Starting phenix.real_space_refine on Sun Feb 18 20:42:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okp_20100/02_2024/6okp_20100.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okp_20100/02_2024/6okp_20100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okp_20100/02_2024/6okp_20100.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okp_20100/02_2024/6okp_20100.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okp_20100/02_2024/6okp_20100.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okp_20100/02_2024/6okp_20100.pdb" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 121 5.16 5 C 14261 2.51 5 N 3750 2.21 5 O 4725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 504": "NH1" <-> "NH2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 504": "NH1" <-> "NH2" Residue "F PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 504": "NH1" <-> "NH2" Residue "K ARG 96": "NH1" <-> "NH2" Residue "K ARG 97": "NH1" <-> "NH2" Residue "K PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 9": "NH1" <-> "NH2" Residue "L ARG 20": "NH1" <-> "NH2" Residue "L ARG 25": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 94": "NH1" <-> "NH2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 94": "NH1" <-> "NH2" Residue "N ARG 93": "NH1" <-> "NH2" Residue "O PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "P ARG 93": "NH1" <-> "NH2" Residue "Q ARG 94": "NH1" <-> "NH2" Residue "R ARG 93": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22857 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 960 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "B" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 960 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "C" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 960 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "D" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3569 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3559 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3569 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "L" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 779 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "M" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1019 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 122} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 797 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Chain: "O" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1019 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 122} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 797 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Chain: "Q" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1019 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 122} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 797 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Chain: "G" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "H" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "a" 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "h" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "i" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "j" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "s" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 12.80, per 1000 atoms: 0.56 Number of scatterers: 22857 At special positions: 0 Unit cell: (154.78, 166.77, 166.77, 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 121 16.00 O 4725 8.00 N 3750 7.00 C 14261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS D 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS F 501 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.01 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.02 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.01 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " 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=3, symmetry=0 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN H 5 " - " MAN H 6 " " MAN g 4 " - " MAN g 5 " " MAN h 4 " - " MAN h 5 " " MAN r 5 " - " MAN r 6 " " MAN s 5 " - " MAN s 6 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 6 " - " MAN G 7 " " BMA H 3 " - " MAN H 8 " " MAN H 4 " - " MAN H 7 " " MAN H 8 " - " MAN H 9 " " BMA I 3 " - " MAN I 7 " " MAN I 4 " - " MAN I 5 " " BMA Z 3 " - " MAN Z 7 " " MAN Z 4 " - " MAN Z 5 " " BMA g 3 " - " MAN g 4 " " MAN g 6 " - " MAN g 7 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 7 " " MAN i 4 " - " MAN i 5 " " BMA j 3 " - " MAN j 7 " " MAN j 4 " - " MAN j 5 " " BMA r 3 " - " MAN r 8 " " MAN r 4 " - " MAN r 7 " " MAN r 8 " - " MAN r 9 " " BMA s 3 " - " MAN s 8 " " MAN s 4 " - " MAN s 7 " " MAN s 8 " - " MAN s 9 " ALPHA1-6 " BMA G 3 " - " MAN G 6 " " MAN G 6 " - " MAN G 8 " " BMA H 3 " - " MAN H 4 " " MAN H 4 " - " MAN H 5 " " BMA I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 6 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 4 " - " MAN Z 6 " " BMA g 3 " - " MAN g 6 " " BMA h 3 " - " MAN h 6 " " BMA i 3 " - " MAN i 4 " " MAN i 4 " - " MAN i 6 " " BMA j 3 " - " MAN j 4 " " MAN j 4 " - " MAN j 6 " " BMA r 3 " - " MAN r 4 " " MAN r 4 " - " MAN r 5 " " BMA s 3 " - " MAN s 4 " " MAN s 4 " - " MAN s 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-ASN " NAG A 701 " - " ASN A 616 " " NAG A 702 " - " ASN A 637 " " NAG B 701 " - " ASN B 616 " " NAG B 702 " - " ASN B 637 " " NAG C 701 " - " ASN C 616 " " NAG C 702 " - " ASN C 637 " " NAG D 627 " - " ASN D 301 " " NAG D 631 " - " ASN D 88 " " NAG D 632 " - " ASN D 241 " " NAG D 635 " - " ASN D 276 " " NAG D 636 " - " ASN D 339 " " NAG D 640 " - " ASN D 396 " " NAG D 647 " - " ASN D 413 " " NAG D 648 " - " ASN D 355 " " NAG D 649 " - " ASN D 197 " " NAG E 610 " - " ASN E 301 " " NAG E 614 " - " ASN E 88 " " NAG E 615 " - " ASN E 241 " " NAG E 618 " - " ASN E 276 " " NAG E 619 " - " ASN E 339 " " NAG E 623 " - " ASN E 396 " " NAG E 630 " - " ASN E 413 " " NAG E 631 " - " ASN E 355 " " NAG E 639 " - " ASN E 197 " " NAG F 617 " - " ASN F 301 " " NAG F 621 " - " ASN F 88 " " NAG F 622 " - " ASN F 241 " " NAG F 625 " - " ASN F 276 " " NAG F 626 " - " ASN F 339 " " NAG F 630 " - " ASN F 396 " " NAG F 637 " - " ASN F 413 " " NAG F 638 " - " ASN F 355 " " NAG F 639 " - " ASN F 197 " " NAG G 1 " - " ASN D 295 " " NAG H 1 " - " ASN D 262 " " NAG I 1 " - " ASN D 448 " " NAG J 1 " - " ASN D 332 " " NAG S 1 " - " ASN D 160 " " NAG T 1 " - " ASN D 234 " " NAG U 1 " - " ASN