Starting phenix.real_space_refine on Mon Mar 18 08:14:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3p_29707/03_2024/8g3p_29707.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3p_29707/03_2024/8g3p_29707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3p_29707/03_2024/8g3p_29707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3p_29707/03_2024/8g3p_29707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3p_29707/03_2024/8g3p_29707.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3p_29707/03_2024/8g3p_29707.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 116 5.16 5 C 12560 2.51 5 N 3448 2.21 5 O 4192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 38": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 87": "NH1" <-> "NH2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "I ARG 18": "NH1" <-> "NH2" Residue "I ARG 24": "NH1" <-> "NH2" Residue "I ARG 27": "NH1" <-> "NH2" Residue "I ARG 45": "NH1" <-> "NH2" Residue "I ARG 54": "NH1" <-> "NH2" Residue "I ARG 61": "NH1" <-> "NH2" Residue "I ARG 109": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B ARG 288": "NH1" <-> "NH2" Residue "B ARG 292": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 364": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ARG 394": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B ARG 430": "NH1" <-> "NH2" Residue "F ARG 38": "NH1" <-> "NH2" Residue "F ARG 63": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 87": "NH1" <-> "NH2" Residue "F ARG 98": "NH1" <-> "NH2" Residue "F ARG 106": "NH1" <-> "NH2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "J ARG 24": "NH1" <-> "NH2" Residue "J ARG 27": "NH1" <-> "NH2" Residue "J ARG 45": "NH1" <-> "NH2" Residue "J ARG 54": "NH1" <-> "NH2" Residue "J ARG 61": "NH1" <-> "NH2" Residue "J ARG 109": "NH1" <-> "NH2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "A PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 224": "NH1" <-> "NH2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "A ARG 292": "NH1" <-> "NH2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 430": "NH1" <-> "NH2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G ARG 63": "NH1" <-> "NH2" Residue "G ARG 67": "NH1" <-> "NH2" Residue "G ARG 87": "NH1" <-> "NH2" Residue "G ARG 98": "NH1" <-> "NH2" Residue "G ARG 106": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K ARG 24": "NH1" <-> "NH2" Residue "K ARG 27": "NH1" <-> "NH2" Residue "K ARG 45": "NH1" <-> "NH2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 61": "NH1" <-> "NH2" Residue "K ARG 109": "NH1" <-> "NH2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 150": "NH1" <-> "NH2" Residue "D ARG 152": "NH1" <-> "NH2" Residue "D ARG 156": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D ARG 224": "NH1" <-> "NH2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 283": "NH1" <-> "NH2" Residue "D ARG 288": "NH1" <-> "NH2" Residue "D ARG 292": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D ARG 364": "NH1" <-> "NH2" Residue "D ARG 371": "NH1" <-> "NH2" Residue "D ARG 394": "NH1" <-> "NH2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D ARG 428": "NH1" <-> "NH2" Residue "D ARG 430": "NH1" <-> "NH2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H ARG 63": "NH1" <-> "NH2" Residue "H ARG 67": "NH1" <-> "NH2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ARG 27": "NH1" <-> "NH2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L ARG 109": "NH1" <-> "NH2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "E ARG 118": "NH1" <-> "NH2" Residue "E PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E ARG 224": "NH1" <-> "NH2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 283": "NH1" <-> "NH2" Residue "E ARG 288": "NH1" <-> "NH2" Residue "E ARG 292": "NH1" <-> "NH2" Residue "E ARG 300": "NH1" <-> "NH2" Residue "E ARG 327": "NH1" <-> "NH2" Residue "E ARG 364": "NH1" <-> "NH2" Residue "E ARG 371": "NH1" <-> "NH2" Residue "E ARG 394": "NH1" <-> "NH2" Residue "E ARG 400": "NH1" <-> "NH2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E ARG 420": "NH1" <-> "NH2" Residue "E ARG 428": "NH1" <-> "NH2" Residue "E ARG 430": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20321 Number of models: 1 Model: "" Number of chains: 40 Chain: "C" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "I" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "B" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "F" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "J" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "A" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "G" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "K" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "D" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "H" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "L" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "E" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "s" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "S" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "Y" 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: "T" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "Z" 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: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "a" 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: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.68, per 1000 atoms: 0.53 Number of scatterers: 20321 At special positions: 0 Unit cell: (166.83, 166.83, 104.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 116 16.00 O 4192 8.00 N 3448 7.00 C 12560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.05 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.08 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.06 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=1.99 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.07 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.07 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.09 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.07 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.09 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.14 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.05 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.08 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.06 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=1.99 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.07 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.07 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.09 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.07 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.09 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.14 