Starting phenix.real_space_refine on Thu Apr 11 04:47:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9b_25755/04_2024/7t9b_25755_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9b_25755/04_2024/7t9b_25755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9b_25755/04_2024/7t9b_25755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9b_25755/04_2024/7t9b_25755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9b_25755/04_2024/7t9b_25755_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9b_25755/04_2024/7t9b_25755_updated.pdb" } resolution = 3.72 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= 0.002 sd= 0.039 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 131 5.16 5 C 13523 2.51 5 N 3572 2.21 5 O 4366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 621": "OE1" <-> "OE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 21592 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3433 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 3 Chain: "B" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "J" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "K" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3425 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 410} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "M" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "N" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3387 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 23, 'TRANS': 405} Chain breaks: 4 Chain: "F" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "O" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "P" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "H" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1051 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 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: "T" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 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 Time building chain proxies: 11.36, per 1000 atoms: 0.53 Number of scatterers: 21592 At special positions: 0 Unit cell: (124.2, 127.65, 188.6, 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 131 16.00 O 4366 8.00 N 3572 7.00 C 13523 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.00 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.10 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.06 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.15 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 7 " " MAN S 4 " - " MAN S 5 " " BMA Y 3 " - " MAN Y 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA S 3 " - " MAN S 4 " " MAN S 4 " - " MAN S 6 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 2 " - " BMA S 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG j 1 " - " NAG j 2 " BETA1-6 " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " FUC T 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG U 1 " - " FUC U 3 " " NAG a 1 " - " FUC a 2 " " NAG b 1 " - " FUC b 3 " " NAG i 1 " - " FUC i 2 " " NAG j 1 " - " FUC j 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 355 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 392 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 301 " " NAG A 611 " - " ASN A 197 " " NAG A 612 " - " ASN A 133 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 625 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 137 " " NAG C 604 " - " ASN C 355 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 448 " " NAG C 610 " - " ASN C 301 " " NAG C 611 " - " ASN C 197 " " NAG C 612 " - " ASN C 133 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 625 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 137 " " NAG E 604 " - " ASN E 355 " " NAG E 605 " - " ASN E 276 " " NAG E 606 " - " ASN E 392 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 133 " " NAG F 701 " - " ASN F 625 " " NAG F 702 " - " ASN F 637 " " NAG G 1 " - " ASN A 386 " " NAG I 1 " - " ASN A 332 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN A 160 " " NAG T 1 " - " ASN B 618 " " NAG U 1 " - " ASN B 611 " " NAG V 1 " - " ASN C 160 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 332 " " NAG Y 1 " - " ASN C 262 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN D 618 " " NAG b 1 " - " ASN D 611 " " NAG c 1 " - " ASN E 386 " " NAG d 1 " - " ASN E 332 " " NAG e 1 " - " ASN E 262 " " NAG f 1 " - " ASN E 197 " " NAG g 1 " - " ASN E 156 " " NAG h 1 " - " ASN E 160 " " NAG i 1 " - " ASN F 618 " " NAG j 1 " - " ASN F 611 " Time building additional restraints: 9.11 Conformation dependent library (CDL) restraints added in 3.7 seconds 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 53 sheets defined 16.8% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.38 Creating SS restraints... Processing helix chain 'A' and resid 100 through 116 removed outlier: 3.743A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 150 No H-bonds generated for 'chain 'A' and resid 140 through 150' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 335 through 351 removed outlier: 4.011A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 475 through 485 removed outlier: 5.054A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 525 removed outlier: 4.355A pdb=" N GLY B 525 " --> pdb=" O GLY B 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 522 through 525' Processing helix chain 'B' and resid 528 through 541 removed outlier: 5.396A pdb=" N MET B 533 " --> pdb=" O GLY B 529 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU B 535 " --> pdb=" O ALA B 531 