D 392 " " NAG V 1 " - " ASN D 362 " " NAG W 1 " - " ASN D 386 " " NAG X 1 " - " ASN D 156 " " NAG Y 1 " - " ASN E 295 " " NAG Z 1 " - " ASN E 448 " " NAG a 1 " - " ASN E 160 " " NAG b 1 " - " ASN E 234 " " NAG c 1 " - " ASN E 392 " " NAG d 1 " - " ASN E 362 " " NAG e 1 " - " ASN E 386 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 332 " " NAG h 1 " - " ASN E 137 " " NAG i 1 " - " ASN F 295 " " NAG j 1 " - " ASN F 448 " " NAG k 1 " - " ASN F 332 " " NAG l 1 " - " ASN F 160 " " NAG m 1 " - " ASN F 234 " " NAG n 1 " - " ASN F 392 " " NAG o 1 " - " ASN F 362 " " NAG p 1 " - " ASN F 386 " " NAG q 1 " - " ASN F 156 " " NAG r 1 " - " ASN E 262 " " NAG s 1 " - " ASN F 262 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.77 Conformation dependent library (CDL) restraints added in 3.7 seconds 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 54 sheets defined 14.1% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 571 through 595 removed outlier: 3.734A pdb=" N GLN A 575 " --> pdb=" O TRP A 571 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 595 " --> pdb=" O GLN A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 635 Processing helix chain 'A' and resid 638 through 648 Processing helix chain 'A' and resid 651 through 663 removed outlier: 3.715A pdb=" N ASN A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU A 657 " --> pdb=" O GLN A 653 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 595 removed outlier: 3.733A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 638 through 648 Processing helix chain 'B' and resid 651 through 663 removed outlier: 3.715A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 595 removed outlier: 3.733A pdb=" N GLN C 575 " --> pdb=" O TRP C 571 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 595 " --> pdb=" O GLN C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 623 Processing helix chain 'C' and resid 628 through 635 Processing helix chain 'C' and resid 638 through 648 Processing helix chain 'C' and resid 651 through 663 removed outlier: 3.714A pdb=" N ASN C 656 " --> pdb=" O GLN C 652 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU C 657 " --> pdb=" O GLN C 653 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 663 " --> pdb=" O GLU C 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 110 removed outlier: 3.611A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.626A pdb=" N LEU D 125 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 353 removed outlier: 3.526A pdb=" N GLU D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS D 348 " --> pdb=" O GLN D 344 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 removed outlier: 3.519A pdb=" N ASN D 478 " --> pdb=" O MET D 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 115 removed outlier: 4.298A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 126 removed outlier: 3.650A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 123 through 126' Processing helix chain 'E' and resid 334 through 353 removed outlier: 3.621A pdb=" N TRP E 338 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS E 348 " --> pdb=" O GLN E 344 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU E 351 " --> pdb=" O ALA E 347 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.580A pdb=" N VAL E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR E 373 " --> pdb=" O PRO E 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 368 through 373' Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'F' and resid 98 through 112 removed outlier: 4.308A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE F 109 " --> pdb=" O HIS F 105 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU F 111 " --> pdb=" O ASP F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 126 Processing helix chain 'F' and resid 335 through 353 removed outlier: 3.971A pdb=" N GLU F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR F 341 " --> pdb=" O ARG F 337 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL F 346 " --> pdb=" O LEU F 342 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA F 347 " --> pdb=" O GLY F 343 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS F 348 " --> pdb=" O GLN F 344 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU F 351 " --> pdb=" O ALA F 347 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN F 352 " --> pdb=" O LYS F 348 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE F 353 " --> pdb=" O LEU F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 429 removed outlier: 4.443A pdb=" N GLY F 429 " --> pdb=" O MET F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 481 removed outlier: 3.759A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.868A pdb=" N ASN K 31 " --> pdb=" O SER K 28 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR K 32 " --> pdb=" O MET K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 32' Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.673A pdb=" N THR K 87 " --> pdb=" O PRO K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 100D through 100H removed outlier: 3.638A pdb=" N PHE K 100G" --> pdb=" O VAL K 100D" (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.353A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 65 No H-bonds generated for 'chain 'M' and resid 63 through 65' Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'Q' and resid 63 through 65 No H-bonds generated for 'chain 'Q' and resid 63 through 65' Processing helix chain 'Q' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 8.529A pdb=" N CYS A 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N TYR D 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N THR A 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N VAL D 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL A 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 609 removed outlier: 8.435A pdb=" N CYS B 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N TYR E 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N THR B 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N VAL E 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL B 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 603 through 609 removed outlier: 5.608A pdb=" N VAL F 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.550A pdb=" N ALA D 224 " --> pdb=" O VAL D 489 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AA6, first strand: chain 'D' and resid 