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.05 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.08 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.06 Simple disulfide: pdb=" SG CYS D 175 " - pdb=" SG CYS D 193 " distance=1.99 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.07 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.07 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.09 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.07 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.09 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.14 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 417 " distance=2.08 Simple disulfide: pdb=" SG CYS E 124 " - pdb=" SG CYS E 129 " distance=2.06 Simple disulfide: pdb=" SG CYS E 175 " - pdb=" SG CYS E 193 " distance=1.99 Simple disulfide: pdb=" SG CYS E 183 " - pdb=" SG CYS E 230 " distance=2.07 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 237 " distance=2.07 Simple disulfide: pdb=" SG CYS E 278 " - pdb=" SG CYS E 291 " distance=2.09 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 289 " distance=2.07 Simple disulfide: pdb=" SG CYS E 318 " - pdb=" SG CYS E 337 " distance=2.09 Simple disulfide: pdb=" SG CYS E 421 " - pdb=" SG CYS E 447 " distance=2.14 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN T 4 " - " MAN T 5 " " MAN U 4 " - " MAN U 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " MAN S 6 " - " MAN S 7 " " BMA T 3 " - " MAN T 4 " " MAN T 6 " - " MAN T 7 " " BMA U 3 " - " MAN U 4 " " MAN U 6 " - " MAN U 7 " " BMA s 3 " - " MAN s 4 " " MAN s 6 " - " MAN s 7 " ALPHA1-6 " BMA S 3 " - " MAN S 6 " " MAN S 6 " - " MAN S 8 " " BMA T 3 " - " MAN T 6 " " MAN T 6 " - " MAN T 8 " " BMA U 3 " - " MAN U 6 " " MAN U 6 " - " MAN U 8 " " BMA s 3 " - " MAN s 6 " " MAN s 6 " - " MAN s 8 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG w 1 " - " NAG w 2 " BETA1-6 " NAG Y 1 " - " FUC Y 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Z 1 " - " FUC Z 3 " " NAG a 1 " - " FUC a 3 " " NAG u 1 " - " FUC u 3 " NAG-ASN " NAG M 1 " - " ASN A 86 " " NAG N 1 " - " ASN D 86 " " NAG O 1 " - " ASN E 86 " " NAG P 1 " - " ASN A 146 " " NAG Q 1 " - " ASN D 146 " " NAG R 1 " - " ASN E 146 " " NAG S 1 " - " ASN A 200 " " NAG T 1 " - " ASN D 200 " " NAG U 1 " - " ASN E 200 " " NAG V 1 " - " ASN A 234 " " NAG W 1 " - " ASN D 234 " " NAG X 1 " - " ASN E 234 " " NAG Y 1 " - " ASN A 245 " " NAG Z 1 " - " ASN D 245 " " NAG a 1 " - " ASN E 245 " " NAG b 1 " - " ASN A 367 " " NAG c 1 " - " ASN D 367 " " NAG d 1 " - " ASN E 367 " " NAG q 1 " - " ASN B 86 " " NAG r 1 " - " ASN B 146 " " NAG s 1 " - " ASN B 200 " " NAG t 1 " - " ASN B 234 " " NAG u 1 " - " ASN B 245 " " NAG w 1 " - " ASN B 367 " Time building additional restraints: 9.60 Conformation dependent library (CDL) restraints added in 3.5 seconds 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 48 sheets defined 5.1% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.747A pdb=" N SER I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.738A pdb=" N ASN B 146 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.746A pdb=" N SER J 83 " --> pdb=" O SER J 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.741A pdb=" N ASN A 146 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.746A pdb=" N SER K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.739A pdb=" N ASN D 146 " --> pdb=" O VAL D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 252 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.746A pdb=" N SER L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 110 Processing helix chain 'E' and resid 142 through 146 removed outlier: 3.737A pdb=" N ASN E 146 " --> pdb=" O VAL E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 252 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.488A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.488A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER C 117 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.624A pdb=" N GLU I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.562A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 102 removed outlier: 3.807A pdb=" N GLY B 96 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 445 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.786A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR B 157 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 158 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS B 172 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 184 removed outlier: 4.048A pdb=" N ASP B 197 " --> pdb=" O ASN B 200 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 231 through 233 removed outlier: 6.454A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.401A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.571A pdb=" N TRP B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 363 " --> pdb=" O TRP B 352 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP B 402 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 9.694A pdb=" N GLU B 375 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N ARG B 400 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 11.435A pdb=" N PHE B 377 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 13.493A pdb=" N VAL B 398 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 15.693A pdb=" N VAL B 379 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 16.303A pdb=" N VAL B 396 " --> pdb=" O VAL B 379 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.488A pdb=" N GLU F 10 " --> pdb=" O THR F 125 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.488A pdb=" N GLU F 10 " --> pdb=" O THR F 125 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER F 117 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 104 through 105 Processing sheet with id=AB8, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.570A pdb=" N GLU J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.558A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.808A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.788A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 157 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU A 158 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS A 172 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 179 through 184 removed outlier: 4.048A pdb=" N ASP A 197 " --> pdb=" O ASN A 200 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 231 through 233 removed outlier: 6.453A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.403A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.571A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP A 402 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N