD2" Residue "Q TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 126": "OE1" <-> "OE2" Residue "Q ASP 147": "OD1" <-> "OD2" Residue "Q GLU 182": "OE1" <-> "OE2" Residue "Q GLU 225": "OE1" <-> "OE2" Residue "Q GLU 233": "OE1" <-> "OE2" Residue "Q GLU 255": "OE1" <-> "OE2" Residue "Q GLU 267": "OE1" <-> "OE2" Residue "Q PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 323": "OE1" <-> "OE2" Residue "Q ASP 382": "OD1" <-> "OD2" Residue "Q TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 419": "OD1" <-> "OD2" Residue "Q TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "S PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 154": "OE1" <-> "OE2" Residue "S ARG 186": "NH1" <-> "NH2" Residue "S PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 309": "OE1" <-> "OE2" Residue "S GLU 323": "OE1" <-> "OE2" Residue "S PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 89": "OD1" <-> "OD2" Residue "V PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 83": "OD1" <-> "OD2" Residue "V TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 29988 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3759 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain: "B" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 797 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 3759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3759 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain: "P" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Q" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "T" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "U" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "V" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 797 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: "0" 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: "1" 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 Time building chain proxies: 15.48, per 1000 atoms: 0.52 Number of scatterers: 29988 At special positions: 0 Unit cell: (162.45, 241.11, 116.28, 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 204 16.00 O 5710 8.00 N 5056 7.00 C 19018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.02 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS C 105 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.04 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 283 " distance=2.03 Simple disulfide: pdb=" SG CYS C 300 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 116 " distance=2.04 Simple disulfide: pdb=" SG CYS E 300 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS O 3 " - pdb=" SG CYS O 30 " distance=2.02 Simple disulfide: pdb=" SG CYS O 60 " - pdb=" SG CYS O 121 " distance=2.03 Simple disulfide: pdb=" SG CYS O 74 " - pdb=" SG CYS O 105 " distance=2.03 Simple disulfide: pdb=" SG CYS O 300 " - pdb=" SG CYS O 331 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 3 " - pdb=" SG CYS Q 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 60 " - pdb=" SG CYS Q 121 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 74 " - pdb=" SG CYS Q 105 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 92 " - pdb=" SG CYS Q 116 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 183 " - pdb=" SG CYS Q 283 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 300 " - pdb=" SG CYS Q 331 " distance=2.03 Simple disulfide: pdb=" SG CYS S 92 " - pdb=" SG CYS S 116 " distance=2.04 Simple disulfide: pdb=" SG CYS S 300 " - pdb=" SG CYS S 331 " distance=2.02 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " NAG-ASN " NAG 0 1 " - " ASN S 67 " " NAG 1 1 " - " ASN S 153 " " NAG G 1 " - " ASN A 67 " " NAG I 1 " - " ASN A 153 " " NAG J 1 " - " ASN C 67 " " NAG K 1 " - " ASN C 153 " " NAG M 1 " - " ASN E 67 " " NAG N 1 " - " ASN E 153 " " NAG W 1 " - " ASN O 67 " " NAG X 1 " - " ASN O 153 " " NAG Y 1 " - " ASN Q 67 " " NAG Z 1 " - " ASN Q 153 " Time building additional restraints: 11.86 Conformation dependent library (CDL) restraints added in 5.1 seconds 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6948 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 76 sheets defined 26.4% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.662A pdb=" N GLN A 150 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL A 151 " --> pdb=" O GLN A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 151' Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 231 through 234 removed outlier: 3.815A pdb=" N LEU A 234 " --> pdb=" O ARG A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 234' Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 394 through 414 removed outlier: 3.627A pdb=" N ILE A 412 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 removed outlier: 3.540A pdb=" N ASP A 419 " --> pdb=" O THR A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 removed outlier: 3.930A pdb=" N ALA A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 466 Processing helix chain 'A' and resid 470 through 489 Processing helix chain 'B' and resid 20 through 39 removed outlier: 4.403A pdb=" N GLN B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N VAL B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.683A pdb=" N ILE B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 75 removed outlier: 3.561A pdb=" N THR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Proline residue: B 72 - end of helix Processing helix chain 'C' and resid 16 through 18 No H-bonds generated for 'chain 'C' and resid 16 through 18' Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.677A pdb=" N GLY C 104 " --> pdb=" O TRP C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 212 removed outlier: 3.640A pdb=" N PHE C 212 " --> pdb=" O ARG C 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 208 through 212' Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 394 through 414 Processing helix chain 'C' and resid 415 through 420 removed outlier: 4.009A pdb=" N TRP C 418 " --> pdb=" O ASP C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 446 Processing helix chain 'C' and resid 450 through 467 Processing helix chain 'C' and resid 470 through 491 Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 26 through 39 Processing helix chain 'D' and resid 40 through 54 removed outlier: 4.239A pdb=" N ILE D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 75 Proline residue: D 72 - end of helix Processing helix chain 'E' and resid 82 through 87 removed outlier: 3.736A pdb=" N GLN E 86 " --> pdb=" O PRO E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 104 removed outlier: 3.602A pdb=" N GLY E 104 " --> pdb=" O TRP E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 135 Processing helix chain 'E' and resid 185 through 188 Processing helix chain 'E' and resid 207 through 213 Processing helix chain 'E' and resid 231 through 235 removed outlier: 3.597A pdb=" N LEU E 235 " --> pdb=" O LYS E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 262 Processing helix chain 'E' and resid 394 through 414 Processing helix chain 'E' and resid 415 through 417 No H-bonds generated for 'chain 'E' and resid 415 through 417' Processing helix chain 'E' and resid 425 through 446 Processing helix chain 'E' and resid 450 through 467 Processing helix chain 'E' and resid 471 through 490 removed outlier: 4.311A pdb=" N PHE E 475 " --> pdb=" O THR E 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 39 Processing helix chain 'F' and resid 40 through 53 removed outlier: 3.872A pdb=" N ILE F 44 " --> pdb=" O PRO F 40 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU F 45 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 71 removed outlier: 3.894A pdb=" N THR F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'O' and resid 100 through 104 Processing helix chain 'O' and resid 131 through 133 No H-bonds generated for 'chain 'O' and resid 131 through 133' Processing helix chain 'O' and resid 147 through 151 removed outlier: 3.662A pdb=" N GLN O 150 " --> pdb=" O ASP O 147 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL O 151 " --> pdb=" O GLN O 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 147 through 151' Processing helix chain 'O' and resid 185 through 188 Processing helix chain 'O' and resid 207 through 213 Processing helix chain 'O' and resid 231 through 234 removed outlier: 3.815A pdb=" N LEU O 234 " --> pdb=" O ARG O 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 231 through 234' Processing helix chain 'O' and resid 254 through 262 Processing helix chain 'O' and resid 394 through 414 removed outlier: 3.627A pdb=" N ILE O 412 " --> pdb=" O ARG O 408 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 419 removed outlier: 3.540A pdb=" N ASP O 419 " --> pdb=" O THR O 416 " (cutoff:3.500A) Processing helix chain 'O' and resid 427 through 444 removed outlier: 3.930A pdb=" N ALA O 441 " --> pdb=" O ILE O 437 " (cutoff:3.500A) Processing helix chain 'O' and resid 450 through 466 Processing helix chain 'O' and resid 470 through 489 Processing helix chain 'P' and resid 20 through 39 removed outlier: 4.403A pdb=" N GLN P 28 " --> pdb=" O GLY P 24 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N VAL P 29 " --> pdb=" O ALA P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 53 removed outlier: 3.683A pdb=" N ILE P 44 " --> pdb=" O PRO P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 75 removed outlier: 3.561A pdb=" N THR P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) Proline residue: P 72 - end of helix Processing helix chain 'Q' and resid 16 through 18 No H-bonds generated for 'chain 'Q' and resid 16 through 18' Processing helix chain 'Q' and resid 100 through 104 removed outlier: 3.677A pdb=" N GLY Q 104 " --> pdb=" O TRP Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 208 through 212 removed outlier: 3.640A pdb=" N PHE Q 212 " --> pdb=" O ARG Q 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 208 through 212' Processing helix chain 'Q' and resid 254 through 262 Processing helix chain 'Q' and resid 394 through 414 Processing helix chain 'Q' and resid 415 through 420 removed outlier: 4.009A pdb=" N TRP Q 418 " --> pdb=" O ASP Q 415 " (cutoff:3.500A) Processing helix chain 'Q' and resid 425 through 446 Processing helix chain 'Q' and resid 450 through 467 Processing helix chain 'Q' and resid 470 through 491 Processing helix chain 'R' and resid 20 through 25 Processing helix chain 'R' and resid 26 through 39 Processing helix chain 'R' and resid 40 through 54 removed outlier: 4.239A pdb=" N ILE R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU R 45 " --> pdb=" O GLY R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 75 Proline residue: R 72 - end of helix Processing helix chain 'S' and resid 82 through 87 removed outlier: 3.736A pdb=" N GLN S 86 " --> pdb=" O PRO S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 100 through 104 removed outlier: 3.602A pdb=" N GLY S 104 " --> pdb=" O TRP S 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 131 through 135 Processing helix chain 'S' and resid 185 through 188 Processing helix chain 'S' and resid 207 through 213 Processing helix chain 'S' and resid 231 through 235 removed outlier: 3.597A pdb=" N LEU S 235 " --> pdb=" O LYS S 232 " (cutoff:3.500A) Processing helix chain 'S' and resid 254 through 262 Processing helix chain 'S' and resid 394 through 414 Processing helix chain 'S' and resid 415 through 417 No H-bonds generated for 'chain 'S' and resid 415 through 417' Processing helix chain 'S' and resid 425 through 446 Processing helix chain 'S' and resid 450 through 467 Processing helix chain 'S' and resid 471 through 490 removed outlier: 4.311A pdb=" N PHE S 475 " --> pdb=" O THR S 471 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 39 Processing helix chain 'T' and resid 40 through 53 removed outlier: 3.872A pdb=" N ILE T 44 " --> pdb=" O PRO T 40 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU T 45 " --> pdb=" O GLY T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 71 removed outlier: 3.894A pdb=" N THR T 71 " --> pdb=" O LEU T 67 " (cutoff:3.500A) Processing helix chain 'V' and resid 80 through 84 Processing sheet with id=1, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.171A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 140 " --> pdb=" O GLU A 44 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N THR A 138 " --> pdb=" O GLN A 46 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR A 48 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LYS A 136 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 20 through 25 removed outlier: 3.564A pdb=" N VAL A 21 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 281 