170 through 177 Processing sheet with id=AA7, first strand: chain 'D' and resid 271 through 273 Processing sheet with id=AA8, first strand: chain 'D' and resid 292 through 293 Processing sheet with id=AA9, first strand: chain 'D' and resid 320 through 322 removed outlier: 5.344A pdb=" N ASP D 321A" --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE D 443 " --> pdb=" O ARG D 298 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 307 through 308 Processing sheet with id=AB2, first strand: chain 'D' and resid 394 through 395 removed outlier: 6.474A pdb=" N THR D 357 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N PHE D 468 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 374 through 378 removed outlier: 3.617A pdb=" N GLU D 381 " --> pdb=" O CYS D 378 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.518A pdb=" N LYS E 487 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'E' and resid 92 through 93 Processing sheet with id=AB7, first strand: chain 'E' and resid 120 through 121 removed outlier: 4.026A pdb=" N VAL E 120 " --> pdb=" O GLN E 203 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AB9, first strand: chain 'E' and resid 154 through 162 Processing sheet with id=AC1, first strand: chain 'E' and resid 259 through 260 removed outlier: 6.732A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.029A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 322 through 323 removed outlier: 4.335A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 307 through 308 Processing sheet with id=AC4, first strand: chain 'E' and resid 394 through 395 removed outlier: 6.626A pdb=" N THR E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N PHE E 468 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.642A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.543A pdb=" N ALA F 224 " --> pdb=" O VAL F 489 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'F' and resid 120 through 121 removed outlier: 3.899A pdb=" N VAL F 120 " --> pdb=" O GLN F 203 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AD1, first strand: chain 'F' and resid 271 through 274 removed outlier: 6.733A pdb=" N THR F 357 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N PHE F 468 " --> pdb=" O THR F 357 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 292 through 294 Processing sheet with id=AD3, first strand: chain 'F' and resid 297 through 298 removed outlier: 3.712A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 302 through 304 removed outlier: 5.060A pdb=" N ASP F 321A" --> pdb=" O THR F 303 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 307 through 308 Processing sheet with id=AD6, first strand: chain 'F' and resid 374 through 378 removed outlier: 3.513A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.623A pdb=" N VAL K 12 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL K 109 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA K 88 " --> pdb=" O VAL K 109 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR K 33 " --> pdb=" O ALA K 95 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.623A pdb=" N VAL K 12 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL K 109 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA K 88 " --> pdb=" O VAL K 109 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER K 100O" --> pdb=" O ARG K 96 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 67 through 68 Processing sheet with id=AE2, first strand: chain 'L' and resid 18 through 22 Processing sheet with id=AE3, first strand: chain 'L' and resid 44 through 46 removed outlier: 3.701A pdb=" N TYR L 36 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.573A pdb=" N GLN M 77 " --> pdb=" O ASP M 72 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.612A pdb=" N ALA M 93 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TRP M 34 " --> pdb=" O PHE M 50 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.387A pdb=" N LEU N 11 " --> pdb=" O GLU N 102 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN N 89 " --> pdb=" O ALA N 34 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA N 34 " --> pdb=" O GLN N 89 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG N 45 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 4 through 7 removed outlier: 3.573A pdb=" N GLN O 77 " --> pdb=" O ASP O 72 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.612A pdb=" N ALA O 93 " --> pdb=" O SER O 35 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TRP O 34 " --> pdb=" O PHE O 50 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'P' and resid 4 through 7 Processing sheet with id=AF4, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.387A pdb=" N LEU P 11 " --> pdb=" O GLU P 102 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR P 87 " --> pdb=" O TYR P 36 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN P 89 " --> pdb=" O ALA P 34 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA P 34 " --> pdb=" O GLN P 89 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG P 45 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 4 through 7 removed outlier: 3.573A pdb=" N GLN Q 77 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.611A pdb=" N ALA Q 93 " --> pdb=" O SER Q 35 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TRP Q 34 " --> pdb=" O PHE Q 50 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE Q 50 " --> pdb=" O TRP Q 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AF9, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.388A pdb=" N LEU R 11 " --> pdb=" O GLU R 102 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR R 87 " --> pdb=" O TYR R 36 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN R 89 " --> pdb=" O ALA R 34 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA R 34 " --> pdb=" O GLN R 89 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG R 45 " --> pdb=" O GLN R 37 " (cutoff:3.500A) 575 hydrogen bonds defined for protein. 1470 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: 7.39 Time building geometry restraints manager: 11.