GLU A 375 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N ARG A 400 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 11.436A pdb=" N PHE A 377 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 13.492A pdb=" N VAL A 398 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 15.692A pdb=" N VAL A 379 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 16.303A pdb=" N VAL A 396 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.489A pdb=" N GLU G 10 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.489A pdb=" N GLU G 10 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER G 117 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 104 through 105 Processing sheet with id=AD2, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.613A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.560A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 96 through 102 removed outlier: 3.808A pdb=" N GLY D 96 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL D 445 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS D 102 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ARG D 420 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.787A pdb=" N TRP D 115 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR D 138 " --> pdb=" O TRP D 115 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N THR D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN D 136 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR D 157 " --> pdb=" O GLY D 135 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU D 158 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS D 172 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 179 through 184 removed outlier: 4.048A pdb=" N ASP D 197 " --> pdb=" O ASN D 200 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR D 207 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 231 through 233 removed outlier: 6.453A pdb=" N GLU D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ILE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 276 through 283 removed outlier: 5.403A pdb=" N GLU D 277 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ARG D 292 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 352 through 356 removed outlier: 4.571A pdb=" N TRP D 352 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY D 363 " --> pdb=" O TRP D 352 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP D 402 " --> pdb=" O GLY D 373 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N GLU D 375 " --> pdb=" O ARG D 400 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N ARG D 400 " --> pdb=" O GLU D 375 " (cutoff:3.500A) removed outlier: 11.436A pdb=" N PHE D 377 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 13.492A pdb=" N VAL D 398 " --> pdb=" O PHE D 377 " (cutoff:3.500A) removed outlier: 15.692A pdb=" N VAL D 379 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 16.303A pdb=" N VAL D 396 " --> pdb=" O VAL D 379 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.480A pdb=" N GLU H 10 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.480A pdb=" N GLU H 10 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER H 117 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AE5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.621A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.562A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 96 through 102 removed outlier: 3.807A pdb=" N GLY E 96 " --> pdb=" O THR E 449 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL E 445 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS E 102 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE E 443 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ARG E 420 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 115 through 124 removed outlier: 4.787A pdb=" N TRP E 115 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR E 138 " --> pdb=" O TRP E 115 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N THR E 117 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN E 136 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU E 119 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU E 134 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR E 157 " --> pdb=" O GLY E 135 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU E 158 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS E 172 " --> pdb=" O MET E 160 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 179 through 184 removed outlier: 4.047A pdb=" N ASP E 197 " --> pdb=" O ASN E 200 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR E 207 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU E 211 " --> pdb=" O TYR E 207 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 231 through 233 removed outlier: 6.454A pdb=" N GLU E 258 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 276 through 283 removed outlier: 5.401A pdb=" N GLU E 277 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ARG E 292 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 352 through 356 removed outlier: 4.571A pdb=" N TRP E 352 " --> pdb=" O GLY E 363 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY E 363 " --> pdb=" O TRP E 352 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP E 402 " --> pdb=" O GLY E 373 " (cutoff:3.500A) removed outlier: 9.694A pdb=" N GLU E 375 " --> pdb=" O ARG E 400 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N ARG E 400 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 11.435A pdb=" N PHE E 377 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 13.493A pdb=" N VAL E 398 " --> pdb=" O PHE E 377 " (cutoff:3.500A) removed outlier: 15.693A pdb=" N VAL E 379 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 16.303A pdb=" N VAL E 396 " --> pdb=" O VAL E 379 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1680 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: 6.94 Time building geometry restraints manager: 10.04 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: 3493 1.32 - 1.44: 5751 1.44 - 1.57: 11360 1.57 - 1.69: 4 1.69 - 1.82: 144 Bond restraints: 20752 Sorted by residual: bond pdb=" N ILE B 176 " pdb=" CA ILE B 176 " ideal model delta sigma weight residual 1.460 1.508 -0.048 1.10e-02 8.26e+03 1.93e+01 bond pdb=" N ILE E 176 " pdb=" CA ILE E 176 " ideal model delta sigma weight residual 1.460 1.507 -0.048 1.10e-02 8.26e+03 1.89e+01 bond pdb=" N ILE D 176 " pdb=" CA ILE D 176 " ideal model delta sigma weight residual 1.460 1.507 -0.047 1.10e-02 8.26e+03 1.86e+01 bond pdb=" N ILE A 176 " pdb=" CA ILE A 176 " ideal model delta sigma weight residual 1.460 1.507 -0.047 1.10e-02 8.26e+03 1.86e+01 bond pdb=" C GLU B 162 " pdb=" O GLU B 162 " ideal model