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL B 537 " --> pdb=" O MET B 533 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 639 through 661 removed outlier: 4.141A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing helix chain 'J' and resid 61 through 63 No H-bonds generated for 'chain 'J' and resid 61 through 63' Processing helix chain 'J' and resid 84 through 86 No H-bonds generated for 'chain 'J' and resid 84 through 86' Processing helix chain 'K' and resid 80 through 82 No H-bonds generated for 'chain 'K' and resid 80 through 82' Processing helix chain 'C' and resid 100 through 116 removed outlier: 3.610A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 150 No H-bonds generated for 'chain 'C' and resid 140 through 150' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 335 through 351 removed outlier: 3.998A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 475 through 485 removed outlier: 5.103A pdb=" N TYR C 484 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 525 removed outlier: 4.278A pdb=" N GLY D 525 " --> pdb=" O GLY D 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 522 through 525' Processing helix chain 'D' and resid 528 through 541 removed outlier: 5.360A pdb=" N MET D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU D 535 " --> pdb=" O ALA D 531 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR D 536 " --> pdb=" O SER D 532 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL D 537 " --> pdb=" O MET D 533 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 595 Processing helix chain 'D' and resid 619 through 622 No H-bonds generated for 'chain 'D' and resid 619 through 622' Processing helix chain 'D' and resid 628 through 634 Processing helix chain 'D' and resid 639 through 661 Processing helix chain 'M' and resid 29 through 31 No H-bonds generated for 'chain 'M' and resid 29 through 31' Processing helix chain 'M' and resid 61 through 63 No H-bonds generated for 'chain 'M' and resid 61 through 63' Processing helix chain 'M' and resid 84 through 86 No H-bonds generated for 'chain 'M' and resid 84 through 86' Processing helix chain 'N' and resid 80 through 82 No H-bonds generated for 'chain 'N' and resid 80 through 82' Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.755A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 150 No H-bonds generated for 'chain 'E' and resid 140 through 150' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 335 through 351 removed outlier: 3.957A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 475 through 485 removed outlier: 5.042A pdb=" N TYR E 484 " --> pdb=" O SER E 481 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS E 485 " --> pdb=" O GLU E 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 525 removed outlier: 4.403A pdb=" N GLY F 525 " --> pdb=" O GLY F 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 522 through 525' Processing helix chain 'F' and resid 528 through 541 removed outlier: 5.375A pdb=" N MET F 533 " --> pdb=" O GLY F 529 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR F 534 " --> pdb=" O ALA F 530 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU F 535 " --> pdb=" O ALA F 531 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR F 536 " --> pdb=" O SER F 532 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL F 537 " --> pdb=" O MET F 533 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN F 541 " --> pdb=" O VAL F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 595 Processing helix chain 'F' and resid 619 through 622 No H-bonds generated for 'chain 'F' and resid 619 through 622' Processing helix chain 'F' and resid 628 through 634 Processing helix chain 'F' and resid 637 through 661 removed outlier: 4.417A pdb=" N GLN F 640 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE F 641 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR F 643 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 31 No H-bonds generated for 'chain 'O' and resid 29 through 31' Processing helix chain 'O' and resid 61 through 63 No H-bonds generated for 'chain 'O' and resid 61 through 63' Processing helix chain 'O' and resid 84 through 86 No H-bonds generated for 'chain 'O' and resid 84 through 86' Processing helix chain 'P' and resid 80 through 82 No H-bonds generated for 'chain 'P' and resid 80 through 82' Processing helix chain 'H' and resid 61 through 63 No H-bonds generated for 'chain 'H' and resid 61 through 63' Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= E, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= F, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= G, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.812A pdb=" N ALA A 433 " --> pdb=" O THR A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 271 through 274 Processing sheet with id= I, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.437A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 301 through 308 removed outlier: 3.988A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 5.974A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'J' and resid 3 through 6 Processing sheet with id= L, first strand: chain 'J' and resid 107 through 109 removed outlier: 5.983A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'J' and resid 93 through 95 Processing sheet with id= N, first strand: chain 'K' and resid 19 through 24 Processing sheet with id= O, first strand: chain 'K' and resid 102 through 104 removed outlier: 3.579A pdb=" N ALA K 84 