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=4, first strand: chain 'A' and resid 65 through 72 removed outlier: 4.583A pdb=" N ILE A 68 " --> pdb=" O CYS A 116 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS A 116 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR A 70 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL A 114 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER A 72 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N SER A 112 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 115 " --> pdb=" O LYS A 93 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 93 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 195 through 196 removed outlier: 3.690A pdb=" N ALA A 203 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 268 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=7, first strand: chain 'A' and resid 240 through 241 removed outlier: 3.541A pdb=" N ALA A 241 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=7 Processing sheet with id=8, first strand: chain 'A' and resid 305 through 308 removed outlier: 3.853A pdb=" N LYS A 307 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N LYS A 321 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A 368 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG A 348 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 336 through 339 removed outlier: 3.667A pdb=" N TRP A 389 " --> pdb=" O SER A 374 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.484A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C 139 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'C' and resid 20 through 26 removed outlier: 3.552A pdb=" N LEU C 281 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 48 through 50 removed outlier: 3.672A pdb=" N THR C 48 " --> pdb=" O ILE C 276 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'C' and resid 54 through 55 removed outlier: 4.062A pdb=" N MET C 205 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR C 266 " --> pdb=" O MET C 205 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=15, first strand: chain 'C' and resid 63 through 64 removed outlier: 3.554A pdb=" N GLN C 120 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 68 through 72 removed outlier: 3.523A pdb=" N ALA C 117 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'C' and resid 68 through 72 removed outlier: 3.515A pdb=" N GLY C 109 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'C' and resid 237 through 240 removed outlier: 4.065A pdb=" N THR C 237 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 249 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 247 " --> pdb=" O LYS C 239 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'C' and resid 304 through 306 removed outlier: 3.524A pdb=" N SER C 311 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'C' and resid 304 through 306 Processing sheet with id=21, first strand: chain 'C' and resid 336 through 338 removed outlier: 3.704A pdb=" N GLY C 372 " --> pdb=" O LYS C 391 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.229A pdb=" N ASP E 10 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR E 138 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR E 48 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LYS E 136 " --> pdb=" O THR E 48 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'E' and resid 20 through 26 Processing sheet with id=24, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=25, first strand: chain 'E' and resid 59 through 62 removed outlier: 3.697A pdb=" N ILE E 61 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLU E 123 " --> pdb=" O ILE E 61 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'E' and resid 65 through 72 removed outlier: 4.713A pdb=" N ILE E 68 " --> pdb=" O CYS E 116 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N CYS E 116 " --> pdb=" O ILE E 68 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N THR E 70 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL E 114 " --> pdb=" O THR E 70 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N SER E 72 " --> pdb=" O SER E 112 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N SER E 112 " --> pdb=" O SER E 72 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR E 115 " --> pdb=" O LYS E 93 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'E' and resid 237 through 239 Processing sheet with id=28, first strand: chain 'E' and resid 269 through 270 removed outlier: 3.626A pdb=" N GLN E 269 " --> pdb=" O SER E 275 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'E' and resid 304 through 306 removed outlier: 3.758A pdb=" N VAL E 305 " --> pdb=" O GLU E 323 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR E 317 " --> pdb=" O THR E 313 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER E 311 " --> pdb=" O LEU E 319 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'E' and resid 304 through 306 removed outlier: 3.758A pdb=" N VAL E 305 " --> pdb=" O GLU E 323 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL E 322 " --> pdb=" O VAL E 363 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'E' and resid 336 through 339 removed outlier: 3.776A pdb=" N SER E 336 " --> pdb=" O VAL E 377 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN E 375 " --> pdb=" O GLU E 338 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'H' and resid 3 through 4 removed outlier: 3.892A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'H' and resid 33 through 34 Processing sheet with id=34, first strand: chain 'H' and resid 45 through 47 Processing sheet with id=35, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.719A pdb=" N LEU L 107 " --> pdb=" O ALA L 85 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA L 85 " --> pdb=" O LEU L 107 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN L 38 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.719A pdb=" N LEU L 107 " --> pdb=" O ALA L 85 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA L 85 " --> pdb=" O LEU L 107 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.847A pdb=" N VAL L 18 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE L 76 " --> pdb=" O VAL L 18 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.847A pdb=" N VAL L 18 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE L 76 " --> pdb=" O VAL L 18 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'O' and resid 10 through 11 removed outlier: 6.171A pdb=" N ASP O 10 " --> pdb=" O THR O 32 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE O 140 " --> pdb=" O GLU O 44 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N THR O 138 " --> pdb=" O GLN O 46 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR O 48 " --> pdb=" O LYS O 136 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LYS O 136 " --> pdb=" O THR O 48 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'O' and resid 20 through 25 removed outlier: 3.564A pdb=" N VAL O 21 " --> pdb=" O LEU O 285 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU O 281 " --> pdb=" O LEU O 25 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'O' and resid 58 through 59 Processing sheet with id=42, first strand: chain 'O' and resid 65 through 72 removed outlier: 4.583A pdb=" N ILE O 68 " --> pdb=" O CYS O 116 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS O 116 " --> pdb=" O ILE O 68 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR O 70 " --> pdb=" O VAL O 114 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL O 114 " --> pdb=" O THR O 70 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER O 72 " --> pdb=" O SER O 112 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N SER O 112 " --> pdb=" O SER O 72 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR O 115 " --> pdb=" O LYS O 93 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS O 93 " --> pdb=" O THR O 115 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'O' and resid 195 through 196 removed outlier: 3.690A pdb=" N ALA O 203 " --> pdb=" O ILE O 268 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE O 268 " --> pdb=" O ALA O 203 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'O' and resid 236 through 237 Processing sheet with id=45, first strand: chain 'O' and resid 240 through 241 removed outlier: 3.541A pdb=" N ALA O 241 " --> pdb=" O LYS O 245 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS O 245 " --> pdb=" O ALA O 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=45 Processing sheet with id=46, first strand: chain 'O' and resid 305 through 308 removed outlier: 3.853A pdb=" N LYS O 307 " --> pdb=" O LYS O 321 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N LYS O 321 " --> pdb=" O LYS O 307 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU O 368 " --> pdb=" O ARG O 348 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG O 348 " --> pdb=" O GLU O 368 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'O' and resid 336 through 339 removed outlier: 3.667A pdb=" N TRP O 389 " --> pdb=" O SER O 374 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'Q' and resid 10 through 11 removed outlier: 6.484A pdb=" N ASP Q 10 " --> pdb=" O THR Q 32 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL Q 139 " --> pdb=" O ALA Q 160 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'Q' and resid 20 through 26 removed outlier: 3.552A pdb=" N LEU Q 281 " --> pdb=" O LEU Q 25 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'Q' and resid 48 through 50 removed outlier: 3.672A pdb=" N THR Q 48 " --> pdb=" O ILE Q 276 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'Q' and resid 54 through 55 removed outlier: 4.062A pdb=" N MET Q 205 " --> pdb=" O THR Q 266 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR Q 266 " --> pdb=" O MET Q 205 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'Q' and resid 59 through 60 Processing sheet with id=53, first strand: chain 'Q' and resid 63 through 64 removed outlier: 3.554A pdb=" N GLN Q 120 " --> pdb=" O LYS Q 64 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'Q' and resid 68 through 72 removed outlier: 3.523A pdb=" N ALA Q 117 " --> pdb=" O VAL Q 91 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'Q' and resid 68 through 72 removed outlier: 3.515A pdb=" N GLY Q 109 " --> pdb=" O ARG Q 99 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'Q' and resid 237 through 240 removed outlier: 4.065A pdb=" N THR Q 237 " --> pdb=" O VAL Q 249 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL Q 249 " --> pdb=" O THR Q 237 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU Q 247 " --> pdb=" O LYS Q 239 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'Q' and resid 304 through 306 removed outlier: 3.524A pdb=" N SER Q 311 " --> pdb=" O LEU Q 319 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'Q' and resid 304 through 306 Processing sheet with id=59, first strand: chain 'Q' and resid 336 through 338 removed outlier: 3.704A pdb=" N GLY Q 372 " --> pdb=" O LYS Q 391 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.229A pdb=" N ASP S 10 " --> pdb=" O THR S 32 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR S 138 " --> pdb=" O GLN S 46 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR S 48 " --> pdb=" O LYS S 136 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LYS S 136 " --> pdb=" O THR S 48 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'S' and resid 20 through 26 Processing sheet with id=62, first strand: chain 'S' and resid 54 through 55 Processing sheet with id=63, first strand: chain 'S' and resid 59 through 62 removed outlier: 3.697A pdb=" N ILE S 61 " --> pdb=" O GLU S 123 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLU S 123 " --> pdb=" O ILE S 61 " (cutoff:3.500A) Processing sheet with id=64, first strand: chain 'S' and resid 65 through 72 removed outlier: 4.713A pdb=" N ILE S 68 " --> pdb=" O CYS S 116 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N CYS S 116 " --> pdb=" O ILE S 68 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N THR S 70 " --> pdb=" O VAL S 114 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL S 114 " --> pdb=" O THR S 70 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N SER S 72 " --> pdb=" O SER S 112 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N SER S 112 " --> pdb=" O SER S 72 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR S 115 " --> pdb=" O LYS S 93 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'S' and resid 237 through 239 Processing sheet with id=66, first strand: chain 'S' and resid 269 through 270 removed outlier: 3.626A pdb=" N GLN S 269 " --> pdb=" O SER S 275 " (cutoff:3.500A) Processing sheet with