delta sigma weight residual 1.234 1.283 -0.049 1.24e-02 6.50e+03 1.59e+01 ... (remaining 20747 not shown) Histogram of bond angle deviations from ideal: 98.31 - 105.70: 418 105.70 - 113.08: 10655 113.08 - 120.46: 9377 120.46 - 127.85: 7469 127.85 - 135.23: 249 Bond angle restraints: 28168 Sorted by residual: angle pdb=" N ILE B 397 " pdb=" CA ILE B 397 " pdb=" C ILE B 397 " ideal model delta sigma weight residual 111.67 106.29 5.38 9.50e-01 1.11e+00 3.21e+01 angle pdb=" N ILE E 397 " pdb=" CA ILE E 397 " pdb=" C ILE E 397 " ideal model delta sigma weight residual 111.67 106.29 5.38 9.50e-01 1.11e+00 3.21e+01 angle pdb=" N ILE D 397 " pdb=" CA ILE D 397 " pdb=" C ILE D 397 " ideal model delta sigma weight residual 111.67 106.32 5.35 9.50e-01 1.11e+00 3.17e+01 angle pdb=" N ILE A 397 " pdb=" CA ILE A 397 " pdb=" C ILE A 397 " ideal model delta sigma weight residual 111.67 106.35 5.32 9.50e-01 1.11e+00 3.14e+01 angle pdb=" CA ASP B 125 " pdb=" CB ASP B 125 " pdb=" CG ASP B 125 " ideal model delta sigma weight residual 112.60 118.00 -5.40 1.00e+00 1.00e+00 2.91e+01 ... (remaining 28163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.63: 12481 19.63 - 39.26: 539 39.26 - 58.90: 116 58.90 - 78.53: 52 78.53 - 98.16: 40 Dihedral angle restraints: 13228 sinusoidal: 6092 harmonic: 7136 Sorted by residual: dihedral pdb=" CA ASN E 441 " pdb=" C ASN E 441 " pdb=" N SER E 442 " pdb=" CA SER E 442 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ASN B 441 " pdb=" C ASN B 441 " pdb=" N SER B 442 " pdb=" CA SER B 442 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ASN D 441 " pdb=" C ASN D 441 " pdb=" N SER D 442 " pdb=" CA SER D 442 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 13225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2162 0.091 - 0.182: 1018 0.182 - 0.273: 92 0.273 - 0.364: 8 0.364 - 0.454: 12 Chirality restraints: 3292 Sorted by residual: chirality pdb=" C1 MAN T 4 " pdb=" O3 BMA T 3 " pdb=" C2 MAN T 4 " pdb=" O5 MAN T 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.79e+01 chirality pdb=" C1 MAN S 4 " pdb=" O3 BMA S 3 " pdb=" C2 MAN S 4 " pdb=" O5 MAN S 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.77e+01 chirality pdb=" C1 MAN s 4 " pdb=" O3 BMA s 3 " pdb=" C2 MAN s 4 " pdb=" O5 MAN s 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.64e+01 ... (remaining 3289 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 281 " -0.084 2.00e-02 2.50e+03 4.41e-02 3.90e+01 pdb=" CG TYR D 281 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR D 281 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR D 281 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR D 281 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR D 281 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR D 281 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 281 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 281 " 0.085 2.00e-02 2.50e+03 4.41e-02 3.90e+01 pdb=" CG TYR B 281 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR B 281 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 281 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 281 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR B 281 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 281 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 281 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 281 " 0.085 2.00e-02 2.50e+03 4.40e-02 3.88e+01 pdb=" CG TYR E 281 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR E 281 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR E 281 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR E 281 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR E 281 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR E 281 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 281 " 0.057 2.00e-02 2.50e+03 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4924 2.83 - 3.35: 19156 3.35 - 3.87: 36030 3.87 - 4.38: 44702 4.38 - 4.90: 72604 Nonbonded interactions: 177416 Sorted by model distance: nonbonded pdb=" O ASP E 293 " pdb="CA CA E2000 " model vdw 2.314 2.510 nonbonded pdb=" O ASP B 293 " pdb="CA CA B2000 " model vdw 2.314 2.510 nonbonded pdb=" O ASP D 293 " pdb="CA CA D2000 " model vdw 2.316 2.510 nonbonded pdb=" O ASP A 293 " pdb="CA CA A 501 " model vdw 2.316 2.510 nonbonded pdb=" O HIS D 347 " pdb="CA CA D2000 " model vdw 2.317 2.510 ... (remaining 177411 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 82 through 469 or resid 501)) selection = chain 'B' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'w' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 's' } ncs_group { reference = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'u' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 18.050 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 55.180 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.400 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:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 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 : 0.015 0.061 20752 Z= 0.947 Angle : 1.637 9.105 28168 Z= 1.062 Chirality : 0.094 0.454 3292 Planarity : 0.010 0.071 3528 Dihedral : 13.928 98.160 8552 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.86 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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: -0.75 (0.16), residues: 2488 helix: -0.11 (0.97), residues: 24 sheet: -0.04 (0.16), residues: 1008 loop : -0.81 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.012 TRP J 97 HIS 0.021 0.006 HIS A 168 PHE 0.060 0.013 PHE E 205 TYR 0.085 0.013 TYR B 281 ARG 0.019 0.003 ARG E 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 LYS cc_start: 0.9335 (ttmt) cc_final: 0.9135 (mtpm) REVERT: I 70 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7808 (mt-10) REVERT: B 400 ARG cc_start: 0.9264 (ptm-80) cc_final: 0.9027 (ptm160) REVERT: F 23 LYS cc_start: 0.9334 (ttmt) cc_final: 0.9132 (mtpm) REVERT: J 70 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7808 (mt-10) REVERT: A 400 ARG cc_start: 0.9263 (ptm-80) cc_final: 0.9029 (ptm160) REVERT: G 23 LYS cc_start: 0.9333 (ttmt) cc_final: 0.9133 (mtpm) REVERT: K 70 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7802 (mt-10) REVERT: D 400 ARG cc_start: 0.9263 (ptm-80) cc_final: 0.9028 (ptm160) REVERT: H 23 LYS cc_start: 0.9334 (ttmt) cc_final: 0.9132 (mtpm) REVERT: L 70 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7811 (mt-10) REVERT: E 400 ARG cc_start: 0.9265 (ptm-80) cc_final: 0.9026 (ptm160) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 1.4676 time to fit residues: 474.2757 Evaluate side-chains 213 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN C 65 