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'K' and resid 89 through 91 Processing sheet with id= Q, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= R, first strand: chain 'C' and resid 45 through 47 Processing sheet with id= S, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= T, first strand: chain 'C' and resid 91 through 94 Processing sheet with id= U, first strand: chain 'C' and resid 130 through 133 Processing sheet with id= V, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= W, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.706A pdb=" N ALA C 433 " --> pdb=" O THR C 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'C' and resid 271 through 274 Processing sheet with id= Y, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.484A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 301 through 308 removed outlier: 3.733A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 5.855A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 3 through 6 Processing sheet with id= AB, first strand: chain 'M' and resid 107 through 109 removed outlier: 5.950A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'M' and resid 93 through 95 Processing sheet with id= AD, first strand: chain 'N' and resid 19 through 24 Processing sheet with id= AE, first strand: chain 'N' and resid 102 through 104 removed outlier: 3.539A pdb=" N ALA N 84 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'N' and resid 89 through 91 Processing sheet with id= AG, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= AH, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.515A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= AJ, first strand: chain 'E' and resid 91 through 94 Processing sheet with id= AK, first strand: chain 'E' and resid 130 through 133 Processing sheet with id= AL, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.688A pdb=" N ALA E 433 " --> pdb=" O THR E 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'E' and resid 271 through 274 Processing sheet with id= AN, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.334A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'E' and resid 301 through 308 removed outlier: 3.796A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 6.021A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'O' and resid 3 through 6 Processing sheet with id= AQ, first strand: chain 'O' and resid 107 through 109 removed outlier: 5.909A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'O' and resid 93 through 95 Processing sheet with id= AS, first strand: chain 'P' and resid 19 through 24 Processing sheet with id= AT, first strand: chain 'P' and resid 102 through 104 removed outlier: 6.083A pdb=" N GLN P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LEU P 46 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'P' and resid 89 through 91 Processing sheet with id= AV, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= AW, first strand: chain 'H' and resid 107 through 109 removed outlier: 6.100A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'H' and resid 93 through 100 Processing sheet with id= AY, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= AZ, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.680A pdb=" N LYS L 103 " --> pdb=" O LEU L 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= AZ Processing sheet with id= BA, first strand: chain 'L' and resid 96 through 98 removed outlier: 3.806A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) 716 hydrogen bonds defined for protein. 1833 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: 8.45 Time building geometry restraints manager: 9.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4674 1.32 - 1.46: 7079 1.46 - 1.59: 10059 1.59 - 1.73: 46 1.73 - 1.87: 175 Bond restraints: 22033 Sorted by residual: bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.00e+01 bond pdb=" CB ASP N 27B" pdb=" CG ASP N 27B" ideal model delta sigma weight residual 1.516 1.361 0.155 2.50e-02 1.60e+03 3.84e+01 bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.393 -0.067 1.10e-02 8.26e+03 3.75e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.392 -0.066 1.10e-02 8.26e+03 3.61e+01 bond pdb=" CB LEU N 107 " pdb=" CG LEU N 107 " ideal model delta sigma weight residual 1.530 1.649 -0.119 2.00e-02 2.50e+03 3.56e+01 ... (remaining 22028 not shown) Histogram of bond angle deviations from ideal: 98.51 - 111.32: 9567 111.32 - 124.14: 19228 124.14 - 136.95: 1122 136.95 - 149.77: 0 149.77 - 162.58: 3 Bond angle restraints: 29920 Sorted by residual: angle pdb=" C2 NAG d 1 " pdb=" N2 NAG d 1 " pdb=" C7 NAG d 1 " ideal model delta sigma weight residual 124.56 162.58 -38.02 3.00e+00 1.11e-01 1.61e+02 angle pdb=" C2 NAG I 1 " pdb=" N2 NAG I 1 " pdb=" C7 NAG I 1 " ideal model delta sigma weight residual 124.56 161.38 -36.82 3.00e+00 1.11e-01 1.51e+02 angle pdb=" C2 NAG X 1 " pdb=" N2 NAG X 1 " pdb=" C7 NAG X 1 " ideal model delta sigma weight residual 124.56 160.89 -36.33 3.00e+00 1.11e-01 1.47e+02 angle pdb=" N HIS C 85 " pdb=" CA HIS C 85 " pdb=" C HIS C 85 " ideal model delta sigma weight residual 111.82 120.98 -9.16 1.16e+00 7.43e-01 6.23e+01 angle pdb=" N GLU C 83 " pdb=" CA GLU C 83 " pdb=" C GLU C 83 " ideal model delta sigma weight residual 109.96 121.71 -11.75 1.50e+00 4.44e-01 6.14e+01 ... (remaining 29915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 13871 21.78 - 43.56: 327 43.56 - 65.34: 102 65.34 - 87.12: 59 87.12 - 108.90: 24 Dihedral angle restraints: 14383 sinusoidal: 6957 