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6778 1.34 - 1.46: 5637 1.46 - 1.58: 10743 1.58 - 1.70: 5 1.70 - 1.82: 160 Bond restraints: 23323 Sorted by residual: bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C1 NAG E 614 " pdb=" O5 NAG E 614 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1 MAN j 6 " pdb=" C2 MAN j 6 " ideal model delta sigma weight residual 1.526 1.593 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C1 MAN I 6 " pdb=" C2 MAN I 6 " ideal model delta sigma weight residual 1.526 1.590 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C3 MAN i 4 " pdb=" O3 MAN i 4 " ideal model delta sigma weight residual 1.408 1.472 -0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 23318 not shown) Histogram of bond angle deviations from ideal: 98.20 - 105.53: 504 105.53 - 112.87: 13154 112.87 - 120.20: 8483 120.20 - 127.53: 9250 127.53 - 134.87: 313 Bond angle restraints: 31704 Sorted by residual: angle pdb=" N ASN F 332 " pdb=" CA ASN F 332 " pdb=" C ASN F 332 " ideal model delta sigma weight residual 111.02 119.54 -8.52 1.25e+00 6.40e-01 4.64e+01 angle pdb=" C GLU D 411 " pdb=" N GLN D 412 " pdb=" CA GLN D 412 " ideal model delta sigma weight residual 121.54 133.48 -11.94 1.91e+00 2.74e-01 3.91e+01 angle pdb=" C PRO D 407 " pdb=" N THR D 408 " pdb=" CA THR D 408 " ideal model delta sigma weight residual 121.54 132.44 -10.90 1.91e+00 2.74e-01 3.25e+01 angle pdb=" CA LEU F 116 " pdb=" CB LEU F 116 " pdb=" CG LEU F 116 " ideal model delta sigma weight residual 116.30 133.17 -16.87 3.50e+00 8.16e-02 2.32e+01 angle pdb=" C PRO F 407 " pdb=" N THR F 408 " pdb=" CA THR F 408 " ideal model delta sigma weight residual 126.45 134.87 -8.42 1.77e+00 3.19e-01 2.26e+01 ... (remaining 31699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.54: 15013 24.54 - 49.07: 542 49.07 - 73.61: 183 73.61 - 98.15: 79 98.15 - 122.69: 69 Dihedral angle restraints: 15886 sinusoidal: 8258 harmonic: 7628 Sorted by residual: dihedral pdb=" CA ASP O 101 " pdb=" C ASP O 101 " pdb=" N PRO O 102 " pdb=" CA PRO O 102 " ideal model delta harmonic sigma weight residual -180.00 -119.65 -60.35 0 5.00e+00 4.00e-02 1.46e+02 dihedral pdb=" CA ASP Q 101 " pdb=" C ASP Q 101 " pdb=" N PRO Q 102 " pdb=" CA PRO Q 102 " ideal model delta harmonic sigma weight residual -180.00 -119.68 -60.32 0 5.00e+00 4.00e-02 1.46e+02 dihedral pdb=" CA ASP M 101 " pdb=" C ASP M 101 " pdb=" N PRO M 102 " pdb=" CA PRO M 102 " ideal model delta harmonic sigma weight residual -180.00 -119.69 -60.31 0 5.00e+00 4.00e-02 1.45e+02 ... (remaining 15883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.259: 3971 0.259 - 0.518: 25 0.518 - 0.777: 3 0.777 - 1.036: 1 1.036 - 1.295: 2 Chirality restraints: 4002 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN D 392 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.11 -1.29 2.00e-01 2.50e+01 4.19e+01 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN E 392 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.19 -1.21 2.00e-01 2.50e+01 3.64e+01 chirality pdb=" C1 NAG e 1 " pdb=" ND2 ASN E 386 " pdb=" C2 NAG e 1 " pdb=" O5 NAG e 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.70e+01 ... (remaining 3999 not shown) Planarity restraints: 3887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG r 2 " -0.040 2.00e-02 2.50e+03 3.32e-02 1.37e+01 pdb=" C7 NAG r 2 " 0.007 2.00e-02 2.50e+03 pdb=" C8 NAG r 2 " -0.029 2.00e-02 2.50e+03 pdb=" N2 NAG r 2 " 0.054 2.00e-02 2.50e+03 pdb=" O7 NAG r 2 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP M 101 " 0.055 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO M 102 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO M 102 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO M 102 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP O 101 " -0.055 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO O 102 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO O 102 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO O 102 " -0.046 5.00e-02 4.00e+02 ... (remaining 3884 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3110 2.76 - 3.29: 19609 3.29 - 3.83: 34443 3.83 - 4.36: 39237 4.36 - 4.90: 69517 Nonbonded interactions: 165916 Sorted by model distance: nonbonded pdb=" O TRP F 69 " pdb=" OG1 THR F 71 " model vdw 2.222 2.440 nonbonded pdb=" O TRP E 69 " pdb=" OG1 THR E 71 " model vdw 2.245 2.440 nonbonded pdb=" OD1 ASP Q 100B" pdb=" O6 NAG s 1 " model vdw 2.258 2.440 nonbonded pdb=" OG SER D 447 " pdb=" O7 NAG H 1 " model vdw 2.276 2.440 nonbonded pdb=" O PRO E 369 " pdb=" OG1 THR E 373 " model vdw 2.294 2.440 ... (remaining 165911 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 32 through 137 or (resid 138 and (name N or name CA or nam \ e C or name O or name CB )) or resid 152 through 505 or resid 627 through 649)) selection = chain 'E' selection = (chain 'F' and (resid 32 through 137 or (resid 138 and (name N or name CA or nam \ e C or name O or name CB )) or resid 152 through 505 or resid 617 through 639)) } ncs_group { reference = (chain 'G' and resid 5 through 8) selection = (chain 'H' and resid 6 through 9) selection = (chain 'I' and resid 4 through 7) selection = (chain 'Z' and resid 4 through 7) selection = (chain 'g' and resid 4 through 7) selection = (chain 'i' and resid 4 through 7) selection = (chain 'j' and resid 4 through 7) selection = (chain 'r' and resid 6 through 9) selection = (chain 's' and resid 6 through 9) } ncs_group { reference = chain 'J' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'k' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'q' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'a' selection = chain 'c' selection = chain 'l' selection = chain 'n' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.030 Extract box with map and model: 6.710 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 62.090 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.090 23323 Z= 0.579 Angle : 1.228 16.875 31704 Z= 0.611 Chirality : 0.079 1.295 4002 Planarity : 0.008 0.085 3823 Dihedral : 16.874 122.686 10909 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.09 % Favored : 88.60 % Rotamer: Outliers : 0.57 % Allowed : 2.62 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.14), residues: 2614 helix: -2.87 (0.21), residues: 301 sheet: -1.54 (0.17), residues: 835 loop : -3.23 (0.13), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP Q 103 HIS 0.012 0.002 HIS M 100G PHE 0.035 0.005 PHE O 100A TYR 0.033 0.003 TYR M 52 ARG 0.021 0.001 ARG F 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 602 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 647 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7757 (tt0) REVERT: D 78 ASP cc_start: 0.7965 (t70) cc_final: 0.7314 (t0) REVERT: E 80 ASN cc_start: 