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS F 32 GLN F 65 GLN ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 HIS G 32 GLN G 65 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 HIS H 32 GLN H 65 GLN ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 347 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20752 Z= 0.273 Angle : 0.690 7.484 28168 Z= 0.371 Chirality : 0.048 0.284 3292 Planarity : 0.004 0.041 3528 Dihedral : 9.127 76.728 4260 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.89 % Favored : 96.95 % Rotamer: Outliers : 1.45 % Allowed : 7.35 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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: -0.22 (0.16), residues: 2488 helix: 0.86 (0.96), residues: 24 sheet: 0.05 (0.15), residues: 1068 loop : -0.23 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 178 HIS 0.004 0.001 HIS D 168 PHE 0.015 0.002 PHE D 410 TYR 0.015 0.002 TYR E 121 ARG 0.008 0.001 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 220 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 17 GLU cc_start: 0.8098 (mp0) cc_final: 0.7855 (mp0) REVERT: I 24 ARG cc_start: 0.8335 (ttm110) cc_final: 0.8131 (ttm110) REVERT: I 81 GLU cc_start: 0.9235 (pm20) cc_final: 0.8921 (pp20) REVERT: J 17 GLU cc_start: 0.8094 (mp0) cc_final: 0.7852 (mp0) REVERT: J 24 ARG cc_start: 0.8327 (ttm110) cc_final: 0.8093 (ttm110) REVERT: J 81 GLU cc_start: 0.9235 (pm20) cc_final: 0.8922 (pp20) REVERT: K 17 GLU cc_start: 0.8095 (mp0) cc_final: 0.7853 (mp0) REVERT: K 24 ARG cc_start: 0.8324 (ttm110) cc_final: 0.8121 (ttm110) REVERT: K 81 GLU cc_start: 0.9235 (pm20) cc_final: 0.8923 (pp20) REVERT: L 17 GLU cc_start: 0.8094 (mp0) cc_final: 0.7852 (mp0) REVERT: L 24 ARG cc_start: 0.8327 (ttm110) cc_final: 0.8123 (ttm110) REVERT: L 81 GLU cc_start: 0.9235 (pm20) cc_final: 0.8923 (pp20) outliers start: 31 outliers final: 12 residues processed: 241 average time/residue: 1.5660 time to fit residues: 420.2557 Evaluate side-chains 222 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 210 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 56 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 225 optimal weight: 0.6980 chunk 243 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 223 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS B 468 HIS ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS G 65 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS D 468 HIS H 65 GLN ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 HIS E 468 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20752 Z= 0.284 Angle : 0.625 6.945 28168 Z= 0.331 Chirality : 0.047 0.264 3292 Planarity : 0.003 0.027 3528 Dihedral : 8.133 65.241 4260 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.54 % Favored : 96.30 % Rotamer: Outliers : 1.54 % Allowed : 9.46 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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: -0.34 (0.16), residues: 2488 helix: 0.60 (0.91), residues: 24 sheet: -0.06 (0.15), residues: 1044 loop : -0.27 (0.15), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 178 HIS 0.004 0.001 HIS B 168 PHE 0.015 0.002 PHE A 410 TYR 0.015 0.002 TYR D 121 ARG 0.008 0.001 ARG J 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 214 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8311 (m-30) cc_final: 0.8041 (m-30) REVERT: I 17 GLU cc_start: 0.8196 (mp0) cc_final: 0.7884 (mp0) REVERT: I 24 ARG cc_start: 0.8484 (ttm110) cc_final: 0.8253 (ttm110) REVERT: I 79 GLN cc_start: 0.8367 (mm-40) cc_final: 0.7819 (mp-120) REVERT: I 81 GLU cc_start: 0.9263 (pm20) cc_final: 0.8928 (pp20) REVERT: I 107 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7050 (mm) REVERT: F 90 ASP cc_start: 0.8306 (m-30) cc_final: 0.8019 (m-30) REVERT: J 17 GLU cc_start: 0.8181 (mp0) cc_final: 0.7867 (mp0) REVERT: J 24 ARG cc_start: 0.8473 (ttm110) cc_final: 0.8172 (ttm110) REVERT: J 79 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7819 (mp-120) REVERT: J 81 GLU cc_start: 0.9263 (pm20) cc_final: 0.8928 (pp20) REVERT: J 107 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7054 (mm) REVERT: G 90 ASP cc_start: 0.8342 (m-30) cc_final: 0.8061 (m-30) REVERT: K 17 GLU cc_start: 0.8191 (mp0) cc_final: 0.7876 (mp0) REVERT: K 24 ARG cc_start: 0.8510 (ttm110) cc_final: 0.8262 (ttm110) REVERT: K 79 GLN cc_start: 0.8370 (mm-40) cc_final: 0.7820 (mp-120) REVERT: K 81 GLU cc_start: 0.9262 (pm20) cc_final: 0.8929 (pp20) REVERT: K 107 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.7049 (mm) REVERT: L 17 GLU cc_start: 0.8196 (mp0) cc_final: 0.7877 (mp0) REVERT: L 24 ARG cc_start: 0.8451 (ttm110) cc_final: 0.8223 (ttm110) REVERT: L 79 GLN cc_start: 0.8368 (mm-40) cc_final: 0.7813 (mp-120) REVERT: L 81 GLU cc_start: 0.9267 (pm20) cc_final: 0.8935 (pp20) REVERT: L 107 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7027 (mm) outliers start: 33 outliers final: 16 residues processed: 231 average time/residue: 1.5218 time to fit residues: 391.8026 Evaluate side-chains 224 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 204 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 151 optimal weight: 0.8980 chunk 226 optimal weight: 0.9980 chunk 239 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 468 HIS ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS A 468 HIS D 468 HIS E 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 20752 Z= 0.258 Angle : 0.598 7.906 28168 Z= 0.314 Chirality : 0.046 0.270 3292 Planarity : 0.004 0.037 3528 Dihedral : 7.727 59.608 4260 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.89 % Favored : 96.95 % Rotamer: Outliers : 0.98 % Allowed : 10.44 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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: -0.31 (0.16), residues: 2488 helix: 0.42 (0.89), residues: 24 sheet: -0.14 (0.15), residues: 1064 loop : -0.15 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 178 HIS 0.002 0.001 HIS B 468 PHE 0.015 0.002 PHE E 410 TYR 0.014 0.001 TYR E 121 ARG 0.010 0.001 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 213 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 GLN cc_start: 0.8531 (tp-100) cc_final: 0.8234 (tp-100) REVERT: I 17 GLU cc_start: 0.8225 (mp0) cc_final: 0.7923 (mp0) REVERT: I 24 ARG cc_start: 0.8496 (ttm110) cc_final: 0.8241 (ttm110) REVERT: I 79 GLN cc_start: 0.8339 (mm-40) cc_final: 0.7771 (mp-120) REVERT: I 81 GLU cc_start: 0.9246 (pm20) cc_final: 0.8934 (pp20) REVERT: I 107 ILE cc_start: 0.7528 (OUTLIER) cc_final: 0.7258 (pp) REVERT: J 17 GLU cc_start: 0.8207 (mp0) cc_final: 0.7898 (mp0) REVERT: J 24 ARG cc_start: 0.8509 (ttm110) cc_final: 0.8129 (ttm110) REVERT: J 81 GLU cc_start: 0.9247 (pm20) cc_final: 0.8952 (pp20) REVERT: J 107 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.7160 (pp) REVERT: G 65 GLN cc_start: 0.8522 (tp-100) cc_final: 0.8230 (tp-100) REVERT: K 17 GLU cc_start: 0.8216 (mp0) cc_final: 0.7910 (mp0) REVERT: K 24 ARG cc_start: 0.8489 (ttm110) cc_final: 0.8175 (ttm110) REVERT: K 79 GLN cc_start: 0.8340 (mm-40) cc_final: 0.7761 (mp-120) REVERT: K 81 GLU cc_start: 0.9247 (pm20) cc_final: 0.8950 (pp20) REVERT: K 107 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7257 (pp) REVERT: H 65 GLN cc_start: 0.8507 (tp-100) cc_final: 0.8228 (tp-100) REVERT: L 17 GLU cc_start: 0.8216 (mp0) cc_final: 0.7908 (mp0) REVERT: L 24 ARG cc_start: 0.8493 (ttm110) cc_final: 0.8215 (ttm110) REVERT: L 81 GLU cc_start: 0.9243 (pm20) cc_final: 0.8974 (pp20) REVERT: L 107 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7260 (pp) outliers start: 21 outliers final: 17 residues processed: 230 average time/residue: 1.6150 time to fit residues: 411.7623 Evaluate side-chains 230 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 209 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS ** J 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** K 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9157 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 20752 Z= 0.518 Angle : 0.686 7.613 28168 Z= 0.360 Chirality : 0.050 0.282 3292 Planarity : 0.004 0.045 3528 Dihedral : 8.305 66.351 4260 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.02 % Favored : 95.82 % Rotamer: Outliers : 1.31 % Allowed : 11.28 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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: -0.42 (0.16), residues: 2488 helix: 0.21 (0.86), residues: 24 sheet: -0.17 (0.15), residues: 1048 loop : -0.28 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 178 HIS 0.003 0.001 HIS D 168 PHE 0.017 0.002 PHE E 410 TYR 0.018 0.002 TYR A 121 ARG 0.011 0.001 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 216 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 GLN cc_start: 0.8586 (tp-100) cc_final: 0.8192 (tp-100) REVERT: I 17 GLU cc_start: 0.8220 (mp0) cc_final: 0.7904 (mp0) REVERT: I 79 GLN cc_start: 0.8345 (mm-40) cc_final: 0.7683 (mp-120) REVERT: I 81 GLU cc_start: 0.9231 (pm20) cc_final: 0.8951 (pp20) REVERT: I 107 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.7180 (pp) REVERT: J 4 MET cc_start: 0.8676 (mmm) cc_final: 0.8209 (mmm) REVERT: J 17 GLU cc_start: 0.8186 (mp0) cc_final: 0.7857 (mp0) REVERT: J 24 ARG cc_start: 0.8614 (ttm110) cc_final: 0.8393 (ttm110) REVERT: J 79 GLN cc_start: 0.8356 (mm-40) cc_final: 0.7706 (mp-120) REVERT: J 81 GLU cc_start: 0.9244 (pm20) cc_final: 0.8948 (pp20) REVERT: J 107 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.7164 (pp) REVERT: G 65 GLN cc_start: 0.8587 (tp-100) cc_final: 0.8201 (tp-100) REVERT: K 17 GLU cc_start: 0.8202 (mp0) cc_final: 0.7877 (mp0) REVERT: K 79 GLN cc_start: 0.8346 (mm-40) cc_final: 0.7695 (mp-120) REVERT: K 81 GLU cc_start: 0.9244 (pm20) cc_final: 0.8950 (pp20) REVERT: K 107 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.7195 (pp) REVERT: H 65 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8215 (tp-100) REVERT: L 17 GLU cc_start: 0.8181 (mp0) cc_final: 0.7852 (mp0) REVERT: L 79 GLN cc_start: 0.8349 (mm-40) cc_final: 0.7697 (mp-120) REVERT: L 81 GLU cc_start: 0.9241 (pm20) cc_final: 0.8948 (pp20) REVERT: L 107 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7183 (pp) outliers start: 28 outliers final: 21 residues processed: 236 average time/residue: 1.5771 time to fit residues: 413.4482 Evaluate side-chains 232 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 207 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 239 optimal weight: 0.8980 chunk 199 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 79 optimal weight: 0.4980 chunk 125 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 92 ASN B 468 HIS F 65 GLN J 92 ASN ** J 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS K 92 ASN D 468 HIS E 468 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20752 Z= 0.190 Angle : 0.593 9.641 28168 Z= 0.305 Chirality : 0.045 0.288 3292 Planarity : 0.003 0.044 3528 Dihedral : 7.446 58.687 4260 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.97 % Favored : 96.86 % Rotamer: Outliers : 1.17 % Allowed : 11.61 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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: -0.32 (0.16), residues: 2488 helix: -0.64 (0.83), residues: 28 sheet: -0.09 (0.15), residues: 1080 loop : -0.19 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 178 HIS 0.003 0.001 HIS E 468 PHE 0.015 0.002 PHE E 410 TYR 0.011 0.001 TYR K 49 ARG 0.012 0.001 ARG J 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 221 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 GLN cc_start: 0.8550 (tp-100) cc_final: 0.8204 (tp-100) REVERT: I 17 GLU cc_start: 0.8303 (mp0) cc_final: 0.8030 (mp0) REVERT: I 79 GLN cc_start: 0.8349 (mm-40) cc_final: 0.7725 (mp-120) REVERT: I 81 GLU cc_start: 0.9246 (pm20) cc_final: 0.8987 (pp20) REVERT: I 107 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7215 (pp) REVERT: J 4 MET cc_start: 0.8605 (mmm) cc_final: 0.8349 (mmm) REVERT: J 17 GLU cc_start: 0.8300 (mp0) cc_final: 0.8019 (mp0) REVERT: J 79 GLN cc_start: 0.8343 (mm-40) cc_final: 0.7733 (mp-120) REVERT: J 81 GLU cc_start: 0.9250 (pm20) cc_final: 0.8988 (pp20) REVERT: J 107 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7210 (pp) REVERT: G 65 GLN cc_start: 0.8565 (tp-100) cc_final: 0.8222 (tp-100) REVERT: K 17 GLU cc_start: 0.8285 (mp0) cc_final: 0.8004 (mp0) REVERT: K 79 GLN cc_start: 0.8349 (mm-40) cc_final: 0.7724 (mp-120) REVERT: K 81 GLU cc_start: 0.9250 (pm20) cc_final: 0.8989 (pp20) REVERT: K 107 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7225 (pp) REVERT: H 65 GLN cc_start: 0.8572 (tp-100) cc_final: 0.8222 (tp-100) REVERT: L 6 GLN cc_start: 0.8902 (tt0) cc_final: 0.8691 (tt0) REVERT: L 17 GLU cc_start: 0.8297 (mp0) cc_final: 0.8017 (mp0) REVERT: L 79 GLN cc_start: 0.8341 (mm-40) cc_final: 0.7726 (mp-120) REVERT: L 81 GLU cc_start: 0.9249 (pm20) cc_final: 0.8986 (pp20) REVERT: L 107 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7208 (pp) outliers start: 25 outliers final: 13 residues processed: 232 average time/residue: 1.6463 time to fit residues: 422.6469 Evaluate side-chains 227 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 210 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 239 optimal weight: 1.9990 chunk 149 optimal weight: 0.2980 chunk 145 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS A 468 HIS ** K 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS L 6 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20752 Z= 0.276 Angle : 0.613 9.423 28168 Z= 0.316 Chirality : 0.046 0.283 3292 Planarity : 0.004 0.051 3528 Dihedral : 7.416 59.873 4260 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.62 % Favored : 96.22 % Rotamer: Outliers : 1.45 % Allowed : 12.55 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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: -0.26 (0.16), residues: 2488 helix: 0.23 (0.85), residues: 24 sheet: -0.14 (0.15), residues: 1048 loop : -0.09 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 178 HIS 0.003 0.001 HIS B 274 PHE 0.015 0.002 PHE B 410 TYR 0.014 0.001 TYR A 121 ARG 0.013 0.001 ARG K 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 215 time to evaluate : 2.