harmonic: 7426 Sorted by residual: dihedral pdb=" CA ASN C 197 " pdb=" C ASN C 197 " pdb=" N THR C 198 " pdb=" CA THR C 198 " ideal model delta harmonic sigma weight residual 180.00 147.63 32.37 0 5.00e+00 4.00e-02 4.19e+01 dihedral pdb=" CA VAL C 68 " pdb=" C VAL C 68 " pdb=" N TRP C 69 " pdb=" CA TRP C 69 " ideal model delta harmonic sigma weight residual -180.00 -151.99 -28.01 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA THR A 198 " pdb=" C THR A 198 " pdb=" N SER A 199 " pdb=" CA SER A 199 " ideal model delta harmonic sigma weight residual -180.00 -153.18 -26.82 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 14380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.218: 3289 0.218 - 0.435: 316 0.435 - 0.653: 24 0.653 - 0.871: 0 0.871 - 1.088: 1 Chirality restraints: 3630 Sorted by residual: chirality pdb=" C1 FUC i 2 " pdb=" O6 NAG i 1 " pdb=" C2 FUC i 2 " pdb=" O5 FUC i 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.31 -1.09 2.00e-02 2.50e+03 2.96e+03 chirality pdb=" C1 NAG S 2 " pdb=" O6 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-02 2.50e+03 6.46e+02 chirality pdb=" C1 MAN S 6 " pdb=" O6 MAN S 4 " pdb=" C2 MAN S 6 " pdb=" O5 MAN S 6 " both_signs ideal model delta sigma weight residual False 2.40 1.93 0.47 2.00e-02 2.50e+03 5.41e+02 ... (remaining 3627 not shown) Planarity restraints: 3736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " 0.348 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG S 2 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " 0.184 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " -0.513 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 2 " 0.318 2.00e-02 2.50e+03 2.78e-01 9.64e+02 pdb=" C7 NAG j 2 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG j 2 " 0.103 2.00e-02 2.50e+03 pdb=" N2 NAG j 2 " -0.498 2.00e-02 2.50e+03 pdb=" O7 NAG j 2 " 0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 701 " -0.324 2.00e-02 2.50e+03 2.75e-01 9.47e+02 pdb=" C7 NAG F 701 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG F 701 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG F 701 " 0.480 2.00e-02 2.50e+03 pdb=" O7 NAG F 701 " -0.055 2.00e-02 2.50e+03 ... (remaining 3733 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5447 2.81 - 3.33: 18984 3.33 - 3.86: 36098 3.86 - 4.38: 43722 4.38 - 4.90: 70105 Nonbonded interactions: 174356 Sorted by model distance: nonbonded pdb=" O5 NAG j 1 " pdb=" O6 NAG j 1 " model vdw 2.289 2.432 nonbonded pdb=" N ASP J 84 " pdb=" OD1 ASP J 84 " model vdw 2.370 2.520 nonbonded pdb=" N ASP O 84 " pdb=" OD1 ASP O 84 " model vdw 2.370 2.520 nonbonded pdb=" N ASP M 84 " pdb=" OD1 ASP M 84 " model vdw 2.370 2.520 nonbonded pdb=" OD1 ASP A 107 " pdb=" NZ LYS B 574 " model vdw 2.411 2.520 ... (remaining 174351 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 57 or resid 72 through 503 or resid 601 through \ 611)) selection = (chain 'C' and (resid 33 through 57 or resid 72 through 503 or resid 601 through \ 611)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'i' and resid 1) } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'K' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'Y' selection = chain 'e' } ncs_group { reference = (chain 'R' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.830 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 59.150 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.021 0.155 22033 Z= 1.347 Angle : 1.775 38.021 29920 Z= 1.147 Chirality : 0.133 1.088 3630 Planarity : 0.015 0.294 3673 Dihedral : 12.572 108.899 9505 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.67 % Allowed : 3.71 % Favored : 95.62 % Rotamer: Outliers : 0.98 % Allowed : 0.76 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.16), residues: 2535 helix: -0.34 (0.24), residues: 385 sheet: 0.93 (0.18), residues: 817 loop : 0.13 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.008 TRP A 96 HIS 0.009 0.002 HIS J 82A PHE 0.044 0.006 PHE L 98 TYR 0.070 0.007 TYR L 87 ARG 0.012 0.001 ARG J 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 395 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.8555 (m-80) cc_final: 0.8237 (m-10) REVERT: A 475 MET cc_start: 0.8713 (mmm) cc_final: 0.8353 (mmm) REVERT: A 482 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7969 (mm-30) REVERT: J 2 VAL cc_start: 0.9262 (t) cc_final: 0.8702 (t) REVERT: K 11 VAL cc_start: 0.8529 (t) cc_final: 0.8194 (p) REVERT: K 47 MET cc_start: 0.8336 (mmm) cc_final: 0.8056 (mmt) REVERT: K 94 ARG cc_start: 0.6115 (mpt180) cc_final: 0.5237 (mmt180) REVERT: K 104 LEU cc_start: 0.8447 (tp) cc_final: 0.7759 (tt) REVERT: C 72 HIS cc_start: 0.6914 (OUTLIER) cc_final: 0.6650 (p90) REVERT: C 107 ASP cc_start: 0.8076 (m-30) cc_final: 0.7734 (t0) REVERT: C 153 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8298 (tt0) REVERT: C 449 ILE cc_start: 0.9419 (mt) cc_final: 0.9217 (mm) REVERT: D 616 ASN cc_start: 0.9247 (p0) cc_final: 0.8814 (p0) REVERT: D 624 ASP cc_start: 0.8310 (p0) cc_final: 0.7721 (p0) REVERT: D 626 MET cc_start: 0.8826 (ttm) cc_final: 0.8613 (ttm) REVERT: M 78 LEU cc_start: 0.9138 (tp) cc_final: 0.8922 (tp) REVERT: N 47 MET cc_start: 0.8484 (mmm) cc_final: 0.8238 (mmp) REVERT: N 58 VAL cc_start: 0.8613 (m) cc_final: 0.8390 (p) REVERT: N 94 ARG cc_start: 0.6713 (mpt180) cc_final: 0.6141 (tpt170) REVERT: N 102 THR cc_start: 0.8431 (m) cc_final: 0.8120 (p) REVERT: E 104 MET cc_start: 0.8272 (ttm) cc_final: 0.8010 (ttt) REVERT: F 571 TRP cc_start: 0.5920 (t-100) cc_final: 0.5585 (p-90) REVERT: F 581 LEU cc_start: 0.8928 (pp) cc_final: 0.8712 (tp) REVERT: O 52 ASN cc_start: 0.8951 (t0) cc_final: 0.8700 (t0) REVERT: P 42 LYS cc_start: 0.8307 (mmtt) cc_final: 0.8034 (ttpt) REVERT: P 94 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7679 (tpt170) REVERT: H 27 PHE cc_start: 0.5955 (t80) cc_final: 0.5594 (t80) REVERT: H 80 LEU cc_start: 0.7504 (tp) cc_final: 0.7066 (tp) REVERT: H 98 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.8063 (p) REVERT: L 42 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8155 (mp10) REVERT: L 71 PHE cc_start: 0.4742 (m-80) cc_final: 0.3278 (m-80) REVERT: L 75 ILE cc_start: 0.7447 (mt) cc_final: 0.6937 (mt) REVERT: L 77 ARG cc_start: 0.7874 (mmt-90) cc_final: 0.7515 (tmm-80) REVERT: L 89 GLN cc_start: 0.8572 (tt0) cc_final: 0.8090 (tm-30) outliers start: 22 outliers final: 2 residues processed: 412 average time/residue: 0.4399 time to fit residues: 266.6141 Evaluate side-chains 195 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 190 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 0.2980 chunk 191 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 229 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 302 ASN A 425 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 258 GLN C 425 ASN D 653 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN E 195 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22033 Z= 0.208 Angle : 0.719 16.645 29920 Z= 0.365 Chirality : 0.048 0.322 3630 Planarity : 0.004 0.068 3673 Dihedral : 9.038 74.118 4866 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.59 % Favored : 96.17 % Rotamer: Outliers : 1.61 % Allowed : 5.80 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.16), residues: 2535 helix: 0.85 (0.26), residues: 390 sheet: 0.79 (0.18), residues: 787 loop : -0.15 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 479 HIS 0.005 0.001 HIS A 105 PHE 0.022 0.002 PHE H 29 TYR 0.017 0.001 TYR L 36 ARG 0.006 0.001 ARG D 588 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 230 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.8376 (m-80) cc_final: 0.7817 (m-80) REVERT: K 27 ASP cc_start: 0.8829 (t70) cc_final: 0.8595 (t70) REVERT: K 94 ARG cc_start: 0.6074 (mpt180) cc_final: 0.5205 (mmt180) REVERT: C 258 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8201 (mt0) REVERT: D 616 ASN cc_start: 0.9104 (p0) cc_final: 0.8707 (p0) REVERT: M 86 ASP cc_start: 0.8413 (m-30) cc_final: 0.8164 (m-30) REVERT: N 94 ARG cc_start: 0.6596 (mpt180) cc_final: 0.6106 (tpt170) REVERT: N 95 THR cc_start: 0.8777 (p) cc_final: 0.8571 (p) REVERT: E 104 MET cc_start: 0.8188 (ttm) cc_final: 0.7972 (ttt) REVERT: F 586 TYR cc_start: 0.9432 (t80) cc_final: 0.9190 (t80) REVERT: O 84 ASP cc_start: 0.7823 (t0) cc_final: 0.7612 (m-30) REVERT: P 94 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7679 (tpt170) REVERT: H 27 PHE cc_start: 0.5659 (t80) cc_final: 0.5261 (t80) REVERT: H 38 ARG cc_start: 0.7880 (ptt180) cc_final: 0.7589 (ptp-170) REVERT: H 80 LEU cc_start: 0.7282 (tp) cc_final: 0.7015 (tp) REVERT: L 89 GLN cc_start: 0.8344 (tt0) cc_final: 0.8091 (tm-30) REVERT: L 104 VAL cc_start: 0.8361 (t) cc_final: 0.8115 (p) outliers start: 36 outliers final: 21 residues processed: 258 average time/residue: 0.3472 time to fit residues: 138.2591 Evaluate side-chains 198 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 175 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain K residue 69 ASN Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 79 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 127 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 191 optimal weight: 0.6980 chunk 156 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 230 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 chunk 204 optimal weight: 3.9990 chunk 228 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 184 optimal weight: 10.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 195 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22033 Z= 0.236 Angle : 0.657 17.094 29920 Z= 0.327 Chirality : 0.045 0.296 3630 Planarity : 0.004 0.044 3673 Dihedral : 7.487 65.203 4861 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.83 % Favored : 96.06 % Rotamer: Outliers : 1.78 % Allowed : 7.18 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.16), residues: 2535 helix: 1.02 (0.27), residues: 378 sheet: 0.61 (0.18), residues: 762 loop : -0.31 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 479 HIS 0.006 0.001 HIS E 105 PHE 0.018 0.002 PHE A 382 TYR 0.020 0.001 TYR L 49 ARG 0.009 0.000 ARG F 588 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 197 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.7103 (t-90) REVERT: A 475 MET cc_start: 0.8703 (mmm) cc_final: 0.8469 (tpp) REVERT: B 648 GLU cc_start: 0.8469 (tp30) cc_final: 0.8006 (tm-30) REVERT: K 27 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8590 (t70) REVERT: K 94 ARG cc_start: 0.6398 (mpt180) cc_final: 0.5228 (mmt180) REVERT: C 434 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8177 (tpp) REVERT: D 616 ASN cc_start: 0.9169 (p0) cc_final: 0.8791 (p0) REVERT: D 626 MET cc_start: 0.8939 (ttm) cc_final: 0.8623 (mtp) REVERT: N 94 ARG cc_start: 0.6833 (mpt180) cc_final: 0.6128 (tpt170) REVERT: E 104 MET cc_start: 0.8335 (ttm) cc_final: 0.8131 (ttt) REVERT: F 586 TYR cc_start: 0.9433 (t80) cc_final: 0.9002 (t80) REVERT: P 94 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7763 (tpt170) REVERT: H 27 PHE cc_start: 0.5343 (t80) cc_final: 