0.7723 (m-40) cc_final: 0.7479 (p0) REVERT: E 432 LYS cc_start: 0.7791 (mmtt) cc_final: 0.7381 (tttm) REVERT: F 78 ASP cc_start: 0.7460 (t70) cc_final: 0.7092 (t0) REVERT: F 325 ASN cc_start: 0.7869 (m-40) cc_final: 0.7653 (m-40) REVERT: F 358 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8152 (pp) REVERT: F 432 LYS cc_start: 0.7727 (mmtt) cc_final: 0.7177 (ptmm) REVERT: F 443 ILE cc_start: 0.8523 (mm) cc_final: 0.8137 (mm) REVERT: K 81 LYS cc_start: 0.7910 (mmtp) cc_final: 0.7665 (tmtt) REVERT: K 99 GLN cc_start: 0.6985 (tt0) cc_final: 0.6736 (tt0) REVERT: L 34 GLN cc_start: 0.7396 (mp-120) cc_final: 0.6928 (mp10) REVERT: L 35 TRP cc_start: 0.7515 (m100) cc_final: 0.7010 (m100) REVERT: L 49 TYR cc_start: 0.7255 (p90) cc_final: 0.6867 (p90) REVERT: N 53 THR cc_start: 0.7902 (m) cc_final: 0.7503 (p) REVERT: O 36 TRP cc_start: 0.7722 (m100) cc_final: 0.7501 (m100) REVERT: P 48 LEU cc_start: 0.7009 (tp) cc_final: 0.6796 (tp) REVERT: Q 5 GLN cc_start: 0.6546 (tt0) cc_final: 0.6223 (pp30) REVERT: R 45 ARG cc_start: 0.6264 (ptt180) cc_final: 0.6009 (mtp180) REVERT: R 53 THR cc_start: 0.7125 (m) cc_final: 0.6910 (p) REVERT: R 63 ILE cc_start: 0.6996 (mt) cc_final: 0.6462 (mt) REVERT: R 65 SER cc_start: 0.8090 (p) cc_final: 0.7770 (m) outliers start: 13 outliers final: 1 residues processed: 613 average time/residue: 0.4060 time to fit residues: 364.8761 Evaluate side-chains 342 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 340 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain F residue 358 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 3.9990 chunk 197 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 236 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN A 658 GLN B 650 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 656 ASN D 98 ASN D 114 GLN D 397 ASN ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN E 114 GLN E 397 ASN ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 ASN F 114 GLN F 397 ASN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN R 6 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 23323 Z= 0.318 Angle : 0.877 11.876 31704 Z= 0.421 Chirality : 0.058 0.820 4002 Planarity : 0.006 0.088 3823 Dihedral : 15.574 116.508 6042 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.60 % Favored : 90.24 % Rotamer: Outliers : 2.92 % Allowed : 10.51 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.15), residues: 2614 helix: -1.36 (0.27), residues: 336 sheet: -0.91 (0.19), residues: 791 loop : -3.03 (0.13), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 395 HIS 0.007 0.002 HIS O 100G PHE 0.031 0.002 PHE P 71 TYR 0.021 0.002 TYR M 52 ARG 0.008 0.001 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 356 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 650 GLN cc_start: 0.4472 (OUTLIER) cc_final: 0.3759 (tm-30) REVERT: C 647 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7837 (tt0) REVERT: D 104 MET cc_start: 0.9065 (ttt) cc_final: 0.8676 (ttt) REVERT: D 208 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8285 (t) REVERT: E 213 ILE cc_start: 0.8749 (pt) cc_final: 0.8534 (mt) REVERT: E 432 LYS cc_start: 0.7673 (mmtt) cc_final: 0.7356 (tttm) REVERT: F 78 ASP cc_start: 0.7382 (t70) cc_final: 0.7057 (t0) REVERT: F 325 ASN cc_start: 0.7913 (m-40) cc_final: 0.7603 (m-40) REVERT: F 432 LYS cc_start: 0.7701 (mmtt) cc_final: 0.7128 (ptmm) REVERT: K 81 LYS cc_start: 0.8142 (mmtp) cc_final: 0.7818 (tmtt) REVERT: L 34 GLN cc_start: 0.7358 (mp-120) cc_final: 0.7143 (mp10) REVERT: L 35 TRP cc_start: 0.7621 (m100) cc_final: 0.7124 (m100) REVERT: L 49 TYR cc_start: 0.7298 (p90) cc_final: 0.6853 (p90) REVERT: M 109 VAL cc_start: 0.7878 (t) cc_final: 0.7633 (p) REVERT: N 35 TRP cc_start: 0.7882 (m100) cc_final: 0.7513 (m100) REVERT: O 36 TRP cc_start: 0.7773 (m100) cc_final: 0.7515 (m100) REVERT: O 43 LYS cc_start: 0.7628 (mtmm) cc_final: 0.6429 (pttp) REVERT: Q 5 GLN cc_start: 0.6521 (tt0) cc_final: 0.6292 (pp30) outliers start: 67 outliers final: 42 residues processed: 401 average time/residue: 0.4164 time to fit residues: 250.3455 Evaluate side-chains 362 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 318 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 67 ASN Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 TRP Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 100 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 0.0470 chunk 73 optimal weight: 0.6980 chunk 196 optimal weight: 2.9990 chunk 160 optimal weight: 0.0070 chunk 65 optimal weight: 6.9990 chunk 236 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 210 optimal weight: 20.0000 chunk 234 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 189 optimal weight: 10.0000 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 ASN E 66 HIS ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23323 Z= 0.192 Angle : 0.754 10.674 31704 Z= 0.362 Chirality : 0.054 0.706 4002 Planarity : 0.005 0.083 3823 Dihedral : 13.568 111.200 6038 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.95 % Favored : 90.93 % Rotamer: Outliers : 2.44 % Allowed : 13.21 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.15), residues: 2614 helix: -0.49 (0.30), residues: 313 sheet: -0.65 (0.19), residues: 779 loop : -2.82 (0.13), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 96 HIS 0.004 0.001 HIS M 100G PHE 0.024 0.002 PHE P 71 TYR 0.018 0.001 TYR Q 52 ARG 0.005 0.000 ARG O 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 356 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 650 GLN cc_start: 0.4613 (OUTLIER) cc_final: 0.4190 (tm-30) REVERT: C 647 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7795 (tt0) REVERT: D 104 MET cc_start: 0.9006 (ttt) cc_final: 0.8644 (ttt) REVERT: E 432 LYS cc_start: 0.7726 (mmtt) cc_final: 0.7420 (tttm) REVERT: F 78 ASP cc_start: 0.7406 (t70) cc_final: 0.7117 (t0) REVERT: F 432 LYS cc_start: 0.7715 (mmtt) cc_final: 0.7180 (ptmm) REVERT: K 81 LYS cc_start: 0.8218 (mmtp) cc_final: 0.7901 (tmtt) REVERT: K 100 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8765 (t) REVERT: L 35 TRP cc_start: 0.7576 (m100) cc_final: 0.7069 (m100) REVERT: L 87 TYR cc_start: 0.6578 (m-80) cc_final: 0.6328 (m-80) REVERT: M 109 VAL cc_start: 0.7777 (t) cc_final: 0.7562 (p) REVERT: N 24 ARG cc_start: 0.6772 (mtp-110) cc_final: 0.6536 (mtp-110) REVERT: N 35 TRP cc_start: 0.7889 (m100) cc_final: 0.7593 (m100) REVERT: N 42 GLN cc_start: 0.6435 (tp40) cc_final: 0.5832 (mt0) REVERT: O 36 TRP cc_start: 0.7689 (m100) cc_final: 0.7486 (m100) REVERT: Q 5 GLN cc_start: 0.6561 (tt0) cc_final: 0.6348 (pp30) outliers start: 56 outliers final: 33 residues processed: 396 average time/residue: 0.3832 time to fit residues: 227.1089 Evaluate side-chains 361 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 326 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 96 TRP Chi-restraints excluded: chain F residue 365 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain R residue 33 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 2.9990 chunk 177 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 158 optimal weight: 5.9990 chunk 237 optimal weight: 0.9980 chunk 251 optimal weight: 6.9990 chunk 124 optimal weight: 0.0570 chunk 224 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 overall best weight: 1.