id=67, first strand: chain 'S' and resid 304 through 306 removed outlier: 3.758A pdb=" N VAL S 305 " --> pdb=" O GLU S 323 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR S 317 " --> pdb=" O THR S 313 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER S 311 " --> pdb=" O LEU S 319 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'S' and resid 304 through 306 removed outlier: 3.758A pdb=" N VAL S 305 " --> pdb=" O GLU S 323 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL S 322 " --> pdb=" O VAL S 363 " (cutoff:3.500A) Processing sheet with id=69, first strand: chain 'S' and resid 336 through 339 removed outlier: 3.776A pdb=" N SER S 336 " --> pdb=" O VAL S 377 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN S 375 " --> pdb=" O GLU S 338 " (cutoff:3.500A) Processing sheet with id=70, first strand: chain 'U' and resid 3 through 4 removed outlier: 3.892A pdb=" N GLN U 3 " --> pdb=" O SER U 25 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER U 25 " --> pdb=" O GLN U 3 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'U' and resid 33 through 34 Processing sheet with id=72, first strand: chain 'U' and resid 45 through 47 Processing sheet with id=73, first strand: chain 'V' and resid 10 through 11 removed outlier: 3.719A pdb=" N LEU V 107 " --> pdb=" O ALA V 85 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA V 85 " --> pdb=" O LEU V 107 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP V 36 " --> pdb=" O LEU V 48 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN V 38 " --> pdb=" O LYS V 46 " (cutoff:3.500A) Processing sheet with id=74, first strand: chain 'V' and resid 10 through 11 removed outlier: 3.719A pdb=" N LEU V 107 " --> pdb=" O ALA V 85 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA V 85 " --> pdb=" O LEU V 107 " (cutoff:3.500A) Processing sheet with id=75, first strand: chain 'V' and resid 18 through 23 removed outlier: 3.847A pdb=" N VAL V 18 " --> pdb=" O ILE V 76 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE V 76 " --> pdb=" O VAL V 18 " (cutoff:3.500A) Processing sheet with id=76, first strand: chain 'V' and resid 18 through 23 removed outlier: 3.847A pdb=" N VAL V 18 " --> pdb=" O ILE V 76 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE V 76 " --> pdb=" O VAL V 18 " (cutoff:3.500A) 1126 hydrogen bonds defined for protein. 3024 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.90 Time building geometry restraints manager: 12.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9604 1.34 - 1.47: 7226 1.47 - 1.59: 13444 1.59 - 1.71: 0 1.71 - 1.83: 322 Bond restraints: 30596 Sorted by residual: bond pdb=" CA ALA O 417 " pdb=" C ALA O 417 " ideal model delta sigma weight residual 1.522 1.485 0.037 1.38e-02 5.25e+03 7.36e+00 bond pdb=" CA ALA A 417 " pdb=" C ALA A 417 " ideal model delta sigma weight residual 1.522 1.485 0.037 1.38e-02 5.25e+03 7.36e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.06e+00 bond pdb=" C1 NAG 1 1 " pdb=" O5 NAG 1 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.06e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 3.93e+00 ... (remaining 30591 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.46: 828 106.46 - 113.39: 17592 113.39 - 120.32: 10204 120.32 - 127.25: 12464 127.25 - 134.18: 396 Bond angle restraints: 41484 Sorted by residual: angle pdb=" N GLY U 56 " pdb=" CA GLY U 56 " pdb=" C GLY U 56 " ideal model delta sigma weight residual 112.37 116.99 -4.62 1.40e+00 5.10e-01 1.09e+01 angle pdb=" N GLY H 56 " pdb=" CA GLY H 56 " pdb=" C GLY H 56 " ideal model delta sigma weight residual 112.37 116.99 -4.62 1.40e+00 5.10e-01 1.09e+01 angle pdb=" CB MET S 473 " pdb=" CG MET S 473 " pdb=" SD MET S 473 " ideal model delta sigma weight residual 112.70 122.58 -9.88 3.00e+00 1.11e-01 1.08e+01 angle pdb=" CB MET E 473 " pdb=" CG MET E 473 " pdb=" SD MET E 473 " ideal model delta sigma weight residual 112.70 122.58 -9.88 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C THR Q 224 " pdb=" N GLU Q 225 " pdb=" CA GLU Q 225 " ideal model delta sigma weight residual 121.54 127.82 -6.28 1.91e+00 2.74e-01 1.08e+01 ... (remaining 41479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.12: 17388 23.12 - 46.24: 924 46.24 - 69.35: 86 69.35 - 92.47: 96 92.47 - 115.59: 40 Dihedral angle restraints: 18534 sinusoidal: 7644 harmonic: 10890 Sorted by residual: dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual 93.00 4.41 88.59 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS O 60 " pdb=" SG CYS O 60 " pdb=" SG CYS O 121 " pdb=" CB CYS O 121 " ideal model delta sinusoidal sigma weight residual 93.00 4.41 88.59 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS C 300 " pdb=" SG CYS C 300 " pdb=" SG CYS C 331 " pdb=" CB CYS C 331 " ideal model delta sinusoidal sigma weight residual 93.00 11.35 81.65 1 1.00e+01 1.00e-02 8.21e+01 ... (remaining 18531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3844 0.053 - 0.107: 884 0.107 - 0.160: 114 0.160 - 0.213: 10 0.213 - 0.267: 10 Chirality restraints: 4862 Sorted by residual: chirality pdb=" C5 BMA W 3 " pdb=" C4 BMA W 3 " pdb=" C6 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C5 BMA Z 3 " pdb=" C4 BMA Z 3 " pdb=" C6 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 4859 not shown) Planarity restraints: 5194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 451 " -0.018 2.00e-02 2.50e+03 1.46e-02 5.34e+00 pdb=" CG TRP E 451 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP E 451 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP E 451 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 451 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 451 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 451 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 451 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 451 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 451 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP S 451 " -0.018 2.00e-02 2.50e+03 1.46e-02 5.34e+00 pdb=" CG TRP S 451 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP S 451 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP S 451 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP S 451 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP S 451 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP S 451 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 451 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 451 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP S 451 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 163 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.63e+00 pdb=" N PRO C 164 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " 0.026 5.00e-02 4.00e+02 ... (remaining 5191 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 485 2.65 - 3.21: 29172 3.21 - 3.78: 43991 3.78 - 4.34: 57725 4.34 - 4.90: 96147 Nonbonded interactions: 227520 Sorted by model distance: nonbonded pdb=" OG1 THR S 48 " pdb=" O ILE S 276 " model vdw 2.089 2.440 nonbonded pdb=" OG1 THR E 48 " pdb=" O ILE E 276 " model vdw 2.089 2.440 nonbonded pdb=" O GLN E 46 " pdb=" OG1 THR E 138 " model vdw 2.103 2.440 nonbonded pdb=" O GLN S 46 " pdb=" OG1 THR S 138 " model vdw 2.103 2.440 nonbonded pdb=" OG SER V 27 " pdb=" OG SER V 95 " model vdw 2.169 2.440 ... (remaining 227515 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 '0' selection = chain '1' selection = chain 'G' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'W' selection = chain 'Z' } ncs_group { reference = (chain 'A' and (resid 1 through 492 or (resid 493 and (name N or name CA or name \ C or name CB )))) selection = chain 'C' selection = chain 'E' selection = (chain 'O' and (resid 1 through 492 or (resid 493 and (name N or name CA or name \ C or name CB )))) selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'H' selection = chain 'U' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'V' } 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.180 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 77.710 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.220 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.005 0.045 30596 Z= 0.298 Angle : 0.760 9.875 41484 Z= 0.419 Chirality : 0.046 0.267 4862 Planarity : 0.004 0.048 5182 Dihedral : 15.804 115.590 11502 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.13), residues: 3838 helix: 0.83 (0.18), residues: 884 sheet: -1.13 (0.17), residues: 972 loop : -2.12 (0.13), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 451 HIS 0.006 0.001 HIS A 27 PHE 0.017 0.002 PHE C 304 TYR 0.014 0.002 TYR C 324 ARG 0.006 0.001 ARG Q 186 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1146 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1146 time to evaluate : 3.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping REVERT: A 42 ASP cc_start: 0.8466 (t0) cc_final: 0.8255 (t0) REVERT: A 49 GLU cc_start: 0.8254 (mp0) cc_final: 0.7865 (mp0) REVERT: A 69 THR cc_start: 0.9207 (p) cc_final: 0.8569 (p) REVERT: A 71 ASP cc_start: 0.8172 (p0) cc_final: 0.7936 (t70) REVERT: A 133 GLU cc_start: 0.8097 (pp20) cc_final: 0.7771 (pp20) REVERT: A 182 GLU cc_start: 0.7581 (mm-30) cc_final: 0.6956 (tp30) REVERT: A 195 ILE cc_start: 0.9014 (mt) cc_final: 0.8349 (tt) REVERT: A 453 MET cc_start: 0.8238 (tpp) cc_final: 0.7945 (tpt) REVERT: A 486 TYR cc_start: 0.8381 (t80) cc_final: 0.8097 (t80) REVERT: A 487 LEU cc_start: 0.8792 (tt) cc_final: 0.8514 (tt) REVERT: A 492 GLN cc_start: 0.8450 (mt0) cc_final: 0.7886 (tm-30) REVERT: B 60 LYS cc_start: 0.7970 (mttt) cc_final: 0.7766 (mttt) REVERT: C 1 MET cc_start: 0.8829 (mmp) cc_final: 0.7900 (mmm) REVERT: C 41 LEU cc_start: 0.9537 (pp) cc_final: 0.9317 (pt) REVERT: C 47 LYS cc_start: 0.8502 (mttp) cc_final: 0.8058 (pttt) REVERT: C 49 GLU cc_start: 0.7949 (mp0) cc_final: 0.7507 (mp0) REVERT: C 148 GLN cc_start: 0.8943 (tt0) cc_final: 0.8414 (tm-30) REVERT: C 196 LEU cc_start: 0.8891 (mt) cc_final: 0.8687 (mp) REVERT: C 237 THR cc_start: 0.9177 (p) cc_final: 0.8890 (p) REVERT: C 366 GLU cc_start: 0.7883 (pm20) cc_final: 0.7602 (pm20) REVERT: D 68 MET cc_start: 0.8613 (mmm) cc_final: 0.7421 (tmm) REVERT: D 74 MET cc_start: 0.8533 (mmm) cc_final: 0.8140 (mmm) REVERT: E 12 VAL cc_start: 0.9540 (p) cc_final: 0.9336 (t) REVERT: E 116 CYS cc_start: 0.5758 (m) cc_final: 0.5478 (m) REVERT: E 125 ILE cc_start: 0.9595 (tt) cc_final: 0.9124 (tt) REVERT: E 183 CYS cc_start: 0.8658 (m) cc_final: 0.8397 (m) REVERT: E 306 LEU cc_start: 0.9204 (tp) cc_final: 0.8920 (tp) REVERT: E 335 PHE cc_start: 0.8435 (t80) cc_final: 0.8179 (t80) REVERT: E 399 MET cc_start: 0.7892 (tmm) cc_final: 0.7442 (tmm) REVERT: E 419 ASP cc_start: 0.7714 (m-30) cc_final: 0.7373 (m-30) REVERT: F 51 HIS cc_start: 0.7549 (t-90) cc_final: 0.7007 (t-90) REVERT: F 59 GLN cc_start: 0.8088 (tt0) cc_final: 0.7184 (tt0) REVERT: F 68 MET cc_start: 0.8592 (tpt) cc_final: 0.8365 (ttt) REVERT: H 3 GLN cc_start: 0.7644 (pm20) cc_final: 0.7295 (pm20) REVERT: H 29 PHE cc_start: 0.6233 (t80) cc_final: 0.5714 (t80) REVERT: H 36 TRP cc_start: 0.6991 (m100) cc_final: 0.6169 (m100) REVERT: H 43 GLN cc_start: 0.7420 (mm-40) cc_final: 0.7053 (mm-40) REVERT: H 81 MET cc_start: 0.7553 (ttt) cc_final: 0.5054 (ttt) REVERT: H 111 TYR cc_start: 0.7820 (m-80) cc_final: 0.7537 (m-80) REVERT: L 3 VAL cc_start: 0.6786 (p) cc_final: 0.6149 (m) REVERT: L 32 ASN cc_start: 0.8135 (m-40) cc_final: 0.7730 (m-40) REVERT: L 52 ASN cc_start: 0.7052 (t0) cc_final: 0.6850 (t0) REVERT: O 42 ASP cc_start: 0.8470 (t0) cc_final: 0.8255 (t0) REVERT: O 49 GLU cc_start: 0.8271 (mp0) cc_final: 0.7840 (mp0) REVERT: O 69 THR cc_start: 0.9205 (p) cc_final: 0.8568 (p) REVERT: O 71 ASP cc_start: 0.8177 (p0) cc_final: 0.7936 (t70) REVERT: O 133 GLU cc_start: 0.8100 (pp20) cc_final: 0.7768 (pp20) REVERT: O 182 GLU cc_start: 0.7563 (mm-30) cc_final: 0.6950 (tp30) REVERT: O 195 ILE cc_start: 0.9011 (mt) cc_final: 0.8370 (tt) REVERT: O 453 MET cc_start: 0.8244 (tpp) cc_final: 0.7938 (tpt) REVERT: O 486 TYR cc_start: 0.8383 (t80) cc_final: 0.8090 (t80) REVERT: O 487 LEU cc_start: 0.8782 (tt) cc_final: 0.8498 (tt) REVERT: O 492 GLN cc_start: 0.8448 (mt0) cc_final: 0.7879 (tm-30) REVERT: P 60 LYS cc_start: 0.7954 (mttt) cc_final: 0.7750 (mttt) REVERT: Q 1 MET cc_start: 0.8827 (mmp) cc_final: 0.7909 (mmm) REVERT: Q 41 LEU cc_start: 0.9535 (pp) cc_final: 0.9317 (pt) REVERT: Q 47 LYS cc_start: 0.8499 (mttp) cc_final: 0.8059 (pttt) REVERT: Q 49 GLU cc_start: 0.7951 (mp0) cc_final: 0.7512 (mp0) REVERT: Q 148 GLN cc_start: 0.8941 (tt0) cc_final: 0.8410 (tm-30) REVERT: Q 196 LEU cc_start: 0.8886 (mt) cc_final: 0.8680 (mp) REVERT: Q 237 THR cc_start: 0.9158 (p) cc_final: 