0.4846 (t80) REVERT: H 100 TYR cc_start: 0.8453 (m-80) cc_final: 0.7979 (m-10) REVERT: L 89 GLN cc_start: 0.8294 (tt0) cc_final: 0.7940 (tt0) outliers start: 40 outliers final: 23 residues processed: 224 average time/residue: 0.3687 time to fit residues: 124.8529 Evaluate side-chains 195 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 168 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 82 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 227 optimal weight: 9.9990 chunk 173 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 154 optimal weight: 0.5980 chunk 230 optimal weight: 20.0000 chunk 244 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN E 99 ASN F 570 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22033 Z= 0.329 Angle : 0.668 16.631 29920 Z= 0.333 Chirality : 0.046 0.295 3630 Planarity : 0.004 0.047 3673 Dihedral : 6.757 57.920 4861 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.14 % Favored : 95.78 % Rotamer: Outliers : 1.87 % Allowed : 7.45 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.16), residues: 2535 helix: 1.13 (0.28), residues: 366 sheet: 0.47 (0.18), residues: 768 loop : -0.51 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 479 HIS 0.007 0.001 HIS E 105 PHE 0.016 0.002 PHE A 382 TYR 0.018 0.001 TYR L 49 ARG 0.011 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 173 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7457 (OUTLIER) cc_final: 0.7238 (t-90) REVERT: K 27 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8522 (t0) REVERT: K 94 ARG cc_start: 0.6551 (mpt180) cc_final: 0.5749 (tpt170) REVERT: D 616 ASN cc_start: 0.9170 (p0) cc_final: 0.8795 (p0) REVERT: D 626 MET cc_start: 0.9015 (ttm) cc_final: 0.8756 (mtp) REVERT: N 94 ARG cc_start: 0.6888 (mpt180) cc_final: 0.6033 (tpt170) REVERT: E 95 MET cc_start: 0.8543 (ptm) cc_final: 0.8318 (ptp) REVERT: F 586 TYR cc_start: 0.9446 (t80) cc_final: 0.9072 (t80) REVERT: O 75 LYS cc_start: 0.9130 (mttm) cc_final: 0.8831 (mttp) REVERT: P 94 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.7876 (tpt170) REVERT: H 27 PHE cc_start: 0.5146 (t80) cc_final: 0.4693 (t80) REVERT: H 38 ARG cc_start: 0.8004 (ptt180) cc_final: 0.7753 (ptp-170) outliers start: 42 outliers final: 30 residues processed: 197 average time/residue: 0.3620 time to fit residues: 109.8546 Evaluate side-chains 192 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 159 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 82 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 203 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 219 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN P 39 HIS L 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22033 Z= 0.242 Angle : 0.604 15.714 29920 Z= 0.301 Chirality : 0.044 0.284 3630 Planarity : 0.004 0.045 3673 Dihedral : 6.229 58.036 4861 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.26 % Favored : 95.70 % Rotamer: Outliers : 1.87 % Allowed : 8.79 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.17), residues: 2535 helix: 1.30 (0.28), residues: 360 sheet: 0.45 (0.19), residues: 754 loop : -0.61 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 479 HIS 0.005 0.001 HIS E 105 PHE 0.014 0.002 PHE L 98 TYR 0.017 0.001 TYR H 100L ARG 0.009 0.000 ARG F 588 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 176 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7423 (OUTLIER) cc_final: 0.7217 (t-90) REVERT: B 586 TYR cc_start: 0.9095 (t80) cc_final: 0.8749 (t80) REVERT: K 27 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8480 (t0) REVERT: K 94 ARG cc_start: 0.6576 (mpt180) cc_final: 0.5720 (tpt170) REVERT: C 434 MET cc_start: 0.8597 (tpp) cc_final: 0.8288 (tpp) REVERT: D 616 ASN cc_start: 0.9097 (p0) cc_final: 0.8710 (p0) REVERT: N 94 ARG cc_start: 0.6911 (mpt180) cc_final: 0.5962 (tpt170) REVERT: F 586 TYR cc_start: 0.9373 (t80) cc_final: 0.9007 (t80) REVERT: O 75 LYS cc_start: 0.9165 (mttm) cc_final: 0.8867 (mttp) REVERT: P 94 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.7966 (tpt170) REVERT: H 3 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7370 (tm-30) REVERT: H 27 PHE cc_start: 0.5128 (t80) cc_final: 0.4617 (t80) REVERT: H 38 ARG cc_start: 0.8035 (ptt180) cc_final: 0.7788 (ptp-170) outliers start: 42 outliers final: 33 residues processed: 206 average time/residue: 0.3737 time to fit residues: 118.0355 Evaluate side-chains 191 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 155 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain J residue 101 ASP Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 82 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 chunk 48 optimal weight: 0.5980 chunk 143 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 22033 Z= 0.293 Angle : 0.621 14.580 29920 Z= 0.310 Chirality : 0.045 0.314 3630 Planarity : 0.004 0.046 3673 Dihedral : 6.190 59.007 4861 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.89 % Favored : 95.07 % Rotamer: Outliers : 2.32 % Allowed : 8.92 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2535 helix: 1.20 (0.28), residues: 363 sheet: 0.39 (0.19), residues: 744 loop : -0.73 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 479 HIS 0.006 0.001 HIS E 105 PHE 0.021 0.002 PHE H 29 TYR 0.014 0.001 TYR A 484 ARG 0.010 0.001 ARG D 588 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 164 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9550 (t) cc_final: 0.9240 (m) REVERT: A 72 HIS cc_start: 0.7460 (OUTLIER) cc_final: 0.7248 (t-90) REVERT: A 452 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8207 (mt) REVERT: B 586 TYR cc_start: 0.9139 (t80) cc_final: 0.8799 (t80) REVERT: K 27 ASP cc_start: 0.8747 (OUTLIER) cc_final: 0.8528 (t0) REVERT: K 94 ARG cc_start: 0.6734 (mpt180) cc_final: 0.5378 (mmt180) REVERT: D 616 ASN cc_start: 0.9105 (p0) cc_final: 0.8657 (p0) REVERT: N 94 ARG cc_start: 0.7007 (mpt180) cc_final: 0.5433 (mmt180) REVERT: F 586 TYR cc_start: 0.9398 (t80) cc_final: 0.9042 (t80) REVERT: O 75 LYS cc_start: 0.9181 (mttm) cc_final: 0.8895 (mttp) REVERT: P 94 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8035 (tpt170) REVERT: H 3 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7539 (tm-30) REVERT: H 27 PHE cc_start: 0.5207 (t80) cc_final: 0.4872 (t80) outliers start: 52 outliers final: 36 residues processed: 203 average time/residue: 0.3420 time to fit residues: 107.9033 Evaluate side-chains 191 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 151 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 101 ASP Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 82 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 236 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 139 optimal weight: 0.3980 chunk 178 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 206 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 243 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN E 82 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 22033 Z= 0.212 Angle : 0.587 13.680 29920 Z= 0.292 Chirality : 0.044 0.322 3630 Planarity : 0.004 0.047 3673 Dihedral : 5.968 58.949 4861 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.46 % Favored : 95.46 % Rotamer: Outliers : 1.74 % Allowed : 9.68 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2535 helix: 1.34 (0.29), residues: 360 sheet: 0.42 (0.19), residues: 744 loop : -0.78 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 479 HIS 0.005 0.001 HIS E 105 PHE 0.019 0.001 PHE H 29 TYR 0.014 0.001 TYR C 217 ARG 0.009 0.000 ARG F 588 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 166 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.7246 (t-90) REVERT: B 586 TYR cc_start: 0.9115 (t80) cc_final: 0.8764 (t80) REVERT: B 648 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8013 (tm-30) REVERT: K 94 ARG cc_start: 0.6575 (mpt180) cc_final: 0.5189 (mmt180) REVERT: D 616 ASN cc_start: 0.9107 (p0) cc_final: 0.8708 (p0) REVERT: N 94 ARG cc_start: 0.6962 (mpt180) cc_final: 0.5859 (tpt170) REVERT: E 138 ILE cc_start: 0.8499 (mp) cc_final: 0.8166 (tt) REVERT: F 586 TYR cc_start: 0.9361 (t80) cc_final: 0.9022 (t80) REVERT: O 75 LYS cc_start: 0.9167 (mttm) cc_final: 0.8880 (mttp) REVERT: P 47 MET cc_start: 0.8591 (mmt) cc_final: 0.8316 (tpp) REVERT: P 94 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8026 (tpt170) REVERT: H 3 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7665 (tm-30) REVERT: H 27 PHE cc_start: 0.5074 (t80) cc_final: 0.4781 (t80) REVERT: H 38 ARG cc_start: 0.8186 (ptt180) cc_final: 0.7857 (ptp-170) outliers start: 39 outliers final: 30 residues processed: 193 average time/residue: 0.3557 time to fit residues: 106.6253 Evaluate side-chains 190 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 158 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 101 ASP Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 150 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 221 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN M 3 GLN E 82 GLN P 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 22033 Z= 0.500 Angle : 0.751 12.450 29920 Z= 0.374 Chirality : 0.048 0.346 3630 Planarity : 0.005 0.052 3673 Dihedral : 6.704 58.414 4861 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.52 % Favored : 94.40 % Rotamer: Outliers : 2.28 % Allowed : 9.33 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.16), residues: 2535 helix: 0.89 (0.27), residues: 363 sheet: 0.14 (0.18), residues: 749 loop : -0.97 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 479 HIS 0.010 0.002 HIS E 85 PHE 0.023 0.002 PHE H 29 TYR 0.023 0.002 TYR A 484 ARG 0.008 0.001 ARG D 588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 156 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7464 (OUTLIER) cc_final: 0.7236 (t-90) REVERT: A 452 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8320 (mt) REVERT: B 586 TYR cc_start: 0.9260 (t80) cc_final: 0.8917 (t80) REVERT: J 83 ARG cc_start: 0.8165 (tpp80) cc_final: 0.7647 (tpp80) REVERT: K 94 ARG cc_start: 0.6706 (mpt180) cc_final: 0.5416 (tpt170) REVERT: C 71 THR cc_start: 0.6756 (OUTLIER) cc_final: 0.6531 (p) REVERT: D 616 ASN cc_start: 0.9134 (p0) cc_final: 0.8727 (p0) REVERT: N 94 ARG cc_start: 0.7073 (mpt180) cc_final: 0.5748 (tpt170) REVERT: E 138 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8269 (tt) REVERT: F 586 TYR cc_start: 0.9484 (t80) cc_final: 0.9168 (t80) REVERT: O 75 LYS cc_start: 0.9203 (mttm) cc_final: 0.8957 (mttp) REVERT: H 27 PHE cc_start: 0.5157 (t80) cc_final: 0.4908 (t80) REVERT: H 38 ARG cc_start: 0.8108 (ptt180) cc_final: 0.7793 (ptp-170) outliers start: 51 outliers final: 40 residues processed: 191 average time/residue: 0.3556 time to fit residues: 105.3815 Evaluate side-chains 192 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 148 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 101 ASP Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 233 optimal weight: 10.0000 chunk 213 optimal weight: 1.9990 chunk 227 optimal weight: 7.9990 chunk 136 