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23323 Z= 0.239 Angle : 0.772 11.070 31704 Z= 0.369 Chirality : 0.055 0.740 4002 Planarity : 0.005 0.084 3823 Dihedral : 12.758 108.988 6038 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.26 % Favored : 90.59 % Rotamer: Outliers : 3.44 % Allowed : 12.69 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.16), residues: 2614 helix: -0.42 (0.29), residues: 328 sheet: -0.53 (0.20), residues: 782 loop : -2.68 (0.14), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 96 HIS 0.005 0.001 HIS F 330 PHE 0.023 0.002 PHE M 100A TYR 0.018 0.001 TYR E 191 ARG 0.008 0.001 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 322 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 663 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7978 (pp) REVERT: D 104 MET cc_start: 0.9029 (ttt) cc_final: 0.8669 (ttt) REVERT: E 432 LYS cc_start: 0.7735 (mmtt) cc_final: 0.7471 (tttm) REVERT: F 78 ASP cc_start: 0.7388 (t70) cc_final: 0.7119 (t0) REVERT: F 432 LYS cc_start: 0.7753 (mmtt) cc_final: 0.7203 (ptmm) REVERT: K 81 LYS cc_start: 0.8238 (mmtp) cc_final: 0.7890 (tmtt) REVERT: K 100 VAL cc_start: 0.9038 (OUTLIER) cc_final: 0.8837 (t) REVERT: L 35 TRP cc_start: 0.7552 (m100) cc_final: 0.7076 (m100) REVERT: L 87 TYR cc_start: 0.6321 (m-80) cc_final: 0.6111 (m-80) REVERT: N 35 TRP cc_start: 0.7903 (m100) cc_final: 0.7669 (m100) REVERT: N 42 GLN cc_start: 0.6433 (tp40) cc_final: 0.5892 (mt0) REVERT: N 100 LYS cc_start: 0.7932 (tttt) cc_final: 0.7104 (mttp) REVERT: Q 5 GLN cc_start: 0.6568 (tt0) cc_final: 0.6353 (pp30) REVERT: R 45 ARG cc_start: 0.7415 (mtp180) cc_final: 0.7207 (mtm110) REVERT: R 69 ARG cc_start: 0.6876 (ttm110) cc_final: 0.6547 (ttm110) REVERT: R 99 THR cc_start: 0.6019 (m) cc_final: 0.5791 (m) outliers start: 79 outliers final: 50 residues processed: 381 average time/residue: 0.3755 time to fit residues: 215.2031 Evaluate side-chains 367 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 315 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 TRP Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 365 SER Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain R residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 3.9990 chunk 142 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 214 optimal weight: 0.2980 chunk 173 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN E 80 ASN E 114 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23323 Z= 0.262 Angle : 0.771 11.201 31704 Z= 0.369 Chirality : 0.055 0.689 4002 Planarity : 0.005 0.084 3823 Dihedral : 12.179 105.909 6038 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.95 % Favored : 89.90 % Rotamer: Outliers : 3.57 % Allowed : 13.64 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.16), residues: 2614 helix: -0.20 (0.29), residues: 328 sheet: -0.51 (0.20), residues: 783 loop : -2.63 (0.14), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 96 HIS 0.005 0.001 HIS E 330 PHE 0.027 0.002 PHE M 100A TYR 0.020 0.001 TYR E 191 ARG 0.009 0.001 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 314 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 663 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7954 (pp) REVERT: C 647 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8041 (tt0) REVERT: D 104 MET cc_start: 0.9033 (ttt) cc_final: 0.8676 (ttt) REVERT: D 228 CYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7895 (t) REVERT: E 113 ASP cc_start: 0.7769 (m-30) cc_final: 0.7521 (m-30) REVERT: F 78 ASP cc_start: 0.7398 (t70) cc_final: 0.7126 (t0) REVERT: F 432 LYS cc_start: 0.7758 (mmtt) cc_final: 0.7227 (ptmm) REVERT: K 81 LYS cc_start: 0.8267 (mmtp) cc_final: 0.7914 (tmtt) REVERT: N 42 GLN cc_start: 0.6410 (tp40) cc_final: 0.5822 (mt0) REVERT: N 100 LYS cc_start: 0.7939 (tttt) cc_final: 0.7098 (mttp) REVERT: O 47 TRP cc_start: 0.7887 (t60) cc_final: 0.7530 (t60) REVERT: Q 5 GLN cc_start: 0.6682 (tt0) cc_final: 0.6450 (pp30) REVERT: R 45 ARG cc_start: 0.7453 (mtp180) cc_final: 0.7193 (mtm110) REVERT: R 99 THR cc_start: 0.6116 (m) cc_final: 0.5659 (m) outliers start: 82 outliers final: 54 residues processed: 379 average time/residue: 0.4125 time to fit residues: 234.7778 Evaluate side-chains 363 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 307 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 386 ASN Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 TRP Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 365 SER Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 33 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 5.9990 chunk 226 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 251 optimal weight: 8.9990 chunk 208 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 GLN E 80 ASN E 308 HIS ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23323 Z= 0.263 Angle : 0.771 13.747 31704 Z= 0.369 Chirality : 0.054 0.663 4002 Planarity : 0.005 0.085 3823 Dihedral : 11.817 101.430 6038 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.98 % Favored : 89.86 % Rotamer: Outliers : 3.88 % Allowed : 13.78 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.16), residues: 2614 helix: -0.04 (0.29), residues: 328 sheet: -0.49 (0.20), residues: 789 loop : -2.58 (0.14), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 96 HIS 0.005 0.001 HIS E 330 PHE 0.027 0.002 PHE M 100A TYR 0.020 0.001 TYR E 191 ARG 0.009 0.001 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 313 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 633 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8305 (ttmt) REVERT: C 647 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7978 (tt0) REVERT: D 104 MET cc_start: 0.9035 (ttt) cc_final: 0.8682 (ttt) REVERT: D 192 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7715 (ttp-110) REVERT: E 113 ASP cc_start: 0.7754 (m-30) cc_final: 0.7535 (m-30) REVERT: E 176 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7324 (p90) REVERT: F 78 ASP cc_start: 0.7416 (t70) cc_final: 0.7162 (t0) REVERT: F 432 LYS cc_start: 0.7772 (mmtt) cc_final: 0.7262 (ptmm) REVERT: K 81 LYS cc_start: 0.8319 (mmtp) cc_final: 0.7902 (tmtt) REVERT: N 42 GLN cc_start: 0.6355 (tp40) cc_final: 0.5839 (mt0) REVERT: N 63 ILE cc_start: 0.8589 (mp) cc_final: 0.8321 (tt) REVERT: N 100 LYS cc_start: 0.7905 (tttt) cc_final: 0.7073 (mttp) REVERT: O 47 TRP cc_start: 0.7876 (t60) cc_final: 0.7540 (t60) REVERT: Q 5 GLN cc_start: 0.6795 (tt0) cc_final: 0.6586 (pp30) REVERT: R 45 ARG cc_start: 0.7370 (mtp180) cc_final: 0.7103 (mtm-85) REVERT: R 99 THR cc_start: 0.6079 (m) cc_final: 0.5861 (m) outliers start: 89 outliers final: 59 residues processed: 378 average time/residue: 0.3955 time to fit residues: 225.7910 Evaluate side-chains 371 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 309 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 TRP Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 365 SER Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain R residue 33 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 143 optimal weight: 0.5980 chunk 183 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 211 optimal weight: 7.9990 chunk 140 optimal weight: 0.0980 chunk 250 optimal weight: 0.5980 chunk 156 optimal weight: 0.7980 chunk 152 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23323 Z= 0.164 Angle : 0.695 15.042 31704 Z= 0.329 Chirality : 0.051 0.576 4002 Planarity : 0.005 0.082 3823 Dihedral : 11.022 94.839 6038 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.15 % Favored : 91.74 % Rotamer: Outliers : 2.83 % Allowed : 14.65 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.16), residues: 2614 helix: 0.37 (0.30), residues: 320 sheet: -0.41 (0.19), residues: 806 loop : -2.43 (0.14), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 628 HIS 0.004 0.001 HIS R 49 PHE 0.027 0.002 PHE P 71 TYR 0.016 0.001 TYR E 191 ARG 0.014 0.000 ARG R 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 334 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 664 ASP cc_start: 0.6859 (OUTLIER) cc_final: 0.6633 (p0) REVERT: C 647 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8020 (tt0) REVERT: D 104 MET cc_start: 0.9002 (ttt) cc_final: 0.8657 (ttt) REVERT: E 113 ASP cc_start: 0.7667 (m-30) cc_final: 0.7415 (m-30) REVERT: E 425 ASN cc_start: 0.8052 (p0) cc_final: 0.7789 (p0) REVERT: F 33 LYS cc_start: 0.8125 (mtpt) cc_final: 0.7779 (mmmt) REVERT: F 78 ASP cc_start: 0.7405 (t70) cc_final: 0.7161 (t0) REVERT: F 432 LYS cc_start: 0.7801 (mmtt) cc_final: 0.7281 (ptmm) REVERT: K 81 LYS cc_start: 0.8185 (mmtp) cc_final: 0.7870 (tmtt) REVERT: N 42 GLN cc_start: 0.6217 (tp40) cc_final: 0.5743 (mt0) REVERT: N 63 ILE cc_start: 0.8538 (mp) cc_final: 0.8263 (tt) REVERT: O 47 TRP cc_start: 0.7790 (t60) cc_final: 0.7381 (t60) REVERT: Q 5 GLN cc_start: 0.6802 (tt0) cc_final: 0.6585 (pp30) REVERT: Q 23 ARG cc_start: 0.8187 (tpt-90) cc_final: 0.7918 (tpt90) REVERT: R 45 ARG cc_start: 0.7337 (mtp180) cc_final: 0.7066 (mtm110) REVERT: R 99 THR cc_start: 0.6107 (m) cc_final: 0.5892 (m) outliers start: 65 outliers final: 47 residues processed: 381 average time/residue: 0.3850 time to fit residues: 220.8723 Evaluate side-chains 359 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 311 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 TRP Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain R residue 33 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 170 optimal weight: 40.0000 chunk 123 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 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 650 GLN A 658 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN F 462 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23323 Z= 0.316 Angle : 0.805 15.948 31704 Z= 0.383 Chirality : 0.056 0.660 4002 Planarity : 0.005 0.087 3823 Dihedral : 11.043 93.575 6038 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.48 % Favored : 89.36 % Rotamer: Outliers : 3.05 % Allowed : 15.34 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.16), residues: 2614 helix: 0.09 (0.29), residues: 328 sheet: -0.51 (0.20), residues: 805 loop : -2.47 (0.14), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 35 HIS 0.006 0.002 HIS E 330 PHE 0.033 0.003 PHE M 100A TYR 0.022 0.002 TYR E 191 ARG 0.010 0.001 ARG E 440 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 316 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 664 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6706 (p0) REVERT: C 647 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8023 (tt0) REVERT: D 104 MET cc_start: 0.9033 (ttt) cc_final: 0.8681 (ttt) REVERT: D 192 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7769 (ttp-170) REVERT: E 113 ASP cc_start: 0.7800 (m-30) cc_final: 0.7589 (m-30) REVERT: E 176 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7495 (p90) REVERT: F 33 LYS cc_start: 0.8174 (mtpt) cc_final: 0.7874 (mmmt) REVERT: F 78 ASP cc_start: 0.7419 (t70) cc_final: 0.7151 (t0) REVERT: F 432 LYS cc_start: 0.7788 (mmtt) cc_final: 0.7336 (ptmm) REVERT: K 81 LYS cc_start: 0.8263 (mmtp) cc_final: 0.7901 (tmtt) REVERT: N 24 ARG cc_start: 0.6869 (mtp-110) cc_final: 0.6641 (mtp-110) REVERT: N 42 GLN cc_start: 0.5815 (tp40) cc_final: 0.5464 (mt0) REVERT: N 63 ILE cc_start: 0.8615 (mp) cc_final: 0.8361 (tt) REVERT: O 47 TRP cc_start: 0.7940 (t60) cc_final: 0.7417 (t60) REVERT: P 78 LEU cc_start: 0.7184 (mt) cc_final: 0.6558 (tt) REVERT: Q 23 ARG cc_start: 0.8176 (tpt-90) cc_final: 0.7868 (tpt90) REVERT: R 99 THR cc_start: 0.6164 (m) cc_final: 0.5960 (m) outliers start: 70 outliers final: 52 residues processed: 369 average time/residue: 0.3990 time to fit residues: 220.0709 Evaluate side-chains 368 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 313 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 TRP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 52 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 6.9990 chunk 240 optimal weight: 10.0000 chunk 219 optimal weight: 0.9980 chunk 233 optimal weight: 8.9990 chunk 140 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 211 optimal weight: 0.0970 chunk 220 optimal weight: 8.9990 chunk 232 optimal weight: 4.