0.8854 (p) REVERT: Q 366 GLU cc_start: 0.7877 (pm20) cc_final: 0.7599 (pm20) REVERT: Q 463 TRP cc_start: 0.8144 (t-100) cc_final: 0.7943 (t-100) REVERT: R 68 MET cc_start: 0.8612 (mmm) cc_final: 0.7416 (tmm) REVERT: R 74 MET cc_start: 0.8536 (mmm) cc_final: 0.8141 (mmm) REVERT: S 12 VAL cc_start: 0.9530 (p) cc_final: 0.9328 (t) REVERT: S 116 CYS cc_start: 0.5734 (m) cc_final: 0.5463 (m) REVERT: S 125 ILE cc_start: 0.9597 (tt) cc_final: 0.9129 (tt) REVERT: S 183 CYS cc_start: 0.8656 (m) cc_final: 0.8389 (m) REVERT: S 306 LEU cc_start: 0.9229 (tp) cc_final: 0.8958 (tp) REVERT: S 335 PHE cc_start: 0.8440 (t80) cc_final: 0.8189 (t80) REVERT: S 399 MET cc_start: 0.7896 (tmm) cc_final: 0.7443 (tmm) REVERT: S 419 ASP cc_start: 0.7726 (m-30) cc_final: 0.7383 (m-30) REVERT: T 51 HIS cc_start: 0.7545 (t-90) cc_final: 0.6999 (t-90) REVERT: T 59 GLN cc_start: 0.8070 (tt0) cc_final: 0.7172 (tt0) REVERT: T 68 MET cc_start: 0.8598 (tpt) cc_final: 0.8369 (ttt) REVERT: U 3 GLN cc_start: 0.7640 (pm20) cc_final: 0.7287 (pm20) REVERT: U 29 PHE cc_start: 0.6252 (t80) cc_final: 0.5729 (t80) REVERT: U 36 TRP cc_start: 0.6990 (m100) cc_final: 0.6167 (m100) REVERT: U 43 GLN cc_start: 0.7417 (mm-40) cc_final: 0.7046 (mm-40) REVERT: U 81 MET cc_start: 0.7562 (ttt) cc_final: 0.5069 (ttt) REVERT: U 111 TYR cc_start: 0.7819 (m-80) cc_final: 0.7539 (m-80) REVERT: V 3 VAL cc_start: 0.6777 (p) cc_final: 0.6145 (m) REVERT: V 32 ASN cc_start: 0.8143 (m-40) cc_final: 0.7732 (m-40) outliers start: 0 outliers final: 0 residues processed: 1146 average time/residue: 0.3829 time to fit residues: 700.8153 Evaluate side-chains 848 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 848 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 8.9990 chunk 288 optimal weight: 20.0000 chunk 159 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 297 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 181 optimal weight: 0.0670 chunk 221 optimal weight: 3.9990 chunk 345 optimal weight: 10.0000 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 HIS ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN E 27 HIS E 201 ASN ** E 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 192 ASN ** O 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 269 GLN P 51 HIS ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 209 GLN ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 467 ASN S 27 HIS S 201 ASN ** S 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30596 Z= 0.238 Angle : 0.687 12.027 41484 Z= 0.351 Chirality : 0.045 0.198 4862 Planarity : 0.004 0.047 5182 Dihedral : 11.418 90.913 4716 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.19 % Allowed : 6.06 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.13), residues: 3838 helix: 0.83 (0.17), residues: 900 sheet: -1.09 (0.17), residues: 956 loop : -1.97 (0.13), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP S 451 HIS 0.005 0.001 HIS U 65 PHE 0.018 0.002 PHE T 42 TYR 0.020 0.002 TYR T 52 ARG 0.005 0.001 ARG Q 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1034 time to evaluate : 3.550 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 TARDY: cannot create tardy model for: "PRO D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D residue: PRO 72 >>> skipping revert: symmetry clash TARDY: cannot create tardy model for: "PRO F 72 " (corrupted residue). Skipping it. Corrupt residue: chain: F residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping revert: symmetry clash TARDY: cannot create tardy model for: "PRO T 72 " (corrupted residue). Skipping it. Corrupt residue: chain: T residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8433 (mmm) cc_final: 0.7804 (mmm) REVERT: A 42 ASP cc_start: 0.8197 (t0) cc_final: 0.7952 (t0) REVERT: A 49 GLU cc_start: 0.8282 (mp0) cc_final: 0.8049 (mp0) REVERT: A 69 THR cc_start: 0.9184 (p) cc_final: 0.8530 (p) REVERT: A 71 ASP cc_start: 0.8193 (p0) cc_final: 0.7815 (t70) REVERT: A 76 THR cc_start: 0.7828 (p) cc_final: 0.7595 (p) REVERT: A 182 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6586 (tp30) REVERT: A 192 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.8174 (t0) REVERT: A 195 ILE cc_start: 0.8995 (mt) cc_final: 0.8474 (mp) REVERT: A 453 MET cc_start: 0.8508 (tpp) cc_final: 0.8249 (tpp) REVERT: A 486 TYR cc_start: 0.8342 (t80) cc_final: 0.8105 (t80) REVERT: A 487 LEU cc_start: 0.8588 (tt) cc_final: 0.8268 (tp) REVERT: A 492 GLN cc_start: 0.8392 (mt0) cc_final: 0.7806 (tm-30) REVERT: C 1 MET cc_start: 0.8809 (mmp) cc_final: 0.7938 (mmm) REVERT: C 47 LYS cc_start: 0.8616 (mttp) cc_final: 0.8102 (pttt) REVERT: C 49 GLU cc_start: 0.7844 (mp0) cc_final: 0.7511 (mp0) REVERT: C 71 ASP cc_start: 0.8940 (t70) cc_final: 0.8725 (t0) REVERT: C 148 GLN cc_start: 0.8997 (tt0) cc_final: 0.8474 (tm-30) REVERT: C 186 ARG cc_start: 0.8781 (mmm160) cc_final: 0.8222 (mmt180) REVERT: C 204 TRP cc_start: 0.9270 (m-90) cc_final: 0.8639 (m-90) REVERT: C 286 LYS cc_start: 0.8311 (tttt) cc_final: 0.7792 (mtpp) REVERT: C 389 TRP cc_start: 0.8004 (t60) cc_final: 0.7713 (t-100) REVERT: C 453 MET cc_start: 0.8941 (mmp) cc_final: 0.8692 (tpp) REVERT: D 68 MET cc_start: 0.8676 (mmm) cc_final: 0.7502 (tmm) REVERT: E 26 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7728 (mt-10) REVERT: E 399 MET cc_start: 0.7956 (tmm) cc_final: 0.7508 (tmm) REVERT: E 419 ASP cc_start: 0.7515 (m-30) cc_final: 0.7312 (m-30) REVERT: E 455 ILE cc_start: 0.9268 (tp) cc_final: 0.9015 (tp) REVERT: F 51 HIS cc_start: 0.7768 (t-90) cc_final: 0.7374 (t-90) REVERT: H 3 GLN cc_start: 0.7599 (pm20) cc_final: 0.7059 (pm20) REVERT: H 21 SER cc_start: 0.8549 (p) cc_final: 0.8308 (p) REVERT: H 27 TYR cc_start: 0.7942 (p90) cc_final: 0.7467 (p90) REVERT: H 29 PHE cc_start: 0.6355 (t80) cc_final: 0.5741 (t80) REVERT: H 43 GLN cc_start: 0.7370 (mm-40) cc_final: 0.7037 (mm-40) REVERT: H 111 TYR cc_start: 0.7715 (m-80) cc_final: 0.7454 (m-80) REVERT: L 3 VAL cc_start: 0.6839 (p) cc_final: 0.6091 (m) REVERT: L 32 ASN cc_start: 0.8079 (m-40) cc_final: 0.7832 (m-40) REVERT: O 1 MET cc_start: 0.8439 (mmm) cc_final: 0.7817 (mmm) REVERT: O 42 ASP cc_start: 0.8208 (t0) cc_final: 0.7959 (t0) REVERT: O 49 GLU cc_start: 0.8295 (mp0) cc_final: 0.8057 (mp0) REVERT: O 69 THR cc_start: 0.9180 (p) cc_final: 0.8513 (p) REVERT: O 71 ASP cc_start: 0.8208 (p0) cc_final: 0.7811 (t70) REVERT: O 76 THR cc_start: 0.7843 (p) cc_final: 0.7606 (p) REVERT: O 182 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6616 (tp30) REVERT: O 190 ASP cc_start: 0.8628 (t0) cc_final: 0.8025 (t0) REVERT: O 192 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8149 (t0) REVERT: O 195 ILE cc_start: 0.8986 (mt) cc_final: 0.8388 (mp) REVERT: O 453 MET cc_start: 0.8508 (tpp) cc_final: 0.8231 (tpp) REVERT: O 486 TYR cc_start: 0.8332 (t80) cc_final: 0.8093 (t80) REVERT: O 487 LEU cc_start: 0.8576 (tt) cc_final: 0.8254 (tp) REVERT: O 492 GLN cc_start: 0.8395 (mt0) cc_final: 0.7806 (tm-30) REVERT: Q 1 MET cc_start: 0.8809 (mmp) cc_final: 0.7950 (mmm) REVERT: Q 47 LYS cc_start: 0.8613 (mttp) cc_final: 0.8101 (pttt) REVERT: Q 49 GLU cc_start: 0.7842 (mp0) cc_final: 0.7510 (mp0) REVERT: Q 71 ASP cc_start: 0.8961 (t70) cc_final: 0.8746 (t0) REVERT: Q 148 GLN cc_start: 0.8996 (tt0) cc_final: 0.8479 (tm-30) REVERT: Q 186 ARG cc_start: 0.8774 (mmm160) cc_final: 0.8488 (mmt180) REVERT: Q 199 MET cc_start: 0.9210 (ptm) cc_final: 0.9004 (ptm) REVERT: Q 204 TRP cc_start: 0.9268 (m-90) cc_final: 0.8647 (m-90) REVERT: Q 286 LYS cc_start: 0.8313 (tttt) cc_final: 0.7791 (mtpp) REVERT: Q 389 TRP cc_start: 0.8009 (t60) cc_final: 0.7718 (t-100) REVERT: Q 453 MET cc_start: 0.8936 (mmp) cc_final: 0.8690 (tpp) REVERT: Q 463 TRP cc_start: 0.8170 (t-100) cc_final: 0.7952 (t-100) REVERT: R 68 MET cc_start: 0.8686 (mmm) cc_final: 0.7495 (tmm) REVERT: S 26 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7732 (mt-10) REVERT: S 399 MET cc_start: 0.7958 (tmm) cc_final: 0.7508 (tmm) REVERT: S 419 ASP cc_start: 0.7543 (m-30) cc_final: 0.7329 (m-30) REVERT: S 455 ILE cc_start: 0.9265 (tp) cc_final: 0.9010 (tp) REVERT: T 43 THR cc_start: 0.8957 (m) cc_final: 0.8713 (m) REVERT: T 51 HIS cc_start: 0.7779 (t-90) cc_final: 0.7370 (t-90) REVERT: U 3 GLN cc_start: 0.7584 (pm20) cc_final: 0.7051 (pm20) REVERT: U 21 SER cc_start: 0.8548 (p) cc_final: 0.8292 (p) REVERT: U 27 TYR cc_start: 0.7946 (p90) cc_final: 0.7468 (p90) REVERT: U 29 PHE cc_start: 0.6369 (t80) cc_final: 0.5769 (t80) REVERT: U 43 GLN cc_start: 0.7369 (mm-40) cc_final: 0.7031 (mm-40) REVERT: U 111 TYR cc_start: 0.7755 (m-80) cc_final: 0.7494 (m-80) REVERT: V 3 VAL cc_start: 0.6828 (p) cc_final: 0.6110 (m) REVERT: V 32 ASN cc_start: 0.8045 (m-40) cc_final: 0.7661 (m-40) REVERT: V 46 LYS cc_start: 0.7658 (pttp) cc_final: 0.7257 (mmtm) outliers start: 6 outliers final: 2 residues processed: 1036 average time/residue: 0.3940 time to fit residues: 652.7352 Evaluate side-chains 857 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 853 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 287 optimal weight: 9.9990 chunk 234 optimal weight: 9.9990 chunk 95 optimal weight: 30.0000 chunk 345 optimal weight: 5.9990 chunk 373 optimal weight: 5.9990 chunk 307 optimal weight: 6.9990 chunk 342 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 277 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN A 269 GLN A 467 ASN ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 ASN ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN O 207 HIS ** O 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 230 ASN O 467 ASN ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 467 ASN ** S 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 192 ASN ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 39 GLN V 52 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 30596 Z= 0.408 Angle : 0.748 8.928 41484 Z= 0.383 Chirality : 0.048 0.244 4862 Planarity : 0.005 0.082 5182 Dihedral : 9.758 81.512 4716 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.16 % Allowed : 6.41 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.13), residues: 3838 helix: 0.64 (0.17), residues: 910 sheet: -1.11 (0.17), residues: 974 loop : -2.08 (0.13), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP S 451 HIS 0.008 0.002 HIS P 7 PHE 0.017 0.002 PHE E 11 TYR 0.019 0.002 TYR A 132 ARG 0.007 0.001 ARG Q 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1008 time to evaluate : 3.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8670 (mmm) cc_final: 0.7623 (mmm) REVERT: A 42 ASP cc_start: 0.8201 (t0) cc_final: 0.7889 (t0) REVERT: A 47 LYS cc_start: 0.9326 (pttm) cc_final: 0.8955 (pttm) REVERT: A 71 ASP cc_start: 0.8105 (p0) cc_final: 0.7680 (t70) REVERT: A 76 THR cc_start: 0.7993 (p) cc_final: 0.7789 (p) REVERT: A 97 VAL cc_start: 0.8980 (t) cc_final: 0.8766 (p) REVERT: A 190 ASP cc_start: 0.8714 (t0) cc_final: 0.8105 (t0) REVERT: A 195 ILE cc_start: 0.8985 (mt) cc_final: 0.8258 (tt) REVERT: A 209 GLN cc_start: 0.7714 (tp40) cc_final: 0.7038 (tm-30) REVERT: A 262 LEU cc_start: 0.9233 (pt) cc_final: 0.8915 (pp) REVERT: A 283 CYS cc_start: 0.8385 (t) cc_final: 0.7953 (t) REVERT: A 453 MET cc_start: 0.8520 (tpp) cc_final: 0.8192 (tpp) REVERT: A 486 TYR cc_start: 0.8375 (t80) cc_final: 0.8111 (t80) REVERT: A 487 LEU cc_start: 0.8772 (tt) cc_final: 0.8547 (tp) REVERT: A 492 GLN cc_start: 0.8487 (mt0) cc_final: 0.8285 (mt0) REVERT: C 1 MET cc_start: 0.8878 (mmp) cc_final: 0.7986 (mmm) REVERT: C 47 LYS cc_start: 0.8750 (mttp) cc_final: 0.8486 (pttt) REVERT: C 193 GLU cc_start: 0.6811 (pm20) cc_final: 0.5633 (pm20) REVERT: C 204 TRP cc_start: 0.9424 (m-90) cc_final: 0.8781 (m-90) REVERT: C 324 TYR cc_start: 0.8892 (t80) cc_final: 0.8001 (t80) REVERT: E 61 ILE cc_start: 0.9329 (tp) cc_final: 0.9124 (tp) REVERT: E 186 ARG cc_start: 0.8258 (mmm160) cc_final: 0.7608 (mmm-85) REVERT: E 205 MET cc_start: 0.8618 (mtp) cc_final: 0.8409 (mtm) REVERT: E 286 LYS cc_start: 0.9136 (mttt) cc_final: 0.8911 (mttm) REVERT: E 399 MET cc_start: 0.7984 (tmm) cc_final: 0.7476 (tmm) REVERT: E 455 ILE cc_start: 0.9434 (tp) cc_final: 0.9075 (tp) REVERT: F 43 THR cc_start: 0.9053 (m) cc_final: 0.8812 (m) REVERT: F 47 LEU cc_start: 0.8315 (mt) cc_final: 0.8104 (mt) REVERT: H 3 GLN cc_start: 0.7748 (pm20) cc_final: 0.7195 (pm20) REVERT: H 27 TYR cc_start: 0.7998 (p90) cc_final: 0.7484 (p90) REVERT: H 29 PHE cc_start: 0.6627 (t80) cc_final: 0.6166 (t80) REVERT: H 45 LEU cc_start: 0.8343 (pp) cc_final: 0.8128 (pp) REVERT: L 3 VAL cc_start: 0.6898 (p) cc_final: 0.6124 (m) REVERT: O 1 MET cc_start: 0.8667 (mmm) cc_final: 0.7599 (mmm) REVERT: O 20 TRP cc_start: 0.8811 (p-90) cc_final: 0.8511 (p-90) REVERT: O 42 ASP cc_start: 0.8197 (t0) cc_final: 