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 226 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22033 Z= 0.183 Angle : 0.595 11.132 29920 Z= 0.296 Chirality : 0.044 0.317 3630 Planarity : 0.004 0.043 3673 Dihedral : 6.076 55.217 4857 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.30 % Favored : 95.62 % Rotamer: Outliers : 1.74 % Allowed : 9.91 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2535 helix: 1.18 (0.28), residues: 369 sheet: 0.28 (0.19), residues: 742 loop : -0.93 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 479 HIS 0.004 0.001 HIS E 105 PHE 0.017 0.001 PHE H 29 TYR 0.021 0.001 TYR L 49 ARG 0.008 0.000 ARG F 588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 164 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7537 (OUTLIER) cc_final: 0.7281 (t-90) REVERT: B 586 TYR cc_start: 0.9142 (t80) cc_final: 0.8803 (t80) REVERT: B 648 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7903 (tm-30) REVERT: J 83 ARG cc_start: 0.8186 (tpp80) cc_final: 0.7605 (tpp80) REVERT: K 94 ARG cc_start: 0.6508 (mpt180) cc_final: 0.5041 (mmt180) REVERT: C 71 THR cc_start: 0.6130 (OUTLIER) cc_final: 0.5894 (p) REVERT: C 72 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.7296 (p90) REVERT: D 616 ASN cc_start: 0.9087 (p0) cc_final: 0.8720 (p0) REVERT: N 94 ARG cc_start: 0.6924 (mpt180) cc_final: 0.5656 (tpt170) REVERT: E 138 ILE cc_start: 0.8492 (mp) cc_final: 0.8240 (tt) REVERT: F 586 TYR cc_start: 0.9366 (t80) cc_final: 0.9030 (t80) REVERT: O 75 LYS cc_start: 0.9173 (mttm) cc_final: 0.8886 (mttp) REVERT: P 47 MET cc_start: 0.8587 (mmt) cc_final: 0.8349 (tpp) REVERT: L 77 ARG cc_start: 0.6695 (tmm-80) cc_final: 0.6188 (ttp80) outliers start: 39 outliers final: 31 residues processed: 193 average time/residue: 0.3579 time to fit residues: 106.9816 Evaluate side-chains 186 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 152 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 101 ASP Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 240 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 113 optimal weight: 0.0170 chunk 167 optimal weight: 7.9990 chunk 252 optimal weight: 3.9990 chunk 231 optimal weight: 0.0370 chunk 200 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 overall best weight: 2.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22033 Z= 0.245 Angle : 0.603 11.034 29920 Z= 0.299 Chirality : 0.044 0.316 3630 Planarity : 0.004 0.042 3673 Dihedral : 6.022 54.569 4857 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.69 % Favored : 95.23 % Rotamer: Outliers : 1.65 % Allowed : 9.91 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.17), residues: 2535 helix: 1.17 (0.28), residues: 369 sheet: 0.28 (0.19), residues: 745 loop : -0.95 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 479 HIS 0.005 0.001 HIS E 105 PHE 0.032 0.001 PHE H 29 TYR 0.023 0.001 TYR L 49 ARG 0.008 0.000 ARG F 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 157 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7544 (OUTLIER) cc_final: 0.7309 (t-90) REVERT: B 586 TYR cc_start: 0.9157 (t80) cc_final: 0.8822 (t80) REVERT: B 648 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8079 (tm-30) REVERT: J 83 ARG cc_start: 0.8170 (tpp80) cc_final: 0.7586 (tpp80) REVERT: K 94 ARG cc_start: 0.6588 (mpt180) cc_final: 0.5082 (mmt180) REVERT: C 71 THR cc_start: 0.6330 (OUTLIER) cc_final: 0.6095 (p) REVERT: C 72 HIS cc_start: 0.7845 (OUTLIER) cc_final: 0.7376 (p90) REVERT: D 616 ASN cc_start: 0.9103 (p0) cc_final: 0.8733 (p0) REVERT: N 94 ARG cc_start: 0.6961 (mpt180) cc_final: 0.5661 (tpt170) REVERT: E 138 ILE cc_start: 0.8507 (mp) cc_final: 0.8259 (tt) REVERT: F 586 TYR cc_start: 0.9373 (t80) cc_final: 0.9051 (t80) REVERT: P 47 MET cc_start: 0.8563 (mmt) cc_final: 0.8325 (tpp) REVERT: L 77 ARG cc_start: 0.6935 (tmm-80) cc_final: 0.6344 (ttp80) outliers start: 37 outliers final: 33 residues processed: 183 average time/residue: 0.3762 time to fit residues: 107.0272 Evaluate side-chains 190 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 154 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 101 ASP Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 185 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 201 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 206 optimal weight: 0.6980 chunk 25 optimal weight: 0.0470 chunk 37 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN C 246 GLN E 82 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.075111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.056457 restraints weight = 63569.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.058246 restraints weight = 36943.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.059445 restraints weight = 26204.235| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 22033 Z= 0.141 Angle : 0.570 12.367 29920 Z= 0.282 Chirality : 0.043 0.295 3630 Planarity : 0.004 0.040 3673 Dihedral : 5.637 52.422 4857 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.30 % Favored : 95.62 % Rotamer: Outliers : 1.34 % Allowed : 10.53 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.17), residues: 2535 helix: 1.53 (0.29), residues: 348 sheet: 0.41 (0.19), residues: 750 loop : -0.90 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 479 HIS 0.003 0.001 HIS E 85 PHE 0.031 0.001 PHE H 29 TYR 0.023 0.001 TYR L 49 ARG 0.010 0.000 ARG F 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3769.90 seconds wall clock time: 70 minutes 59.63 seconds (4259.63 seconds total)