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 GLN cc_start: 0.8569 (tp-100) cc_final: 0.8226 (tp-100) REVERT: I 4 MET cc_start: 0.8690 (mmm) cc_final: 0.8400 (mmm) REVERT: I 17 GLU cc_start: 0.8307 (mp0) cc_final: 0.7991 (mp0) REVERT: I 79 GLN cc_start: 0.8418 (mm-40) cc_final: 0.7973 (mm-40) REVERT: I 81 GLU cc_start: 0.9251 (pm20) cc_final: 0.8954 (pp20) REVERT: I 107 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7234 (pp) REVERT: J 4 MET cc_start: 0.8617 (mmm) cc_final: 0.8340 (mmm) REVERT: J 17 GLU cc_start: 0.8299 (mp0) cc_final: 0.7980 (mp0) REVERT: J 79 GLN cc_start: 0.8414 (mm-40) cc_final: 0.7969 (mm-40) REVERT: J 81 GLU cc_start: 0.9252 (pm20) cc_final: 0.8957 (pp20) REVERT: J 107 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7250 (pp) REVERT: G 65 GLN cc_start: 0.8505 (tp-100) cc_final: 0.8182 (tp-100) REVERT: K 17 GLU cc_start: 0.8301 (mp0) cc_final: 0.7983 (mp0) REVERT: K 79 GLN cc_start: 0.8420 (mm-40) cc_final: 0.7971 (mm-40) REVERT: K 81 GLU cc_start: 0.9250 (pm20) cc_final: 0.8959 (pp20) REVERT: K 107 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7254 (pp) REVERT: H 65 GLN cc_start: 0.8589 (tp-100) cc_final: 0.8222 (tp-100) REVERT: L 4 MET cc_start: 0.8672 (mmm) cc_final: 0.8249 (mmm) REVERT: L 17 GLU cc_start: 0.8302 (mp0) cc_final: 0.7994 (mp0) REVERT: L 79 GLN cc_start: 0.8376 (mm-40) cc_final: 0.7930 (mm-40) REVERT: L 81 GLU cc_start: 0.9246 (pm20) cc_final: 0.8956 (pp20) REVERT: L 107 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7249 (pp) outliers start: 31 outliers final: 23 residues processed: 238 average time/residue: 1.4972 time to fit residues: 397.7249 Evaluate side-chains 234 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 207 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 142 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 468 HIS ** J 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** K 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS E 441 ASN E 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9103 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20752 Z= 0.228 Angle : 0.602 9.726 28168 Z= 0.308 Chirality : 0.045 0.282 3292 Planarity : 0.004 0.052 3528 Dihedral : 7.107 56.904 4260 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.62 % Favored : 96.22 % Rotamer: Outliers : 1.54 % Allowed : 12.50 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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: -0.21 (0.16), residues: 2488 helix: -0.59 (0.84), residues: 28 sheet: -0.10 (0.15), residues: 1048 loop : -0.04 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 178 HIS 0.003 0.001 HIS A 468 PHE 0.014 0.002 PHE E 410 TYR 0.012 0.001 TYR A 121 ARG 0.014 0.001 ARG J 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 222 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.9338 (mt-10) cc_final: 0.9052 (mp0) REVERT: C 65 GLN cc_start: 0.8495 (tp-100) cc_final: 0.8201 (tp-100) REVERT: I 4 MET cc_start: 0.8622 (mmm) cc_final: 0.8377 (mmm) REVERT: I 17 GLU cc_start: 0.8329 (mp0) cc_final: 0.8023 (mp0) REVERT: I 79 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7924 (mm-40) REVERT: I 81 GLU cc_start: 0.9227 (pm20) cc_final: 0.8981 (pp20) REVERT: I 107 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7298 (pp) REVERT: F 13 GLU cc_start: 0.9341 (mt-10) cc_final: 0.9053 (mp0) REVERT: J 4 MET cc_start: 0.8605 (mmm) cc_final: 0.8299 (mmm) REVERT: J 17 GLU cc_start: 0.8325 (mp0) cc_final: 0.8007 (mp0) REVERT: J 79 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7922 (mm-40) REVERT: J 81 GLU cc_start: 0.9233 (pm20) cc_final: 0.8984 (pp20) REVERT: J 107 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7290 (pp) REVERT: G 13 GLU cc_start: 0.9343 (mt-10) cc_final: 0.9057 (mp0) REVERT: G 65 GLN cc_start: 0.8505 (tp-100) cc_final: 0.8244 (tp-100) REVERT: K 17 GLU cc_start: 0.8320 (mp0) cc_final: 0.8014 (mp0) REVERT: K 79 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7913 (mm-40) REVERT: K 81 GLU cc_start: 0.9226 (pm20) cc_final: 0.8982 (pp20) REVERT: K 107 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7307 (pp) REVERT: H 13 GLU cc_start: 0.9344 (mt-10) cc_final: 0.9061 (mp0) REVERT: H 65 GLN cc_start: 0.8518 (tp-100) cc_final: 0.8216 (tp-100) REVERT: L 4 MET cc_start: 0.8616 (mmm) cc_final: 0.8188 (mmm) REVERT: L 17 GLU cc_start: 0.8323 (mp0) cc_final: 0.8017 (mp0) REVERT: L 79 GLN cc_start: 0.8374 (mm-40) cc_final: 0.7922 (mm-40) REVERT: L 81 GLU cc_start: 0.9233 (pm20) cc_final: 0.8982 (pp20) REVERT: L 107 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7309 (pp) outliers start: 33 outliers final: 25 residues processed: 246 average time/residue: 1.4583 time to fit residues: 406.9227 Evaluate side-chains 244 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 215 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.9990 chunk 208 optimal weight: 0.4980 chunk 222 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 210 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 ASN B 468 HIS ** J 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** K 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS L 92 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 468 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9089 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20752 Z= 0.192 Angle : 0.590 9.846 28168 Z= 0.300 Chirality : 0.044 0.277 3292 Planarity : 0.004 0.057 3528 Dihedral : 6.764 51.572 4260 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.18 % Favored : 96.66 % Rotamer: Outliers : 1.45 % Allowed : 12.69 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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: -0.15 (0.17), residues: 2488 helix: -0.55 (0.84), residues: 28 sheet: -0.10 (0.16), residues: 1056 loop : 0.04 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 178 HIS 0.004 0.001 HIS A 468 PHE 0.013 0.002 PHE B 410 TYR 0.011 0.001 TYR E 121 ARG 