0.7872 (t0) REVERT: O 47 LYS cc_start: 0.9305 (pttm) cc_final: 0.8964 (pttm) REVERT: O 49 GLU cc_start: 0.8547 (mp0) cc_final: 0.8338 (mp0) REVERT: O 71 ASP cc_start: 0.8125 (p0) cc_final: 0.7699 (t70) REVERT: O 76 THR cc_start: 0.8004 (p) cc_final: 0.7757 (p) REVERT: O 97 VAL cc_start: 0.8982 (t) cc_final: 0.8771 (p) REVERT: O 190 ASP cc_start: 0.8716 (t0) cc_final: 0.8060 (t0) REVERT: O 195 ILE cc_start: 0.8988 (mt) cc_final: 0.8189 (tt) REVERT: O 209 GLN cc_start: 0.7717 (tp40) cc_final: 0.7085 (tm-30) REVERT: O 283 CYS cc_start: 0.8364 (t) cc_final: 0.7917 (t) REVERT: O 453 MET cc_start: 0.8527 (tpp) cc_final: 0.8187 (tpp) REVERT: O 486 TYR cc_start: 0.8370 (t80) cc_final: 0.8109 (t80) REVERT: O 487 LEU cc_start: 0.8763 (tt) cc_final: 0.8528 (tp) REVERT: O 492 GLN cc_start: 0.8491 (mt0) cc_final: 0.8289 (mt0) REVERT: Q 1 MET cc_start: 0.8886 (mmp) cc_final: 0.8197 (mmm) REVERT: Q 47 LYS cc_start: 0.8746 (mttp) cc_final: 0.8483 (pttt) REVERT: Q 71 ASP cc_start: 0.8986 (t70) cc_final: 0.8760 (t0) REVERT: Q 186 ARG cc_start: 0.8707 (mmm160) cc_final: 0.8292 (mmt180) REVERT: Q 193 GLU cc_start: 0.6829 (pm20) cc_final: 0.5662 (pm20) REVERT: Q 204 TRP cc_start: 0.9415 (m-90) cc_final: 0.8784 (m-90) REVERT: Q 229 TRP cc_start: 0.8962 (m100) cc_final: 0.8758 (m100) REVERT: S 186 ARG cc_start: 0.8258 (mmm160) cc_final: 0.7629 (mmm-85) REVERT: S 205 MET cc_start: 0.8599 (mtp) cc_final: 0.8387 (mtm) REVERT: S 286 LYS cc_start: 0.9139 (mttt) cc_final: 0.8918 (mttm) REVERT: S 399 MET cc_start: 0.7985 (tmm) cc_final: 0.7473 (tmm) REVERT: S 455 ILE cc_start: 0.9433 (tp) cc_final: 0.9069 (tp) REVERT: T 43 THR cc_start: 0.9042 (m) cc_final: 0.8798 (m) REVERT: T 47 LEU cc_start: 0.8320 (mt) cc_final: 0.8111 (mt) REVERT: U 3 GLN cc_start: 0.7756 (pm20) cc_final: 0.7185 (pm20) REVERT: U 27 TYR cc_start: 0.8026 (p90) cc_final: 0.7508 (p90) REVERT: U 29 PHE cc_start: 0.6640 (t80) cc_final: 0.6191 (t80) REVERT: U 45 LEU cc_start: 0.8362 (pp) cc_final: 0.8146 (pp) REVERT: U 111 TYR cc_start: 0.7982 (m-80) cc_final: 0.7770 (m-80) REVERT: V 3 VAL cc_start: 0.6901 (p) cc_final: 0.6121 (m) REVERT: V 47 LEU cc_start: 0.8090 (tt) cc_final: 0.7741 (tt) outliers start: 5 outliers final: 0 residues processed: 1011 average time/residue: 0.3829 time to fit residues: 626.3448 Evaluate side-chains 844 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 844 time to evaluate : 4.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 6.9990 chunk 259 optimal weight: 7.9990 chunk 179 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 chunk 346 optimal weight: 2.9990 chunk 367 optimal weight: 20.0000 chunk 181 optimal weight: 0.0060 chunk 328 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 HIS ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 GLN C 280 HIS ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 ASN ** O 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 HIS ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 209 GLN Q 280 HIS ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 GLN ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 16 GLN ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30596 Z= 0.291 Angle : 0.696 11.465 41484 Z= 0.353 Chirality : 0.046 0.210 4862 Planarity : 0.004 0.070 5182 Dihedral : 8.312 72.606 4716 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.54 % Favored : 93.41 % Rotamer: Outliers : 0.09 % Allowed : 5.12 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.13), residues: 3838 helix: 0.76 (0.17), residues: 910 sheet: -1.04 (0.17), residues: 940 loop : -2.08 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 229 HIS 0.006 0.001 HIS B 51 PHE 0.019 0.002 PHE T 42 TYR 0.014 0.002 TYR Q 324 ARG 0.006 0.001 ARG H 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1011 time to evaluate : 3.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping revert: symmetry clash REVERT: A 1 MET cc_start: 0.8474 (mmm) cc_final: 0.8242 (mmm) REVERT: A 20 TRP cc_start: 0.8694 (p-90) cc_final: 0.8466 (p-90) REVERT: A 42 ASP cc_start: 0.8141 (t0) cc_final: 0.7784 (t0) REVERT: A 47 LYS cc_start: 0.9415 (pttm) cc_final: 0.9094 (pttm) REVERT: A 69 THR cc_start: 0.9150 (p) cc_final: 0.8627 (p) REVERT: A 71 ASP cc_start: 0.8048 (p0) cc_final: 0.7828 (t70) REVERT: A 76 THR cc_start: 0.8031 (p) cc_final: 0.7806 (p) REVERT: A 176 TYR cc_start: 0.8950 (m-80) cc_final: 0.8664 (m-80) REVERT: A 190 ASP cc_start: 0.8603 (t0) cc_final: 0.8106 (t0) REVERT: A 210 TRP cc_start: 0.9125 (t60) cc_final: 0.8804 (t60) REVERT: A 262 LEU cc_start: 0.9243 (pt) cc_final: 0.8981 (pp) REVERT: A 453 MET cc_start: 0.8501 (tpp) cc_final: 0.8192 (tpp) REVERT: A 486 TYR cc_start: 0.8381 (t80) cc_final: 0.8075 (t80) REVERT: A 487 LEU cc_start: 0.8748 (tt) cc_final: 0.8540 (tp) REVERT: A 492 GLN cc_start: 0.8453 (mt0) cc_final: 0.7777 (tm-30) REVERT: C 1 MET cc_start: 0.8685 (mmp) cc_final: 0.7957 (mmm) REVERT: C 22 ASP cc_start: 0.7787 (m-30) cc_final: 0.7458 (m-30) REVERT: C 47 LYS cc_start: 0.8749 (mttp) cc_final: 0.8194 (tmmt) REVERT: C 148 GLN cc_start: 0.8823 (tt0) cc_final: 0.8412 (tm-30) REVERT: C 204 TRP cc_start: 0.9397 (m-90) cc_final: 0.8754 (m-90) REVERT: C 286 LYS cc_start: 0.8400 (tttm) cc_final: 0.8046 (mtpp) REVERT: C 324 TYR cc_start: 0.8473 (t80) cc_final: 0.7549 (t80) REVERT: E 26 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8084 (mt-10) REVERT: E 96 TYR cc_start: 0.8888 (m-80) cc_final: 0.8650 (m-80) REVERT: E 132 TYR cc_start: 0.8426 (t80) cc_final: 0.8145 (t80) REVERT: E 186 ARG cc_start: 0.8227 (mmm160) cc_final: 0.7708 (mpt180) REVERT: E 205 MET cc_start: 0.8553 (mtp) cc_final: 0.8282 (mtm) REVERT: E 286 LYS cc_start: 0.9210 (mttt) cc_final: 0.8934 (mttm) REVERT: E 399 MET cc_start: 0.7840 (tmm) cc_final: 0.7372 (tmm) REVERT: F 28 GLN cc_start: 0.7307 (mm-40) cc_final: 0.7067 (mm-40) REVERT: F 47 LEU cc_start: 0.8312 (mt) cc_final: 0.8078 (mt) REVERT: F 68 MET cc_start: 0.8455 (ttt) cc_final: 0.8254 (ttp) REVERT: H 3 GLN cc_start: 0.7752 (pm20) cc_final: 0.7194 (pm20) REVERT: H 21 SER cc_start: 0.8507 (p) cc_final: 0.8255 (p) REVERT: H 27 TYR cc_start: 0.8011 (p90) cc_final: 0.7651 (p90) REVERT: H 29 PHE cc_start: 0.6640 (t80) cc_final: 0.6165 (t80) REVERT: H 98 ARG cc_start: 0.6865 (ttp-170) cc_final: 0.6590 (ttp-110) REVERT: L 3 VAL cc_start: 0.6886 (p) cc_final: 0.6126 (m) REVERT: O 1 MET cc_start: 0.8458 (mmm) cc_final: 0.8258 (mmm) REVERT: O 20 TRP cc_start: 0.8744 (p-90) cc_final: 0.8488 (p-90) REVERT: O 42 ASP cc_start: 0.8101 (t0) cc_final: 0.7778 (t0) REVERT: O 47 LYS cc_start: 0.9269 (pttm) cc_final: 0.8859 (pttm) REVERT: O 69 THR cc_start: 0.9135 (p) cc_final: 0.8609 (p) REVERT: O 71 ASP cc_start: 0.8067 (p0) cc_final: 0.7833 (t70) REVERT: O 76 THR cc_start: 0.8005 (p) cc_final: 0.7781 (p) REVERT: O 176 TYR cc_start: 0.8953 (m-80) cc_final: 0.8673 (m-80) REVERT: O 190 ASP cc_start: 0.8608 (t0) cc_final: 0.8060 (t0) REVERT: O 195 ILE cc_start: 0.8872 (mt) cc_final: 0.8335 (mp) REVERT: O 210 TRP cc_start: 0.9134 (t60) cc_final: 0.8771 (t60) REVERT: O 262 LEU cc_start: 0.9226 (pt) cc_final: 0.8949 (pp) REVERT: O 453 MET cc_start: 0.8599 (tpp) cc_final: 0.8274 (tpp) REVERT: O 486 TYR cc_start: 0.8371 (t80) cc_final: 0.8067 (t80) REVERT: O 487 LEU cc_start: 0.8736 (tt) cc_final: 0.8517 (tp) REVERT: O 492 GLN cc_start: 0.8464 (mt0) cc_final: 0.7772 (tm-30) REVERT: Q 1 MET cc_start: 0.8688 (mmp) cc_final: 0.8187 (mmm) REVERT: Q 22 ASP cc_start: 0.7773 (m-30) cc_final: 0.7443 (m-30) REVERT: Q 47 LYS cc_start: 0.8746 (mttp) cc_final: 0.8186 (tmmt) REVERT: Q 71 ASP cc_start: 0.8935 (t70) cc_final: 0.8714 (t0) REVERT: Q 148 GLN cc_start: 0.8836 (tt0) cc_final: 0.8413 (tm-30) REVERT: Q 204 TRP cc_start: 0.9381 (m-90) cc_final: 0.8781 (m-90) REVERT: Q 286 LYS cc_start: 0.8407 (tttm) cc_final: 0.8042 (mtpp) REVERT: Q 324 TYR cc_start: 0.8834 (t80) cc_final: 0.7735 (t80) REVERT: R 38 ARG cc_start: 0.8046 (ttp-170) cc_final: 0.7738 (ttp-170) REVERT: S 26 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8091 (mt-10) REVERT: S 96 TYR cc_start: 0.8887 (m-80) cc_final: 0.8655 (m-80) REVERT: S 132 TYR cc_start: 0.8422 (t80) cc_final: 0.8145 (t80) REVERT: S 186 ARG cc_start: 0.8236 (mmm160) cc_final: 0.7711 (mpt180) REVERT: S 205 MET cc_start: 0.8541 (mtp) cc_final: 0.8248 (mtm) REVERT: S 286 LYS cc_start: 0.9206 (mttt) cc_final: 0.8940 (mttm) REVERT: S 399 MET cc_start: 0.7834 (tmm) cc_final: 0.7379 (tmm) REVERT: T 10 MET cc_start: 0.8389 (mmp) cc_final: 0.7989 (mmt) REVERT: T 28 GLN cc_start: 0.7304 (mm-40) cc_final: 0.7075 (mm-40) REVERT: T 47 LEU cc_start: 0.8324 (mt) cc_final: 0.8090 (mt) REVERT: U 3 GLN cc_start: 0.7729 (pm20) cc_final: 0.7188 (pm20) REVERT: U 21 SER cc_start: 0.8494 (p) cc_final: 0.8252 (p) REVERT: U 27 TYR cc_start: 0.8016 (p90) cc_final: 0.7667 (p90) REVERT: U 29 PHE cc_start: 0.6663 (t80) cc_final: 0.6187 (t80) REVERT: U 98 ARG cc_start: 0.6947 (ttp-170) cc_final: 0.6586 (ttp-110) REVERT: U 111 TYR cc_start: 0.7825 (m-80) cc_final: 0.7472 (m-80) REVERT: V 3 VAL cc_start: 0.6921 (p) cc_final: 0.6132 (m) REVERT: V 28 ASN cc_start: 0.8170 (p0) cc_final: 0.7717 (p0) REVERT: V 32 ASN cc_start: 0.8069 (m-40) cc_final: 0.7862 (m-40) outliers start: 3 outliers final: 3 residues processed: 1012 average time/residue: 0.4023 time to fit residues: 657.1432 Evaluate side-chains 839 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 836 time to evaluate : 3.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 0.5980 chunk 208 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 273 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 313 optimal weight: 9.9990 chunk 253 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 187 optimal weight: 5.9990 chunk 329 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 467 ASN ** S 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 GLN V 16 GLN ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30596 Z= 0.297 Angle : 0.696 11.674 41484 Z= 0.351 Chirality : 0.046 0.214 4862 Planarity : 0.004 0.061 5182 Dihedral : 7.332 62.346 4716 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.03 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.13), residues: 3838 helix: 0.73 (0.17), residues: 906 sheet: -1.03 (0.17), residues: 928 loop : -2.11 (0.12), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP U 47 HIS 0.005 0.001 HIS P 7 PHE 0.020 0.002 PHE F 42 TYR 0.020 0.002 TYR B 52 ARG 0.006 0.001 ARG Q 186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1004 time to evaluate : 3.252 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 TARDY: cannot create tardy model for: "PRO D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D residue: PRO 72 >>> skipping revert: symmetry clash TARDY: cannot create tardy model for: "PRO F 72 " (corrupted residue). Skipping it. Corrupt residue: chain: F residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO T 72 " (corrupted residue). Skipping it. Corrupt residue: chain: T residue: PRO 72 >>> skipping revert: symmetry clash REVERT: A 1 MET cc_start: 0.8561 (mmm) cc_final: 0.8210 (mmm) REVERT: A 49 GLU cc_start: 0.8429 (mp0) cc_final: 0.7705 (mp0) REVERT: A 69 THR cc_start: 0.9182 (p) cc_final: 0.8629 (p) REVERT: A 71 ASP cc_start: 0.8068 (p0) cc_final: 0.7833 (t70) REVERT: A 190 ASP cc_start: 0.8581 (t0) cc_final: 0.8141 (t0) REVERT: A 209 GLN cc_start: 0.7124 (tm-30) cc_final: 0.6874 (tm-30) REVERT: A 210 TRP cc_start: 0.9218 (t60) cc_final: 0.8757 (t60) REVERT: A 262 LEU cc_start: 0.9248 (pt) cc_final: 0.8867 (pp) REVERT: A 283 CYS cc_start: 0.8466 (t) cc_final: 0.8242 (t) REVERT: A 323 GLU cc_start: 0.8397 (tp30) cc_final: 0.8167 (tp30) REVERT: A 408 ARG cc_start: 0.8050 (ttm170) cc_final: 0.7704 (tpp80) REVERT: A 453 MET cc_start: 0.8535 (tpp) cc_final: 0.8242 (tpp) REVERT: A 486 TYR cc_start: 0.8376 (t80) cc_final: 0.8130 (t80) REVERT: A 487 LEU cc_start: 0.8540 (tt) cc_final: 0.8268 (tp) REVERT: A 492 GLN cc_start: 0.8494 (mt0) cc_final: 0.8186 (mt0) REVERT: B 60 LYS cc_start: 0.8202 (mttm) cc_final: 0.7973 (mtpt) REVERT: C 1 MET cc_start: 0.8683 (mmp) cc_final: 0.7913 (mmm) REVERT: C 20 TRP cc_start: 0.8430 (p-90) cc_final: 0.8072 (p-90) REVERT: C 137 TYR cc_start: 0.8941 (m-80) cc_final: 0.8504 (m-10) REVERT: C 204 TRP cc_start: 0.9389 (m-90) cc_final: 0.8795 (m-90) REVERT: C 209 GLN cc_start: 0.8658 (tp-100) cc_final: 0.8427 (tp40) REVERT: C 286 LYS cc_start: 0.8142 (tttm) cc_final: 0.7804 (mtpp) REVERT: C 389 TRP cc_start: 0.7757 (t-100) cc_final: 0.7329 (t-100) REVERT: D 30 GLU cc_start: 0.8287 (tp30) cc_final: 0.7915 (tp30) REVERT: E 26 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8075 (mt-10) REVERT: E 132 TYR cc_start: 0.8448 (t80) cc_final: 0.8244 (t80) REVERT: E 186 ARG cc_start: 0.8260 (mmm160) cc_final: 0.7719 (mpt180) REVERT: E 205 MET cc_start: 0.8536 (mtp) cc_final: 0.8314 (mtm) REVERT: E 286 LYS cc_start: 0.9243 (mttt) cc_final: 0.8993 (mttm) REVERT: E 399 MET cc_start: 0.7814 (tmm) cc_final: 0.7370 (tmm) REVERT: F 10 MET cc_start: 0.7806 (mmp) cc_final: 0.7357 (mmt) REVERT: F 43 THR cc_start: 0.9021 (m) cc_final: 0.8801 (m) REVERT: F 68 MET cc_start: 0.8591 (ttt) cc_final: 0.8210 (ttp) REVERT: H 3 GLN cc_start: 0.7771 (pm20) cc_final: 0.7210 (pm20) REVERT: H 21 SER cc_start: 0.8466 (p) cc_final: 0.8251 (p) REVERT: H 27 TYR cc_start: 0.7998 (p90) cc_final: 0.7553 (p90) REVERT: H 29 PHE cc_start: 0.6698 (t80) cc_final: 0.6103 (t80) REVERT: H 84 LYS cc_start: 0.8132 (pttm) cc_final: 0.7915 (pttm) REVERT: L 3 VAL cc_start: 0.6923 (p) cc_final: 0.6050 (m) REVERT: L 28 ASN cc_start: 0.8379 (p0) cc_final: 0.8019 (p0) REVERT: L 32 ASN cc_start: 0.8105 (m-40) cc_final: 0.7892 (m-40) REVERT: O 1 MET cc_start: 0.8568 (mmm) cc_final: 0.8237 (mmm) REVERT: O 69 THR cc_start: 0.9166 (p) cc_final: 0.8612 (p) REVERT: O 71 ASP cc_start: 0.8072 (p0) cc_final: 0.7823 (t70) REVERT: O 190 ASP cc_start: 0.8552 (t0) cc_final: 0.8142 (t0) REVERT: O 210 TRP cc_start: 0.9210 (t60) cc_final: 0.8886 (t60) REVERT: O 262 LEU cc_start: 0.9221 (pt) cc_final: 0.8817 (pp) REVERT: O 283 CYS cc_start: 0.8446 (t) cc_final: 0.8226 (t) REVERT: O 323 GLU cc_start: 0.8415 (tp30) cc_final: 0.8184 (tp30) REVERT: O 408 ARG cc_start: 0.8055 (ttm170) cc_final: 0.7697 (tpp80) REVERT: O 453 MET cc_start: 0.8599 (tpp) cc_final: 0.8301 (tpp) REVERT: O 486 TYR cc_start: 0.8376 (t80) cc_final: 0.8132 (t80) REVERT: O 487 LEU cc_start: 0.8521 (tt) cc_final: 0.8248 (tp) REVERT: O 492 GLN cc_start: 0.8478 (mt0) cc_final: 0.8177 (mt0) REVERT: P 60 LYS cc_start: 0.8196 (mttm) cc_final: 0.7970 (mttt) REVERT: Q 1 MET cc_start: 0.8687 (mmp) cc_final: 0.7925 (mmm) REVERT: Q 20 TRP cc_start: 0.8433 (p-90) cc_final: 0.8077 (p-90) REVERT: Q 71 ASP cc_start: 0.8890 (t70) cc_final: 0.8684 (t0) REVERT: Q 137 TYR cc_start: 0.8953 (m-80) cc_final: 0.8538 (m-10) REVERT: Q 204 TRP cc_start: 0.9392 (m-90) cc_final: 0.8797 (m-90) REVERT: Q 286 LYS cc_start: 0.8138 (tttm) cc_final: 0.7798 (mtpp) REVERT: Q 389 TRP cc_start: 0.7753 (t-100) cc_final: 0.7326 (t-100) REVERT: R 30 GLU cc_start: 0.8300 (tp30) cc_final: 0.7916 (tp30) REVERT: S 26 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8055 (mt-10) REVERT: S 61 ILE cc_start: 0.9261 (tp) cc_final: 0.9060 (tp) REVERT: S 186 ARG cc_start: 0.8266 (mmm160) cc_final: 0.7720 (mpt180) REVERT: S 205 MET cc_start: 0.8516 (mtp) cc_final: 0.8289 (mtm) REVERT: S 399 MET cc_start: 0.7818 (tmm) cc_final: 0.7371 (tmm) REVERT: T 10 MET cc_start: 0.8427 (mmp) cc_final: 0.7964 (mmt) REVERT: T 43 THR cc_start: 0.9030 (m) cc_final: 0.8795 (m) REVERT: U 3 GLN cc_start: 0.7739 (pm20) cc_final: 0.7210 (pm20) REVERT: U 21 SER cc_start: 0.8466 (p) cc_final: 0.8263 (p) REVERT: U 27 TYR cc_start: 0.8019 (p90) cc_final: 0.7645 (p90) REVERT: U 29 PHE cc_start: 0.6677 (t80) cc_final: 0.6087 (t80) REVERT: U 50 TRP cc_start: 0.8557 (m-10) cc_final: 0.8108 (m-10) REVERT: U 98 ARG cc_start: 0.6927 (ttp-170) cc_final: 0.6528 (ttp-110) REVERT: U 111 TYR cc_start: 0.7821 (m-80) cc_final: 0.7472 (m-80) REVERT: U 118 VAL cc_start: 0.9195 (p) cc_final: 0.8993 (m) REVERT: V 3 VAL cc_start: 0.6907 (p) cc_final: 0.6054 (m) REVERT: V 28 ASN cc_start: 0.8214 (p0) cc_final: 0.7722 (p0) outliers start: 0 outliers final: 0 residues processed: 1004 average time/residue: 0.3751 time to fit residues: 609.3081 Evaluate side-chains 838 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 838 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 20.0000 chunk 330 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 90 optimal weight: 30.0000 chunk 367 optimal weight: 20.0000 chunk 305 optimal weight: 7.9990 chunk 170 optimal weight: 8.9990 chunk 30 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 51 HIS ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN L 16 GLN L 39 GLN L 52 ASN O 89 ASN O 246 GLN ** O 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 HIS ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 209 GLN ** Q 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 207 HIS T 59 GLN ** U 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 16 GLN ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 30596 Z= 0.324 Angle : 0.700 10.687 41484 Z= 0.356 Chirality : 0.046 0.180 4862 Planarity : 0.004 0.060 5182 Dihedral : 6.944 52.869 4716 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.14 % Favored : 92.81 % Rotamer: Outliers : 0.09 % Allowed : 3.84 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 3838 helix: 0.72 (0.17), residues: 906 sheet: -1.02 (0.17), residues: 944 loop : -2.10 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP S 451 HIS 0.009 0.001 HIS C 280 PHE 0.017 0.002 PHE P 42 TYR 0.018 0.002 TYR S 297 ARG 0.007 0.001 ARG E 2 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 990 time to evaluate : 3.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D residue: PRO 72 >>> skipping revert: symmetry clash TARDY: cannot create tardy model for: "PRO F 72 " (corrupted residue). Skipping it. Corrupt residue: chain: F residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping revert: symmetry clash TARDY: cannot create tardy model for: "PRO T 72 " (corrupted residue). Skipping it. Corrupt residue: chain: T residue: PRO 72 >>> skipping revert: symmetry clash REVERT: A 69 THR cc_start: 0.9000 (p) cc_final: 0.8487 (p) REVERT: A 71 ASP cc_start: 0.8077 (p0) cc_final: 0.7869 (t70) REVERT: A 209 GLN cc_start: 0.7246 (tm-30) cc_final: 0.6888 (tm-30) REVERT: A 262 LEU cc_start: 0.9317 (pt) cc_final: 0.9049 (pp) REVERT: A 312 GLU cc_start: 0.8782 (tp30) cc_final: 0.8249 (tp30) REVERT: A 357 THR cc_start: 0.8307 (p) cc_final: 0.8106 (p) REVERT: A 453 MET cc_start: 0.8577 (tpp) cc_final: 0.8241 (tpp) REVERT: A 486 TYR cc_start: 0.8386 (t80) cc_final: 0.8082 (t80) REVERT: A 487 LEU cc_start: 0.8625 (tt) cc_final: 0.8369 (tp) REVERT: A 492 GLN cc_start: 0.8524 (mt0) cc_final: 0.8199 (mt0) REVERT: B 12 LEU cc_start: 0.8561 (tt) cc_final: 0.7837 (tt) REVERT: C 1 MET cc_start: 0.8684 (mmp) cc_final: 0.7932 (mmm) REVERT: C 57 ARG cc_start: 0.9256 (tpp80) cc_final: 0.9011 (tpp80) REVERT: C 137 TYR cc_start: 0.9006 (m-80) cc_final: 0.8744 (m-10) REVERT: C 193 GLU cc_start: 0.6784 (pm20) cc_final: 0.5448 (pm20) REVERT: C 204 TRP cc_start: 0.9399 (m-90) cc_final: 0.8834 (m-90) REVERT: C 286 LYS cc_start: 0.8156 (tttm) cc_final: 0.7776 (mtpp) REVERT: C 375 ASN cc_start: 0.8028 (m-40) cc_final: 0.7801 (m-40) REVERT: C 408 ARG cc_start: 0.8985 (tpp80) cc_final: 0.8775 (tpp80) REVERT: D 30 GLU cc_start: 0.8224 (tp30) cc_final: 0.7799 (tp30) REVERT: E 26 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7905 (mt-10) REVERT: E 186 ARG cc_start: 0.8300 (mmm160) cc_final: 0.7678 (mmt-90) REVERT: E 205 MET cc_start: 0.8563 (mtp) cc_final: 0.8348 (mtm) REVERT: E 399 MET cc_start: 0.7791 (tmm) cc_final: 0.7360 (tmm) REVERT: F 10 MET cc_start: 0.8194 (mmp) cc_final: 0.7775 (mmp) REVERT: F 28 GLN cc_start: 0.7128 (mm-40) cc_final: 0.6728 (mm-40) REVERT: F 68 MET cc_start: 0.8576 (ttt) cc_final: 0.8133 (ttp) REVERT: H 3 GLN cc_start: 0.7807 (pm20) cc_final: 0.7238 (pm20) REVERT: H 21 SER cc_start: 0.8491 (p) cc_final: 0.8209 (p) REVERT: H 27 TYR cc_start: 0.7989 (p90) cc_final: 0.7588 (p90) REVERT: H 29 PHE cc_start: 0.6731 (t80) cc_final: 0.6236 (t80) REVERT: H 36 TRP cc_start: 0.7585 (m100) cc_final: 0.6570 (m100) REVERT: H 50 TRP cc_start: 0.8436 (m-10) cc_final: 0.8110 (m-10) REVERT: H 84 LYS cc_start: 0.8094 (pttm) cc_final: 0.7878 (pttm) REVERT: L 3 VAL cc_start: 0.6889 (p) cc_final: 0.6077 (m) REVERT: O 47 LYS cc_start: 0.9311 (pttm) cc_final: 0.8995 (pttm) REVERT: O 49 GLU cc_start: 0.8402 (mp0) cc_final: 0.8128 (mp0) REVERT: O 69 THR cc_start: 0.9005 (p) cc_final: 0.8503 (p) REVERT: O 71 ASP cc_start: 0.8089 (p0) cc_final: 0.7839 (t70) REVERT: O 190 ASP cc_start: 0.8478 (t0) cc_final: 0.8154 (t0) REVERT: O 262 LEU cc_start: 0.9279 (pt) cc_final: 0.8991 (pp) REVERT: O 357 THR cc_start: 0.8328 (p) cc_final: 0.8121 (p) REVERT: O 453 MET cc_start: 0.8644 (tpp) cc_final: 0.8358 (tpp) REVERT: O 486 TYR cc_start: 0.8389 (t80) cc_final: 0.8091 (t80) REVERT: O 487 LEU cc_start: 0.8596 (tt) cc_final: 0.8335 (tp) REVERT: O 492 GLN cc_start: 0.8508 (mt0) cc_final: 0.8178 (mt0) REVERT: Q 1 MET cc_start: 0.8683 (mmp) cc_final: 0.7953 (mmm) REVERT: Q 57 ARG cc_start: 0.9252 (tpp80) cc_final: 0.9027 (tpp80) REVERT: Q 137 TYR cc_start: 0.9026 (m-80) cc_final: 0.8770 (m-10) REVERT: Q 193 GLU cc_start: 0.6808 (pm20) cc_final: 0.5450 (pm20) REVERT: Q 204 TRP cc_start: 0.9403 (m-90) cc_final: 0.8841 (m-90) REVERT: Q 286 LYS cc_start: 0.8164 (tttm) cc_final: 0.7814 (mtpp) REVERT: Q 375 ASN cc_start: 0.8035 (m-40) cc_final: 0.7809 (m-40) REVERT: Q 413 LEU cc_start: 0.8993 (mt) cc_final: 0.8701 (mt) REVERT: R 30 GLU cc_start: 0.8229 (tp30) cc_final: 0.7823 (tp30) REVERT: S 26 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7882 (mt-10) REVERT: S 41 LEU cc_start: 0.9037 (pt) cc_final: 0.8812 (pt) REVERT: S 61 ILE cc_start: 0.9201 (tp) cc_final: 0.8989 (tp) REVERT: S 205 MET cc_start: 0.8551 (mtp) cc_final: 0.8334 (mtm) REVERT: S 399 MET cc_start: 0.7788 (tmm) cc_final: 0.7371 (tmm) REVERT: T 10 MET cc_start: 0.8282 (mmp) cc_final: 0.7960 (mmt) REVERT: T 28 GLN cc_start: 0.7144 (mm-40) cc_final: 0.6747 (mm-40) REVERT: T 43 THR cc_start: 0.9097 (m) cc_final: 0.8876 (m) REVERT: U 3 GLN cc_start: 0.7760 (pm20) cc_final: 0.7233 (pm20) REVERT: U 21 SER cc_start: 0.8510 (p) cc_final: 0.8202 (p) REVERT: U 27 TYR cc_start: 0.8032 (p90) cc_final: 0.7608 (p90) REVERT: U 29 PHE cc_start: 0.6694 (t80) cc_final: 0.6255 (t80) REVERT: U 36 TRP cc_start: 0.7605 (m100) cc_final: 0.6552 (m100) REVERT: U 50 TRP cc_start: 0.8421 (m-10) cc_final: 0.8104 (m-10) REVERT: U 98 ARG cc_start: 0.6852 (ttp-170) cc_final: 0.6498 (ttp-110) REVERT: U 111 TYR cc_start: 0.7872 (m-80) cc_final: 0.7478 (m-80) REVERT: V 3 VAL cc_start: 0.6914 (p) cc_final: 0.6056 (m) REVERT: V 28 ASN cc_start: 0.8192 (p0) cc_final: 0.7771 (p0) outliers start: 3 outliers final: 3 residues processed: 991 average time/residue: 0.3709 time to fit residues: 595.6418 Evaluate side-chains 839 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 836 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 209 optimal weight: 0.8980 chunk 268 optimal weight: 7.9990 chunk 208 optimal weight: 9.9990 chunk 309 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 366 optimal weight: 30.0000 chunk 229 optimal weight: 6.9990 chunk 223 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN C 77 GLN C 209 GLN ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN F 59 GLN ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 ASN ** O 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 467 ASN ** S 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 GLN ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 16 GLN ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30596 Z= 0.341 Angle : 0.723 11.100 41484 Z= 0.366 Chirality : 0.047 0.212 4862 Planarity : 0.004 0.056 5182 Dihedral : 6.730 52.721 4716 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.32 % Favored : 92.63 % Rotamer: Outliers : 0.03 % Allowed : 2.22 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.13), residues: 3838 helix: 0.64 (0.17), residues: 908 sheet: -1.04 (0.17), residues: 944 loop : -2.10 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 451 HIS 0.007 0.001 HIS Q 280 PHE 0.016 0.002 PHE C 335 TYR 0.027 0.002 TYR P 52 ARG 0.011 0.001 ARG C 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 992 time to evaluate : 3.