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 658 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23323 Z= 0.236 Angle : 0.753 15.423 31704 Z= 0.360 Chirality : 0.054 0.629 4002 Planarity : 0.005 0.107 3823 Dihedral : 10.867 93.217 6038 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.18 % Favored : 90.67 % Rotamer: Outliers : 2.83 % Allowed : 15.61 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.16), residues: 2614 helix: 0.37 (0.30), residues: 322 sheet: -0.44 (0.20), residues: 786 loop : -2.43 (0.14), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 35 HIS 0.004 0.001 HIS F 330 PHE 0.030 0.002 PHE P 71 TYR 0.023 0.001 TYR O 100H ARG 0.013 0.001 ARG R 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 315 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 662 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8204 (mm-30) REVERT: B 664 ASP cc_start: 0.6834 (OUTLIER) cc_final: 0.6609 (p0) REVERT: C 647 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8036 (tt0) REVERT: D 104 MET cc_start: 0.9019 (ttt) cc_final: 0.8666 (ttt) REVERT: E 113 ASP cc_start: 0.7738 (m-30) cc_final: 0.7520 (m-30) REVERT: E 176 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7524 (p90) REVERT: F 33 LYS cc_start: 0.8152 (mtpt) cc_final: 0.7837 (mmmt) REVERT: F 78 ASP cc_start: 0.7419 (t70) cc_final: 0.7155 (t0) REVERT: F 432 LYS cc_start: 0.7787 (mmtt) cc_final: 0.7350 (ptmm) REVERT: K 81 LYS cc_start: 0.8254 (mmtp) cc_final: 0.7901 (tmtt) REVERT: N 24 ARG cc_start: 0.6923 (mtp-110) cc_final: 0.6707 (mtp-110) REVERT: N 42 GLN cc_start: 0.5699 (tp40) cc_final: 0.5324 (mt0) REVERT: N 63 ILE cc_start: 0.8607 (mp) cc_final: 0.8349 (tt) REVERT: O 47 TRP cc_start: 0.7897 (t60) cc_final: 0.7595 (t60) REVERT: P 78 LEU cc_start: 0.7213 (mt) cc_final: 0.6657 (tt) REVERT: R 45 ARG cc_start: 0.6649 (mtm110) cc_final: 0.5984 (mtm-85) REVERT: R 69 ARG cc_start: 0.6618 (ttm-80) cc_final: 0.6404 (ttm-80) REVERT: R 99 THR cc_start: 0.6190 (m) cc_final: 0.5888 (m) outliers start: 65 outliers final: 51 residues processed: 363 average time/residue: 0.3958 time to fit residues: 213.5454 Evaluate side-chains 363 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 310 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 TRP Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain R residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 2.9990 chunk 246 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 171 optimal weight: 20.0000 chunk 259 optimal weight: 4.9990 chunk 238 optimal weight: 0.7980 chunk 206 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 GLN B 658 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 HIS ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 23323 Z= 0.375 Angle : 0.856 16.157 31704 Z= 0.411 Chirality : 0.057 0.707 4002 Planarity : 0.006 0.110 3823 Dihedral : 11.181 92.649 6038 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.48 % Favored : 88.37 % Rotamer: Outliers : 2.75 % Allowed : 15.74 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.16), residues: 2614 helix: 0.22 (0.30), residues: 313 sheet: -0.46 (0.20), residues: 788 loop : -2.54 (0.14), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP N 35 HIS 0.007 0.002 HIS F 330 PHE 0.034 0.003 PHE M 100A TYR 0.021 0.002 TYR E 191 ARG 0.012 0.001 ARG R 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 320 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 664 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6777 (p0) REVERT: D 104 MET cc_start: 0.9034 (ttt) cc_final: 0.8654 (ttt) REVERT: E 176 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7601 (p90) REVERT: F 33 LYS cc_start: 0.8169 (mtpt) cc_final: 0.7886 (mmmt) REVERT: F 78 ASP cc_start: 0.7364 (t70) cc_final: 0.7122 (t0) REVERT: F 432 LYS cc_start: 0.7690 (mmtt) cc_final: 0.7328 (ptmm) REVERT: K 81 LYS cc_start: 0.8272 (mmtp) cc_final: 0.7825 (tmtt) REVERT: L 35 TRP cc_start: 0.7470 (m100) cc_final: 0.6908 (m100) REVERT: N 24 ARG cc_start: 0.6914 (mtp-110) cc_final: 0.6674 (mtp-110) REVERT: N 42 GLN cc_start: 0.5769 (tp40) cc_final: 0.5382 (mt0) REVERT: N 63 ILE cc_start: 0.8646 (mp) cc_final: 0.8410 (tt) REVERT: O 47 TRP cc_start: 0.7937 (t60) cc_final: 0.7426 (t60) REVERT: P 37 GLN cc_start: 0.7305 (tt0) cc_final: 0.6890 (tt0) REVERT: P 69 ARG cc_start: 0.5844 (tpp80) cc_final: 0.5513 (tpp80) REVERT: P 78 LEU cc_start: 0.7261 (mt) cc_final: 0.6656 (tt) REVERT: R 45 ARG cc_start: 0.6909 (mtm110) cc_final: 0.6226 (mtm-85) REVERT: R 69 ARG cc_start: 0.6806 (ttm-80) cc_final: 0.6581 (ttm-80) REVERT: R 99 THR cc_start: 0.6243 (m) cc_final: 0.6041 (m) outliers start: 63 outliers final: 52 residues processed: 367 average time/residue: 0.3775 time to fit residues: 206.4139 Evaluate side-chains 367 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 313 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 TRP Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain R residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 3.9990 chunk 219 optimal weight: 0.0170 chunk 63 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 206 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 212 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 658 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.161464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.122000 restraints weight = 34345.450| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.89 r_work: 0.3147 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23323 Z= 0.190 Angle : 0.739 15.352 31704 Z= 0.352 Chirality : 0.053 0.608 4002 Planarity : 0.005 0.112 3823 Dihedral : 10.714 92.264 6038 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.07 % Favored : 90.78 % Rotamer: Outliers : 2.48 % Allowed : 16.04 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.16), residues: 2614 helix: 0.41 (0.30), residues: 321 sheet: -0.37 (0.20), residues: 778 loop : -2.47 (0.14), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 35 HIS 0.005 0.001 HIS E 330 PHE 0.023 0.002 PHE O 50 TYR 0.023 0.001 TYR O 100H ARG 0.012 0.001 ARG R 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5428.99 seconds wall clock time: 99 minutes 15.68 seconds (5955.68 seconds total)