0.015 0.001 ARG K 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 226 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.9326 (mt-10) cc_final: 0.9044 (mp0) REVERT: C 65 GLN cc_start: 0.8448 (tp-100) cc_final: 0.8240 (tp-100) REVERT: I 4 MET cc_start: 0.8584 (mmm) cc_final: 0.8384 (mmm) REVERT: I 17 GLU cc_start: 0.8329 (mp0) cc_final: 0.7994 (mp0) REVERT: I 79 GLN cc_start: 0.8440 (mm-40) cc_final: 0.7797 (mp-120) REVERT: I 81 GLU cc_start: 0.9226 (pm20) cc_final: 0.8986 (pp20) REVERT: I 107 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7459 (pp) REVERT: F 13 GLU cc_start: 0.9326 (mt-10) cc_final: 0.9057 (mp0) REVERT: J 4 MET cc_start: 0.8604 (mmm) cc_final: 0.8332 (mmm) REVERT: J 17 GLU cc_start: 0.8321 (mp0) cc_final: 0.7982 (mp0) REVERT: J 79 GLN cc_start: 0.8432 (mm-40) cc_final: 0.7974 (mm-40) REVERT: J 81 GLU cc_start: 0.9229 (pm20) cc_final: 0.8986 (pp20) REVERT: J 107 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7481 (pp) REVERT: G 13 GLU cc_start: 0.9333 (mt-10) cc_final: 0.9055 (mp0) REVERT: G 65 GLN cc_start: 0.8464 (tp-100) cc_final: 0.8200 (tp-100) REVERT: K 17 GLU cc_start: 0.8320 (mp0) cc_final: 0.7986 (mp0) REVERT: K 79 GLN cc_start: 0.8442 (mm-40) cc_final: 0.7967 (mm-40) REVERT: K 81 GLU cc_start: 0.9225 (pm20) cc_final: 0.8986 (pp20) REVERT: K 107 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7494 (pp) REVERT: H 13 GLU cc_start: 0.9338 (mt-10) cc_final: 0.9060 (mp0) REVERT: H 65 GLN cc_start: 0.8538 (tp-100) cc_final: 0.8242 (tp-100) REVERT: L 4 MET cc_start: 0.8564 (mmm) cc_final: 0.8174 (mmm) REVERT: L 17 GLU cc_start: 0.8321 (mp0) cc_final: 0.7980 (mp0) REVERT: L 79 GLN cc_start: 0.8435 (mm-40) cc_final: 0.7795 (mp-120) REVERT: L 81 GLU cc_start: 0.9228 (pm20) cc_final: 0.8986 (pp20) REVERT: L 107 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7488 (pp) outliers start: 31 outliers final: 24 residues processed: 249 average time/residue: 1.4804 time to fit residues: 412.4486 Evaluate side-chains 241 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 213 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.1980 chunk 143 optimal weight: 10.0000 chunk 111 optimal weight: 0.3980 chunk 163 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 156 optimal weight: 0.3980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 468 HIS ** J 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** K 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS E 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9103 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20752 Z= 0.249 Angle : 0.607 9.642 28168 Z= 0.310 Chirality : 0.045 0.276 3292 Planarity : 0.004 0.062 3528 Dihedral : 6.768 48.630 4260 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.26 % Favored : 96.58 % Rotamer: Outliers : 1.50 % Allowed : 12.64 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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: -0.12 (0.17), residues: 2488 helix: -0.52 (0.85), residues: 28 sheet: -0.06 (0.16), residues: 1048 loop : 0.04 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 178 HIS 0.004 0.001 HIS D 468 PHE 0.014 0.002 PHE A 410 TYR 0.013 0.001 TYR B 121 ARG 0.018 0.001 ARG L 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 223 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.9328 (mt-10) cc_final: 0.9050 (mp0) REVERT: C 65 GLN cc_start: 0.8478 (tp-100) cc_final: 0.8255 (tp-100) REVERT: I 17 GLU cc_start: 0.8338 (mp0) cc_final: 0.8017 (mp0) REVERT: I 79 GLN cc_start: 0.8443 (mm-40) cc_final: 0.7983 (mm-40) REVERT: I 81 GLU cc_start: 0.9219 (pm20) cc_final: 0.8984 (pp20) REVERT: I 107 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7500 (pp) REVERT: F 13 GLU cc_start: 0.9329 (mt-10) cc_final: 0.9062 (mp0) REVERT: J 4 MET cc_start: 0.8627 (mmm) cc_final: 0.8297 (mmm) REVERT: J 17 GLU cc_start: 0.8335 (mp0) cc_final: 0.7994 (mp0) REVERT: J 79 GLN cc_start: 0.8434 (mm-40) cc_final: 0.7977 (mm-40) REVERT: J 81 GLU cc_start: 0.9223 (pm20) cc_final: 0.8987 (pp20) REVERT: J 107 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7393 (pp) REVERT: G 13 GLU cc_start: 0.9329 (mt-10) cc_final: 0.9051 (mp0) REVERT: G 65 GLN cc_start: 0.8467 (tp-100) cc_final: 0.8210 (tp-100) REVERT: K 4 MET cc_start: 0.8357 (tpp) cc_final: 0.8016 (mmm) REVERT: K 17 GLU cc_start: 0.8333 (mp0) cc_final: 0.7998 (mp0) REVERT: K 79 GLN cc_start: 0.8441 (mm-40) cc_final: 0.7980 (mm-40) REVERT: K 81 GLU cc_start: 0.9219 (pm20) cc_final: 0.8986 (pp20) REVERT: K 107 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7513 (pp) REVERT: H 13 GLU cc_start: 0.9333 (mt-10) cc_final: 0.9053 (mp0) REVERT: H 65 GLN cc_start: 0.8542 (tp-100) cc_final: 0.8262 (tp-100) REVERT: L 4 MET cc_start: 0.8569 (mmm) cc_final: 0.8150 (mmm) REVERT: L 17 GLU cc_start: 0.8332 (mp0) cc_final: 0.8005 (mp0) REVERT: L 79 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8017 (mm-40) REVERT: L 81 GLU cc_start: 0.9218 (pm20) cc_final: 0.8948 (pp20) REVERT: L 107 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7345 (pp) outliers start: 32 outliers final: 24 residues processed: 247 average time/residue: 1.4838 time to fit residues: 409.4682 Evaluate side-chains 243 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 215 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.7980 chunk 60 optimal weight: 0.0970 chunk 181 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 197 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 202 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 173 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 468 HIS ** J 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 ASN A 468 HIS ** K 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.086483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.056424 restraints weight = 37554.352| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.66 r_work: 0.2676 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20752 Z= 0.173 Angle : 0.585 9.929 28168 Z= 0.298 Chirality : 0.044 0.272 3292 Planarity : 0.004 0.075 3528 Dihedral : 6.386 44.166 4260 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.05 % Favored : 96.78 % Rotamer: Outliers : 1.45 % Allowed : 13.06 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % 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: -0.06 (0.17), residues: 2488 helix: -0.47 (0.86), residues: 28 sheet: -0.03 (0.16), residues: 1064 loop : 0.10 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 178 HIS 0.004 0.001 HIS A 468 PHE 0.012 0.001 PHE E 410 TYR 0.011 0.001 TYR A 121 ARG 0.016 0.001 ARG J 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7317.69 seconds wall clock time: 130 minutes 50.87 seconds (7850.87 seconds total)