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D residue: PRO 72 >>> skipping revert: symmetry clash TARDY: cannot create tardy model for: "PRO F 72 " (corrupted residue). Skipping it. Corrupt residue: chain: F residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping revert: symmetry clash TARDY: cannot create tardy model for: "PRO T 72 " (corrupted residue). Skipping it. Corrupt residue: chain: T residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8506 (mmm) cc_final: 0.7899 (mmm) REVERT: A 49 GLU cc_start: 0.8372 (mp0) cc_final: 0.8136 (mp0) REVERT: A 69 THR cc_start: 0.9064 (p) cc_final: 0.8477 (p) REVERT: A 262 LEU cc_start: 0.9179 (pt) cc_final: 0.8949 (pp) REVERT: A 283 CYS cc_start: 0.8520 (t) cc_final: 0.8288 (t) REVERT: A 312 GLU cc_start: 0.8793 (tp30) cc_final: 0.8312 (tp30) REVERT: A 323 GLU cc_start: 0.8438 (tp30) cc_final: 0.8126 (tp30) REVERT: A 453 MET cc_start: 0.8601 (tpp) cc_final: 0.8248 (tpp) REVERT: A 486 TYR cc_start: 0.8400 (t80) cc_final: 0.8113 (t80) REVERT: A 487 LEU cc_start: 0.8663 (tt) cc_final: 0.8433 (tp) REVERT: A 492 GLN cc_start: 0.8536 (mt0) cc_final: 0.8187 (mt0) REVERT: C 1 MET cc_start: 0.8645 (mmp) cc_final: 0.7983 (mmm) REVERT: C 22 ASP cc_start: 0.7797 (m-30) cc_final: 0.7458 (m-30) REVERT: C 49 GLU cc_start: 0.7456 (pp20) cc_final: 0.7252 (pp20) REVERT: C 57 ARG cc_start: 0.9278 (tpp80) cc_final: 0.8989 (tpp80) REVERT: C 137 TYR cc_start: 0.9008 (m-80) cc_final: 0.8699 (m-10) REVERT: C 193 GLU cc_start: 0.6787 (pm20) cc_final: 0.5474 (pm20) REVERT: C 204 TRP cc_start: 0.9403 (m-90) cc_final: 0.8836 (m-90) REVERT: C 286 LYS cc_start: 0.8162 (tttm) cc_final: 0.7799 (mtpp) REVERT: C 375 ASN cc_start: 0.7860 (m-40) cc_final: 0.7532 (m-40) REVERT: C 408 ARG cc_start: 0.8992 (tpp80) cc_final: 0.8757 (tpp80) REVERT: C 486 TYR cc_start: 0.8922 (t80) cc_final: 0.8697 (t80) REVERT: D 30 GLU cc_start: 0.8238 (tp30) cc_final: 0.7827 (tp30) REVERT: E 26 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7890 (mt-10) REVERT: E 199 MET cc_start: 0.8187 (tpp) cc_final: 0.7983 (mmm) REVERT: E 205 MET cc_start: 0.8609 (mtp) cc_final: 0.8349 (mtm) REVERT: E 399 MET cc_start: 0.7873 (tmm) cc_final: 0.7334 (tmm) REVERT: F 10 MET cc_start: 0.8212 (mmp) cc_final: 0.7823 (mmp) REVERT: F 28 GLN cc_start: 0.7030 (mm-40) cc_final: 0.6357 (mm-40) REVERT: F 68 MET cc_start: 0.8617 (ttt) cc_final: 0.8146 (ttp) REVERT: H 3 GLN cc_start: 0.7639 (pm20) cc_final: 0.7149 (pm20) REVERT: H 12 LYS cc_start: 0.6763 (mmtm) cc_final: 0.6289 (mmtm) REVERT: H 21 SER cc_start: 0.8495 (p) cc_final: 0.8262 (p) REVERT: H 27 TYR cc_start: 0.8516 (p90) cc_final: 0.7758 (p90) REVERT: H 29 PHE cc_start: 0.6736 (t80) cc_final: 0.6185 (t80) REVERT: H 50 TRP cc_start: 0.8379 (m-10) cc_final: 0.8118 (m-10) REVERT: H 84 LYS cc_start: 0.8131 (pttm) cc_final: 0.7920 (pttm) REVERT: H 118 VAL cc_start: 0.9193 (p) cc_final: 0.8968 (m) REVERT: L 3 VAL cc_start: 0.6942 (p) cc_final: 0.6059 (m) REVERT: O 1 MET cc_start: 0.8435 (mmm) cc_final: 0.7806 (mmm) REVERT: O 49 GLU cc_start: 0.8443 (mp0) cc_final: 0.8120 (mp0) REVERT: O 69 THR cc_start: 0.9062 (p) cc_final: 0.8498 (p) REVERT: O 190 ASP cc_start: 0.8500 (t0) cc_final: 0.8296 (t0) REVERT: O 262 LEU cc_start: 0.9163 (pt) cc_final: 0.8922 (pp) REVERT: O 283 CYS cc_start: 0.8513 (t) cc_final: 0.8279 (t) REVERT: O 323 GLU cc_start: 0.8459 (tp30) cc_final: 0.8134 (tp30) REVERT: O 453 MET cc_start: 0.8666 (tpp) cc_final: 0.8379 (tpp) REVERT: O 486 TYR cc_start: 0.8396 (t80) cc_final: 0.8106 (t80) REVERT: O 487 LEU cc_start: 0.8639 (tt) cc_final: 0.8389 (tp) REVERT: O 492 GLN cc_start: 0.8543 (mt0) cc_final: 0.8204 (mt0) REVERT: Q 1 MET cc_start: 0.8661 (mmp) cc_final: 0.8015 (mmm) REVERT: Q 22 ASP cc_start: 0.7860 (m-30) cc_final: 0.7554 (m-30) REVERT: Q 49 GLU cc_start: 0.7454 (pp20) cc_final: 0.7226 (pp20) REVERT: Q 137 TYR cc_start: 0.9043 (m-80) cc_final: 0.8758 (m-10) REVERT: Q 204 TRP cc_start: 0.9390 (m-90) cc_final: 0.8835 (m-90) REVERT: Q 286 LYS cc_start: 0.8185 (tttm) cc_final: 0.7792 (mtpp) REVERT: Q 375 ASN cc_start: 0.7851 (m-40) cc_final: 0.7525 (m-40) REVERT: Q 486 TYR cc_start: 0.8941 (t80) cc_final: 0.8720 (t80) REVERT: R 30 GLU cc_start: 0.8250 (tp30) cc_final: 0.7826 (tp30) REVERT: S 26 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7900 (mt-10) REVERT: S 61 ILE cc_start: 0.9295 (tp) cc_final: 0.8964 (tp) REVERT: S 132 TYR cc_start: 0.8520 (t80) cc_final: 0.8191 (t80) REVERT: S 181 LEU cc_start: 0.9322 (mm) cc_final: 0.9105 (mp) REVERT: S 192 ASN cc_start: 0.8135 (t0) cc_final: 0.7885 (t0) REVERT: S 205 MET cc_start: 0.8616 (mtp) cc_final: 0.8309 (mtm) REVERT: S 399 MET cc_start: 0.7877 (tmm) cc_final: 0.7345 (tmm) REVERT: T 10 MET cc_start: 0.8350 (mmp) cc_final: 0.8048 (mmt) REVERT: T 28 GLN cc_start: 0.7013 (mm-40) cc_final: 0.6390 (mm-40) REVERT: T 43 THR cc_start: 0.9102 (m) cc_final: 0.8880 (m) REVERT: U 3 GLN cc_start: 0.7588 (pm20) cc_final: 0.7119 (pm20) REVERT: U 21 SER cc_start: 0.8472 (p) cc_final: 0.8263 (p) REVERT: U 27 TYR cc_start: 0.7987 (p90) cc_final: 0.7490 (p90) REVERT: U 29 PHE cc_start: 0.6722 (t80) cc_final: 0.6166 (t80) REVERT: U 50 TRP cc_start: 0.8495 (m-10) cc_final: 0.8257 (m-10) REVERT: V 3 VAL cc_start: 0.6902 (p) cc_final: 0.6036 (m) REVERT: V 28 ASN cc_start: 0.8226 (p0) cc_final: 0.7883 (p0) outliers start: 1 outliers final: 0 residues processed: 992 average time/residue: 0.3757 time to fit residues: 605.9297 Evaluate side-chains 803 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 803 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 71 optimal weight: 30.0000 chunk 70 optimal weight: 7.9990 chunk 232 optimal weight: 8.9990 chunk 249 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 287 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 HIS B 59 GLN ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN F 59 GLN L 16 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 ASN ** O 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 HIS P 59 GLN Q 209 GLN ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 GLN S 364 ASN T 59 GLN V 16 GLN V 39 GLN ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 30596 Z= 0.434 Angle : 0.782 12.058 41484 Z= 0.398 Chirality : 0.048 0.253 4862 Planarity : 0.005 0.059 5182 Dihedral : 6.783 52.404 4716 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.39 % Favored : 91.56 % Rotamer: Outliers : 0.12 % Allowed : 1.97 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.13), residues: 3838 helix: 0.48 (0.17), residues: 914 sheet: -1.09 (0.17), residues: 948 loop : -2.15 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 218 HIS 0.007 0.002 HIS P 7 PHE 0.017 0.002 PHE A 119 TYR 0.017 0.002 TYR A 132 ARG 0.009 0.001 ARG E 2 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 966 time to evaluate : 3.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D residue: PRO 72 >>> skipping revert: symmetry clash TARDY: cannot create tardy model for: "PRO F 72 " (corrupted residue). Skipping it. Corrupt residue: chain: F residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO T 72 " (corrupted residue). Skipping it. Corrupt residue: chain: T residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7835 (t0) cc_final: 0.7357 (t0) REVERT: A 49 GLU cc_start: 0.8437 (mp0) cc_final: 0.8104 (mp0) REVERT: A 69 THR cc_start: 0.9218 (p) cc_final: 0.8636 (p) REVERT: A 312 GLU cc_start: 0.8855 (tp30) cc_final: 0.8378 (tp30) REVERT: A 418 TRP cc_start: 0.8254 (t-100) cc_final: 0.7818 (t-100) REVERT: A 453 MET cc_start: 0.8661 (tpp) cc_final: 0.8345 (tpp) REVERT: A 486 TYR cc_start: 0.8439 (t80) cc_final: 0.8143 (t80) REVERT: A 487 LEU cc_start: 0.8802 (tt) cc_final: 0.8570 (tp) REVERT: A 492 GLN cc_start: 0.8571 (mt0) cc_final: 0.8302 (mt0) REVERT: B 31 LYS cc_start: 0.8842 (tmmt) cc_final: 0.8576 (ttpt) REVERT: C 1 MET cc_start: 0.8656 (mmp) cc_final: 0.7972 (mmm) REVERT: C 22 ASP cc_start: 0.7951 (m-30) cc_final: 0.7721 (m-30) REVERT: C 57 ARG cc_start: 0.9299 (tpp80) cc_final: 0.9065 (tpp80) REVERT: C 137 TYR cc_start: 0.9031 (m-10) cc_final: 0.8691 (m-10) REVERT: C 204 TRP cc_start: 0.9424 (m-90) cc_final: 0.8798 (m-90) REVERT: C 375 ASN cc_start: 0.7870 (m-40) cc_final: 0.7591 (m-40) REVERT: C 486 TYR cc_start: 0.8948 (t80) cc_final: 0.8748 (t80) REVERT: D 30 GLU cc_start: 0.8247 (tp30) cc_final: 0.7872 (tp30) REVERT: D 68 MET cc_start: 0.8514 (mmm) cc_final: 0.7331 (tmm) REVERT: E 26 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7709 (mt-10) REVERT: E 205 MET cc_start: 0.8658 (mtp) cc_final: 0.8399 (mtm) REVERT: E 254 GLN cc_start: 0.8859 (mm110) cc_final: 0.8657 (mm110) REVERT: E 399 MET cc_start: 0.7937 (tmm) cc_final: 0.7641 (tmm) REVERT: F 28 GLN cc_start: 0.7468 (mm-40) cc_final: 0.7206 (mm-40) REVERT: F 43 THR cc_start: 0.9187 (m) cc_final: 0.8927 (m) REVERT: F 68 MET cc_start: 0.8668 (ttt) cc_final: 0.8218 (ttp) REVERT: H 3 GLN cc_start: 0.7911 (pm20) cc_final: 0.7407 (pm20) REVERT: H 12 LYS cc_start: 0.6761 (mmtm) cc_final: 0.6376 (mmtt) REVERT: H 27 TYR cc_start: 0.8320 (p90) cc_final: 0.7915 (p90) REVERT: H 29 PHE cc_start: 0.6756 (t80) cc_final: 0.6248 (t80) REVERT: H 50 TRP cc_start: 0.8519 (m-10) cc_final: 0.8218 (m-10) REVERT: H 118 VAL cc_start: 0.9213 (p) cc_final: 0.8996 (m) REVERT: L 3 VAL cc_start: 0.6868 (p) cc_final: 0.6022 (m) REVERT: L 47 LEU cc_start: 0.7506 (tt) cc_final: 0.7246 (tt) REVERT: O 1 MET cc_start: 0.8474 (mmm) cc_final: 0.7935 (mmm) REVERT: O 49 GLU cc_start: 0.8491 (mp0) cc_final: 0.8159 (mp0) REVERT: O 69 THR cc_start: 0.9206 (p) cc_final: 0.8648 (p) REVERT: O 209 GLN cc_start: 0.7687 (tm-30) cc_final: 0.7382 (tm-30) REVERT: O 283 CYS cc_start: 0.8563 (t) cc_final: 0.8342 (t) REVERT: O 357 THR cc_start: 0.8295 (p) cc_final: 0.8062 (p) REVERT: O 418 TRP cc_start: 0.8254 (t-100) cc_final: 0.7808 (t-100) REVERT: O 453 MET cc_start: 0.8734 (tpp) cc_final: 0.8469 (tpp) REVERT: O 486 TYR cc_start: 0.8437 (t80) cc_final: 0.8148 (t80) REVERT: O 487 LEU cc_start: 0.8785 (tt) cc_final: 0.8554 (tp) REVERT: O 492 GLN cc_start: 0.8588 (mt0) cc_final: 0.8298 (mt0) REVERT: P 31 LYS cc_start: 0.8818 (tmmt) cc_final: 0.8567 (ttpt) REVERT: Q 1 MET cc_start: 0.8676 (mmp) cc_final: 0.8004 (mmm) REVERT: Q 137 TYR cc_start: 0.9066 (m-80) cc_final: 0.8755 (m-10) REVERT: Q 204 TRP cc_start: 0.9413 (m-90) cc_final: 0.8833 (m-90) REVERT: Q 233 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7271 (tm-30) REVERT: Q 375 ASN cc_start: 0.7880 (m-40) cc_final: 0.7601 (m-40) REVERT: Q 486 TYR cc_start: 0.8960 (t80) cc_final: 0.8758 (t80) REVERT: R 30 GLU cc_start: 0.8261 (tp30) cc_final: 0.7894 (tp30) REVERT: R 68 MET cc_start: 0.8503 (mmm) cc_final: 0.7322 (tmm) REVERT: S 26 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7755 (mt-10) REVERT: S 61 ILE cc_start: 0.9270 (tp) cc_final: 0.9009 (tp) REVERT: S 181 LEU cc_start: 0.9343 (mm) cc_final: 0.9103 (mp) REVERT: S 205 MET cc_start: 0.8630 (mtp) cc_final: 0.8376 (mtm) REVERT: S 399 MET cc_start: 0.7953 (tmm) cc_final: 0.7654 (tmm) REVERT: T 28 GLN cc_start: 0.7483 (mm-40) cc_final: 0.7232 (mm-40) REVERT: T 43 THR cc_start: 0.9203 (m) cc_final: 0.8925 (m) REVERT: U 3 GLN cc_start: 0.7696 (pm20) cc_final: 0.7088 (pm20) REVERT: U 29 PHE cc_start: 0.6738 (t80) cc_final: 0.6426 (t80) REVERT: U 36 TRP cc_start: 0.7699 (m100) cc_final: 0.6765 (m100) REVERT: U 50 TRP cc_start: 0.8509 (m-10) cc_final: 0.8190 (m-10) REVERT: U 98 ARG cc_start: 0.6885 (ttp-170) cc_final: 0.6299 (ttp-110) REVERT: V 3 VAL cc_start: 0.6818 (p) cc_final: 0.6007 (m) REVERT: V 28 ASN cc_start: 0.8525 (p0) cc_final: 0.8015 (p0) REVERT: V 47 LEU cc_start: 0.7549 (tt) cc_final: 0.7312 (tt) outliers start: 4 outliers final: 3 residues processed: 968 average time/residue: 0.3722 time to fit residues: 586.4523 Evaluate side-chains 820 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 817 time to evaluate : 3.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 4.9990 chunk 350 optimal weight: 2.9990 chunk 320 optimal weight: 8.9990 chunk 341 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 148 optimal weight: 0.1980 chunk 268 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 308 optimal weight: 0.9980 chunk 322 optimal weight: 1.9990 chunk 340 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS F 59 GLN ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 ASN ** O 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 GLN Q 77 GLN Q 207 HIS ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 27 HIS T 59 GLN V 16 GLN V 53 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30596 Z= 0.215 Angle : 0.692 12.516 41484 Z= 0.346 Chirality : 0.046 0.187 4862 Planarity : 0.004 0.052 5182 Dihedral : 6.234 53.749 4716 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.73 % Favored : 94.22 % Rotamer: Outliers : 0.06 % Allowed : 1.00 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.13), residues: 3838 helix: 0.72 (0.17), residues: 908 sheet: -0.87 (0.18), residues: 924 loop : -2.07 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 451 HIS 0.008 0.001 HIS S 259 PHE 0.019 0.002 PHE C 335 TYR 0.029 0.001 TYR P 52 ARG 0.006 0.001 ARG C 405 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1002 time to evaluate : 3.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 THR cc_start: 0.9293 (p) cc_final: 0.9076 (p) REVERT: A 323 GLU cc_start: 0.8277 (tp30) cc_final: 0.8044 (tp30) REVERT: A 453 MET cc_start: 0.8470 (tpp) cc_final: 0.8192 (tpp) REVERT: A 471 THR cc_start: 0.8148 (m) cc_final: 0.7909 (t) REVERT: A 486 TYR cc_start: 0.8336 (t80) cc_final: 0.8020 (t80) REVERT: A 487 LEU cc_start: 0.8736 (tt) cc_final: 0.8477 (tp) REVERT: A 492 GLN cc_start: 0.8513 (mt0) cc_final: 0.8244 (mt0) REVERT: C 1 MET cc_start: 0.8615 (mmp) cc_final: 0.7952 (mmm) REVERT: C 22 ASP cc_start: 0.7794 (m-30) cc_final: 0.7482 (m-30) REVERT: C 47 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8337 (tmmt) REVERT: C 101 TRP cc_start: 0.8579 (m-10) cc_final: 0.8144 (m-10) REVERT: C 137 TYR cc_start: 0.9010 (m-10) cc_final: 0.8651 (m-10) REVERT: C 204 TRP cc_start: 0.9389 (m-90) cc_final: 0.8876 (m-90) REVERT: C 286 LYS cc_start: 0.8243 (tttm) cc_final: 0.8002 (mtpp) REVERT: C 375 ASN cc_start: 0.7802 (m-40) cc_final: 0.7474 (m-40) REVERT: C 408 ARG cc_start: 0.8999 (tpp80) cc_final: 0.8752 (tpp80) REVERT: D 30 GLU cc_start: 0.8270 (tp30) cc_final: 0.7917 (tp30) REVERT: D 39 HIS cc_start: 0.7543 (m-70) cc_final: 0.6615 (m-70) REVERT: D 68 MET cc_start: 0.8481 (mmm) cc_final: 0.7224 (tmm) REVERT: E 26 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8039 (mt-10) REVERT: E 41 LEU cc_start: 0.8986 (pt) cc_final: 0.8680 (pt) REVERT: E 61 ILE cc_start: 0.9227 (tp) cc_final: 0.8923 (tp) REVERT: E 186 ARG cc_start: 0.8507 (mmt-90) cc_final: 0.8086 (mmm160) REVERT: E 335 PHE cc_start: 0.8132 (t80) cc_final: 0.7911 (t80) REVERT: E 399 MET cc_start: 0.7945 (tmm) cc_final: 0.7665 (tmm) REVERT: E 455 ILE cc_start: 0.9470 (tp) cc_final: 0.9248 (tp) REVERT: F 43 THR cc_start: 0.9039 (m) cc_final: 0.8806 (m) REVERT: F 68 MET cc_start: 0.8628 (ttt) cc_final: 0.8153 (ttp) REVERT: H 3 GLN cc_start: 0.7872 (pm20) cc_final: 0.7352 (pm20) REVERT: H 12 LYS cc_start: 0.6672 (mmtm) cc_final: 0.6185 (mmtt) REVERT: H 21 SER cc_start: 0.8438 (p) cc_final: 0.8206 (p) REVERT: H 27 TYR cc_start: 0.8422 (p90) cc_final: 0.7558 (p90) REVERT: H 29 PHE cc_start: 0.6738 (t80) cc_final: 0.6154 (t80) REVERT: H 50 TRP cc_start: 0.8443 (m-10) cc_final: 0.8053 (m-10) REVERT: H 118 VAL cc_start: 0.9204 (p) cc_final: 0.8943 (m) REVERT: L 3 VAL cc_start: 0.6825 (p) cc_final: 0.5950 (m) REVERT: L 32 ASN cc_start: 0.7855 (m-40) cc_final: 0.7580 (m-40) REVERT: O 49 GLU cc_start: 0.8294 (mp0) cc_final: 0.8094 (mp0) REVERT: O 204 TRP cc_start: 0.9394 (m-90) cc_final: 0.9174 (m-90) REVERT: O 323 GLU cc_start: 0.8297 (tp30) cc_final: 0.8095 (tp30) REVERT: O 453 MET cc_start: 0.8492 (tpp) cc_final: 0.8196 (tpp) REVERT: O 471 THR cc_start: 0.8121 (m) cc_final: 0.7904 (t) REVERT: O 486 TYR cc_start: 0.8326 (t80) cc_final: 0.8023 (t80) REVERT: O 487 LEU cc_start: 0.8726 (tt) cc_final: 0.8420 (tp) REVERT: Q 1 MET cc_start: 0.8633 (mmp) cc_final: 0.7968 (mmm) REVERT: Q 22 ASP cc_start: 0.8000 (m-30) cc_final: 0.7637 (m-30) REVERT: Q 47 LYS cc_start: 0.8721 (ttmm) cc_final: 0.8358 (tmmt) REVERT: Q 101 TRP cc_start: 0.8507 (m-10) cc_final: 0.8101 (m-10) REVERT: Q 137 TYR cc_start: 0.9048 (m-10) cc_final: 0.8692 (m-10) REVERT: Q 204 TRP cc_start: 0.9378 (m-90) cc_final: 0.8869 (m-90) REVERT: Q 233 GLU cc_start: 0.7348 (tm-30) cc_final: 0.7138 (tm-30) REVERT: Q 375 ASN cc_start: 0.7802 (m-40) cc_final: 0.7466 (m-40) REVERT: R 30 GLU cc_start: 0.8288 (tp30) cc_final: 0.7917 (tp30) REVERT: R 68 MET cc_start: 0.8457 (mmm) cc_final: 0.7220 (tmm) REVERT: S 26 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7971 (mt-10) REVERT: S 41 LEU cc_start: 0.8676 (pt) cc_final: 0.8220 (pt) REVERT: S 61 ILE cc_start: 0.9256 (tp) cc_final: 0.9001 (tp) REVERT: S 132 TYR cc_start: 0.8544 (t80) cc_final: 0.7413 (t80) REVERT: S 181 LEU cc_start: 0.9305 (mm) cc_final: 0.8976 (mt) REVERT: S 335 PHE cc_start: 0.8140 (t80) cc_final: 0.7902 (t80) REVERT: S 399 MET cc_start: 0.7938 (tmm) cc_final: 0.7666 (tmm) REVERT: S 455 ILE cc_start: 0.9470 (tp) cc_final: 0.9241 (tp) REVERT: T 10 MET cc_start: 0.8105 (mmp) cc_final: 0.7681 (mmp) REVERT: T 43 THR cc_start: 0.9050 (m) cc_final: 0.8771 (m) REVERT: U 3 GLN cc_start: 0.7856 (pm20) cc_final: 0.7355 (pm20) REVERT: U 21 SER cc_start: 0.8427 (p) cc_final: 0.8214 (p) REVERT: U 27 TYR cc_start: 0.8343 (p90) cc_final: 0.7611 (p90) REVERT: U 29 PHE cc_start: 0.6679 (t80) cc_final: 0.6071 (t80) REVERT: U 50 TRP cc_start: 0.8459 (m-10) cc_final: 0.8043 (m-10) REVERT: U 98 ARG cc_start: 0.6758 (ttp-170) cc_final: 0.6175 (ttp-110) REVERT: V 3 VAL cc_start: 0.6711 (p) cc_final: 0.5718 (m) REVERT: V 28 ASN cc_start: 0.8420 (p0) cc_final: 0.7919 (p0) outliers start: 2 outliers final: 0 residues processed: 1002 average time/residue: 0.3840 time to fit residues: 627.5348 Evaluate side-chains 826 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 826 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 40.0000 chunk 360 optimal weight: 40.0000 chunk 220 optimal weight: 9.9990 chunk 171 optimal weight: 20.0000 chunk 250 optimal weight: 4.9990 chunk 378 optimal weight: 6.9990 chunk 348 optimal weight: 0.6980 chunk 301 optimal weight: 0.8980 chunk 31 optimal weight: 0.0000 chunk 232 optimal weight: 9.9990 chunk 184 optimal weight: 20.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 51 HIS C 149 HIS C 207 HIS ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS E 77 GLN F 59 GLN L 16 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 ASN O 388 ASN P 51 HIS Q 149 HIS Q 207 HIS Q 209 GLN ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 27 HIS T 59 GLN ** U 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 16 GLN V 53 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 30596 Z= 0.236 Angle : 0.709 12.213 41484 Z= 0.353 Chirality : 0.046 0.195 4862 Planarity : 0.004 0.054 5182 Dihedral : 6.051 52.935 4716 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.85 % Favored : 93.10 % Rotamer: Outliers : 0.12 % Allowed : 0.62 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.13), residues: 3838 helix: 0.77 (0.17), residues: 908 sheet: -0.84 (0.18), residues: 908 loop : -2.03 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP O 451 HIS 0.023 0.001 HIS Q 149 PHE 0.046 0.002 PHE C 304 TYR 0.030 0.002 TYR S 132 ARG 0.013 0.001 ARG S 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 947 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8071 (mp0) cc_final: 0.7739 (mp0) REVERT: A 194 MET cc_start: 0.8259 (mmp) cc_final: 0.7563 (mmt) REVERT: A 205 MET cc_start: 0.8718 (ttp) cc_final: 0.7613 (ttp) REVERT: A 209 GLN cc_start: 0.6975 (tm-30) cc_final: 0.6756 (tm-30) REVERT: A 246 GLN cc_start: 0.9014 (pt0) cc_final: 0.8813 (pt0) REVERT: A 323 GLU cc_start: 0.8269 (tp30) cc_final: 0.8022 (tp30) REVERT: A 357 THR cc_start: 0.8237 (p) cc_final: 0.8022 (p) REVERT: A 453 MET cc_start: 0.8483 (tpp) cc_final: 0.8219 (tpp) REVERT: A 471 THR cc_start: 0.8135 (m) cc_final: 0.7892 (t) REVERT: A 486 TYR cc_start: 0.8348 (t80) cc_final: 0.8054 (t80) REVERT: A 487 LEU cc_start: 0.8702 (tt) cc_final: 0.8433 (tp) REVERT: A 492 GLN cc_start: 0.8556 (mt0) cc_final: 0.8255 (mt0) REVERT: C 22 ASP cc_start: 0.7776 (m-30) cc_final: 0.7459 (m-30) REVERT: C 47 LYS cc_start: 0.8734 (ttmm) cc_final: 0.8351 (tmmt) REVERT: C 101 TRP cc_start: 0.8621 (m-10) cc_final: 0.8174 (m-10) REVERT: C 137 TYR cc_start: 0.8975 (m-10) cc_final: 0.8629 (m-10) REVERT: C 204 TRP cc_start: 0.9381 (m-90) cc_final: 0.8846 (m-90) REVERT: C 205 MET cc_start: 0.8944 (ptp) cc_final: 0.8659 (ptp) REVERT: C 408 ARG cc_start: 0.9037 (tpp80) cc_final: 0.8730 (tpp80) REVERT: C 433 MET cc_start: 0.7912 (tpp) cc_final: 0.7638 (tpp) REVERT: D 30 GLU cc_start: 0.8215 (tp30) cc_final: 0.7809 (tp30) REVERT: D 39 HIS cc_start: 0.7401 (m-70) cc_final: 0.6458 (m-70) REVERT: D 68 MET cc_start: 0.8524 (mmm) cc_final: 0.7253 (tmm) REVERT: E 26 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8023 (mt-10) REVERT: E 41 LEU cc_start: 0.9011 (pt) cc_final: 0.8674 (pt) REVERT: E 335 PHE cc_start: 0.8279 (t80) cc_final: 0.7991 (t80) REVERT: E 399 MET cc_start: 0.7938 (tmm) cc_final: 0.7644 (tmm) REVERT: E 455 ILE cc_start: 0.9481 (tp) cc_final: 0.9247 (tp) REVERT: F 10 MET cc_start: 0.7994 (mmp) cc_final: 0.7717 (mmp) REVERT: F 68 MET cc_start: 0.8587 (ttt) cc_final: 0.8381 (ttp) REVERT: H 3 GLN cc_start: 0.7825 (pm20) cc_final: 0.7319 (pm20) REVERT: H 12 LYS cc_start: 0.6675 (mmtm) cc_final: 0.6233 (mmtm) REVERT: H 21 SER cc_start: 0.8442 (p) cc_final: 0.8216 (p) REVERT: H 27 TYR cc_start: 0.8430 (p90) cc_final: 0.7554 (p90) REVERT: H 29 PHE cc_start: 0.6718 (t80) cc_final: 0.6118 (t80) REVERT: H 45 LEU cc_start: 0.8498 (pp) cc_final: 0.8271 (pp) REVERT: H 50 TRP cc_start: 0.8261 (m-10) cc_final: 0.7879 (m-10) REVERT: H 118 VAL cc_start: 0.9114 (p) cc_final: 0.8904 (m) REVERT: L 3 VAL cc_start: 0.6767 (p) cc_final: 0.5884 (m) REVERT: L 32 ASN cc_start: 0.7775 (m-40) cc_final: 0.7550 (m-40) REVERT: O 323 GLU cc_start: 0.8315 (tp30) cc_final: 0.8052 (tp30) REVERT: O 357 THR cc_start: 0.8245 (p) cc_final: 0.8025 (p) REVERT: O 453 MET cc_start: 0.8555 (tpp) cc_final: 0.8287 (tpp) REVERT: O 471 THR cc_start: 0.8120 (m) cc_final: 0.7889 (t) REVERT: O 486 TYR cc_start: 0.8348 (t80) cc_final: 0.8087 (t80) REVERT: O 487 LEU cc_start: 0.8636 (tt) cc_final: 0.8343 (tp) REVERT: Q 22 ASP cc_start: 0.7855 (m-30) cc_final: 0.7587 (m-30) REVERT: Q 47 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8390 (tmmt) REVERT: Q 101 TRP cc_start: 0.8494 (m-10) cc_final: 0.8020 (m-10) REVERT: Q 137 TYR cc_start: 0.9024 (m-10) cc_final: 0.8695 (m-10) REVERT: Q 204 TRP cc_start: 0.9412 (m-90) cc_final: 0.8858 (m-90) REVERT: Q 233 GLU cc_start: 0.7322 (tm-30) cc_final: 0.7113 (tm-30) REVERT: Q 433 MET cc_start: 0.7926 (tpp) cc_final: 0.7665 (tpp) REVERT: R 30 GLU cc_start: 0.8229 (tp30) cc_final: 0.7811 (tp30) REVERT: R 68 MET cc_start: 0.8501 (mmm) cc_final: 0.7223 (tmm) REVERT: S 26 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8326 (mt-10) REVERT: S 41 LEU cc_start: 0.8713 (pt) cc_final: 0.8314 (pt) REVERT: S 116 CYS cc_start: 0.5546 (m) cc_final: 0.4955 (m) REVERT: S 335 PHE cc_start: 0.8284 (t80) cc_final: 0.8001 (t80) REVERT: S 399 MET cc_start: 0.7955 (tmm) cc_final: 0.7655 (tmm) REVERT: S 455 ILE cc_start: 0.9484 (tp) cc_final: 0.9242 (tp) REVERT: T 10 MET cc_start: 0.8010 (mmp) cc_final: 0.7575 (mmp) REVERT: T 43 THR cc_start: 0.9067 (m) cc_final: 0.8852 (m) REVERT: U 3 GLN cc_start: 0.7983 (pm20) cc_final: 0.7494 (pm20) REVERT: U 21 SER cc_start: 0.8443 (p) cc_final: 0.8221 (p) REVERT: U 27 TYR cc_start: 0.8285 (p90) cc_final: 0.7749 (p90) REVERT: U 29 PHE cc_start: 0.6635 (t80) cc_final: 0.6049 (t80) REVERT: U 45 LEU cc_start: 0.8507 (pp) cc_final: 0.8293 (pp) REVERT: U 50 TRP cc_start: 0.8239 (m-10) cc_final: 0.7848 (m-10) REVERT: U 98 ARG cc_start: 0.6730 (ttp-170) cc_final: 0.6211 (ttp-110) REVERT: V 3 VAL cc_start: 0.6827 (p) cc_final: 0.6007 (m) REVERT: V 28 ASN cc_start: 0.8449 (p0) cc_final: 0.7980 (p0) REVERT: V 32 ASN cc_start: 0.7882 (m-40) cc_final: 0.7533 (m-40) outliers start: 4 outliers final: 3 residues processed: 949 average time/residue: 0.3704 time to fit residues: 574.6515 Evaluate side-chains 807 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 804 time to evaluate : 3.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 0.6980 chunk 321 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 277 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 0.0770 chunk 301 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 310 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 overall best weight: 1.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 207 HIS ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS F 59 GLN L 16 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 492 GLN Q 94 HIS Q 150 GLN Q 207 HIS ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 27 HIS S 77 GLN S 144 HIS T 59 GLN V 16 GLN ** V 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.134736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.116998 restraints weight = 51144.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.119678 restraints weight = 28354.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121456 restraints weight = 18288.825| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30596 Z= 0.200 Angle : 0.695 12.445 41484 Z= 0.343 Chirality : 0.046 0.195 4862 Planarity : 0.004 0.047 5182 Dihedral : 5.860 53.768 4716 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.63 % Favored : 94.32 % Rotamer: Outliers : 0.03 % Allowed : 0.66 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.13), residues: 3838 helix: 0.86 (0.17), residues: 916 sheet: -0.71 (0.18), residues: 882 loop : -2.02 (0.12), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 451 HIS 0.014 0.001 HIS O 207 PHE 0.024 0.001 PHE Q 304 TYR 0.016 0.001 TYR Q 486 ARG 0.007 0.001 ARG Q 405 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9058.46 seconds wall clock time: 160 minutes 58.89 seconds (9658.89 seconds total)