Starting phenix.real_space_refine on Sat Feb 17 12:41:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g40_29712/02_2024/8g40_29712.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g40_29712/02_2024/8g40_29712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g40_29712/02_2024/8g40_29712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g40_29712/02_2024/8g40_29712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g40_29712/02_2024/8g40_29712.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g40_29712/02_2024/8g40_29712.pdb" } resolution = 2.8 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= 0.017 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 109 5.16 5 C 11569 2.51 5 N 3120 2.21 5 O 3847 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 85": "NH1" <-> "NH2" Residue "G ARG 107": "NH1" <-> "NH2" Residue "G ARG 118": "NH1" <-> "NH2" Residue "G ARG 150": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 156": "NH1" <-> "NH2" Residue "G ARG 210": "NH1" <-> "NH2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "G TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 283": "NH1" <-> "NH2" Residue "G ARG 288": "NH1" <-> "NH2" Residue "G ARG 292": "NH1" <-> "NH2" Residue "G ARG 300": "NH1" <-> "NH2" Residue "G ARG 327": "NH1" <-> "NH2" Residue "G PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 364": "NH1" <-> "NH2" Residue "G ARG 371": "NH1" <-> "NH2" Residue "G ARG 394": "NH1" <-> "NH2" Residue "G ARG 400": "NH1" <-> "NH2" Residue "G ARG 403": "NH1" <-> "NH2" Residue "G ARG 420": "NH1" <-> "NH2" Residue "G ARG 428": "NH1" <-> "NH2" Residue "G ARG 430": "NH1" <-> "NH2" Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "A 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 TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 85": "NH1" <-> "NH2" Residue "H ARG 107": "NH1" <-> "NH2" Residue "H ARG 118": "NH1" <-> "NH2" Residue "H ARG 150": "NH1" <-> "NH2" Residue "H ARG 152": "NH1" <-> "NH2" Residue "H ARG 156": "NH1" <-> "NH2" Residue "H ARG 210": "NH1" <-> "NH2" Residue "H ARG 224": "NH1" <-> "NH2" Residue "H TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 283": "NH1" <-> "NH2" Residue "H ARG 288": "NH1" <-> "NH2" Residue "H ARG 292": "NH1" <-> "NH2" Residue "H ARG 300": "NH1" <-> "NH2" Residue "H ARG 327": "NH1" <-> "NH2" Residue "H ARG 364": "NH1" <-> "NH2" Residue "H ARG 371": "NH1" <-> "NH2" Residue "H ARG 394": "NH1" <-> "NH2" Residue "H ARG 400": "NH1" <-> "NH2" Residue "H ARG 403": "NH1" <-> "NH2" Residue "H ARG 420": "NH1" <-> "NH2" Residue "H ARG 428": "NH1" <-> "NH2" Residue "H ARG 430": "NH1" <-> "NH2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 24": "NH1" <-> "NH2" Residue "M ARG 27": "NH1" <-> "NH2" Residue "M ARG 45": "NH1" <-> "NH2" Residue "M ARG 54": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 85": "NH1" <-> "NH2" Residue "I PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 107": "NH1" <-> "NH2" Residue "I ARG 118": "NH1" <-> "NH2" Residue "I ARG 150": "NH1" <-> "NH2" Residue "I ARG 152": "NH1" <-> "NH2" Residue "I ARG 156": "NH1" <-> "NH2" Residue "I ARG 210": "NH1" <-> "NH2" Residue "I ARG 224": "NH1" <-> "NH2" Residue "I TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 283": "NH1" <-> "NH2" Residue "I ARG 288": "NH1" <-> "NH2" Residue "I ARG 292": "NH1" <-> "NH2" Residue "I ARG 300": "NH1" <-> "NH2" Residue "I ARG 327": "NH1" <-> "NH2" Residue "I ARG 364": "NH1" <-> "NH2" Residue "I ARG 371": "NH1" <-> "NH2" Residue "I ARG 394": "NH1" <-> "NH2" Residue "I ARG 400": "NH1" <-> "NH2" Residue "I ARG 403": "NH1" <-> "NH2" Residue "I ARG 420": "NH1" <-> "NH2" Residue "I ARG 428": "NH1" <-> "NH2" Residue "I ARG 430": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 87": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N ARG 24": "NH1" <-> "NH2" Residue "N ARG 27": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N ARG 54": "NH1" <-> "NH2" Residue "N ARG 61": "NH1" <-> "NH2" Residue "N TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 85": "NH1" <-> "NH2" Residue "J ARG 107": "NH1" <-> "NH2" Residue "J ARG 118": "NH1" <-> "NH2" Residue "J PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 150": "NH1" <-> "NH2" Residue "J ARG 152": "NH1" <-> "NH2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "J ARG 210": "NH1" <-> "NH2" Residue "J ARG 224": "NH1" <-> "NH2" Residue "J TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 283": "NH1" <-> "NH2" Residue "J ARG 288": "NH1" <-> "NH2" Residue "J ARG 292": "NH1" <-> "NH2" Residue "J ARG 300": "NH1" <-> "NH2" Residue "J ARG 327": "NH1" <-> "NH2" Residue "J ARG 364": "NH1" <-> "NH2" Residue "J ARG 371": "NH1" <-> "NH2" Residue "J ARG 394": "NH1" <-> "NH2" Residue "J ARG 400": "NH1" <-> "NH2" Residue "J ARG 403": "NH1" <-> "NH2" Residue "J ARG 420": "NH1" <-> "NH2" Residue "J ARG 428": "NH1" <-> "NH2" Residue "J ARG 430": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18650 Number of models: 1 Model: "" Number of chains: 38 Chain: "G" 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: "A" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "L" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "H" 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: "B" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "M" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "I" 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: "C" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "N" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "J" 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: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" 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: "k" 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: "s" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "3" 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: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" 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: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "l" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "2" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "4" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "5" 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: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: 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: "G" 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: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "J" 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: 10.18, per 1000 atoms: 0.55 Number of scatterers: 18650 At special positions: 0 Unit cell: (117.03, 142.76, 169.32, 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 109 16.00 O 3847 8.00 N 3120 7.00 C 11569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 417 " distance=2.06 Simple disulfide: pdb=" SG CYS G 124 " - pdb=" SG CYS G 129 " distance=2.07 Simple disulfide: pdb=" SG CYS G 175 " - pdb=" SG CYS G 193 " distance=2.04 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 230 " distance=2.08 Simple disulfide: pdb=" SG CYS G 232 " - pdb=" SG CYS G 237 " distance=2.07 Simple disulfide: pdb=" SG CYS G 278 " - pdb=" SG CYS G 291 " distance=2.07 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 289 " distance=2.09 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.08 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 447 " distance=2.14 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.07 Simple disulfide: pdb=" SG CYS H 92 " - pdb=" SG CYS H 417 " distance=2.05 Simple disulfide: pdb=" SG CYS H 124 " - pdb=" SG CYS H 129 " distance=2.07 Simple disulfide: pdb=" SG CYS H 175 " - pdb=" SG CYS H 193 " distance=2.03 Simple disulfide: pdb=" SG CYS H 183 " - pdb=" SG CYS H 230 " distance=2.10 Simple disulfide: pdb=" SG CYS H 232 " - pdb=" SG CYS H 237 " distance=2.08 Simple disulfide: pdb=" SG CYS H 278 " - pdb=" SG CYS H 291 " distance=2.07 Simple disulfide: pdb=" SG CYS H 280 " - pdb=" SG CYS H 289 " distance=2.09 Simple disulfide: pdb=" SG CYS H 318 " - pdb=" SG CYS H 337 " distance=2.09 Simple disulfide: pdb=" SG CYS H 421 " - pdb=" SG CYS H 447 " distance=2.15 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.05 Simple disulfide: pdb=" SG CYS I 92 " - pdb=" SG CYS I 417 " distance=2.03 Simple disulfide: pdb=" SG CYS I 124 " - pdb=" SG CYS I 129 " distance=2.11 Simple disulfide: pdb=" SG CYS I 175 " - pdb=" SG CYS I 193 " distance=2.05 Simple disulfide: pdb=" SG CYS I 183 " - pdb=" SG CYS I 230 " distance=2.08 Simple disulfide: pdb=" SG CYS I 232 " - pdb=" SG CYS I 237 " distance=2.06 Simple disulfide: pdb=" SG CYS I 278 " - pdb=" SG CYS I 291 " distance=2.08 Simple disulfide: pdb=" SG CYS I 280 " - pdb=" SG CYS I 289 " distance=2.09 Simple disulfide: pdb=" SG CYS I 318 " - pdb=" SG CYS I 337 " distance=2.09 Simple disulfide: pdb=" SG CYS I 421 " - pdb=" SG CYS I 447 " distance=2.16 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.05 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.07 Simple disulfide: pdb=" SG CYS J 92 " - pdb=" SG CYS J 417 " distance=2.02 Simple disulfide: pdb=" SG CYS J 124 " - pdb=" SG CYS J 129 " distance=2.07 Simple disulfide: pdb=" SG CYS J 175 " - pdb=" SG CYS J 193 " distance=2.03 Simple disulfide: pdb=" SG CYS J 183 " - pdb=" SG CYS J 230 " distance=2.09 Simple disulfide: pdb=" SG CYS J 232 " - pdb=" SG CYS J 237 " distance=2.06 Simple disulfide: pdb=" SG CYS J 278 " - pdb=" SG CYS J 291 " distance=2.08 Simple disulfide: pdb=" SG CYS J 280 " - pdb=" SG CYS J 289 " distance=2.09 Simple disulfide: pdb=" SG CYS J 318 " - pdb=" SG CYS J 337 " distance=2.08 Simple disulfide: pdb=" SG CYS J 421 " - pdb=" SG CYS J 447 " distance=2.13 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 3 4 " - " MAN 3 5 " " MAN c 4 " - " MAN c 5 " " MAN k 4 " - " MAN k 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA 3 3 " - " MAN 3 4 " " MAN 3 6 " - " MAN 3 7 " " BMA c 3 " - " MAN c 4 " " MAN c 6 " - " MAN c 7 " " BMA k 3 " - " MAN k 4 " " MAN k 6 " - " MAN k 7 " " BMA s 3 " - " MAN s 4 " " MAN s 6 " - " MAN s 7 " ALPHA1-6 " BMA 3 3 " - " MAN 3 6 " " MAN 3 6 " - " MAN 3 8 " " BMA c 3 " - " MAN c 6 " " MAN c 6 " - " MAN c 8 " " BMA j 3 " - " MAN j 4 " " BMA k 3 " - " MAN k 6 " " MAN k 6 " - " MAN k 8 " " BMA s 3 " - " MAN s 6 " BETA1-4 " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 7 1 " - " NAG 7 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG o 1 " - " NAG o 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 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 w 1 " - " NAG w 2 " BETA1-6 " NAG 4 1 " - " FUC 4 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG 5 1 " - " FUC 5 3 " " NAG d 1 " - " FUC d 4 " " NAG e 1 " - " FUC e 3 " " NAG l 1 " - " FUC l 4 " " NAG m 1 " - " FUC m 3 " " NAG t 1 " - " FUC t 4 " " NAG u 1 " - " FUC u 3 " NAG-ASN " NAG 1 1 " - " ASN J 86 " " NAG 2 1 " - " ASN J 146 " " NAG 3 1 " - " ASN J 200 " " NAG 4 1 " - " ASN J 234 " " NAG 5 1 " - " ASN J 245 " " NAG 7 1 " - " ASN J 367 " " NAG a 1 " - " ASN G 86 " " NAG b 1 " - " ASN G 146 " " NAG c 1 " - " ASN G 200 " " NAG d 1 " - " ASN G 234 " " NAG e 1 " - " ASN G 245 " " NAG g 1 " - " ASN G 367 " " NAG i 1 " - " ASN H 86 " " NAG j 1 " - " ASN H 146 " " NAG k 1 " - " ASN H 200 " " NAG l 1 " - " ASN H 234 " " NAG m 1 " - " ASN H 245 " " NAG o 1 " - " ASN H 367 " " NAG q 1 " - " ASN I 86 " " NAG r 1 " - " ASN I 146 " " NAG s 1 " - " ASN I 200 " " NAG t 1 " - " ASN I 234 " " NAG u 1 " - " ASN I 245 " " NAG w 1 " - " ASN I 367 " Time building additional restraints: 9.59 Conformation dependent library (CDL) restraints added in 4.3 seconds 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4096 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 41 sheets defined 5.0% alpha, 41.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'G' and resid 104 through 110 Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.696A pdb=" N ASN G 146 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 251 Processing helix chain 'A' and resid 27 through 32 removed outlier: 3.711A pdb=" N LYS A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.955A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 110 Processing helix chain 'H' and resid 142 through 146 removed outlier: 3.729A pdb=" N ASN H 146 " --> pdb=" O VAL H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 251 Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.687A pdb=" N LYS B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.985A pdb=" N PHE M 83 " --> pdb=" O SER M 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 110 Processing helix chain 'I' and resid 247 through 251 Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.704A pdb=" N LYS C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.877A pdb=" N PHE N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 110 Processing helix chain 'J' and resid 142 through 146 removed outlier: 3.733A pdb=" N ASN J 146 " --> pdb=" O VAL J 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 96 through 102 removed outlier: 5.422A pdb=" N PHE G 97 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR G 449 " --> pdb=" O PHE G 97 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N CYS G 447 " --> pdb=" O PRO G 99 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ARG G 420 " --> pdb=" O GLY G 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 115 through 124 removed outlier: 4.818A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS G 172 " --> pdb=" O MET G 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 179 through 184 removed outlier: 4.154A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR G 207 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU G 211 " --> pdb=" O TYR G 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 231 through 233 removed outlier: 3.503A pdb=" N VAL G 231 " --> pdb=" O THR G 238 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ILE G 262 " --> pdb=" O GLU G 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 276 through 283 removed outlier: 5.406A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 352 through 356 removed outlier: 4.591A pdb=" N TRP G 352 " --> pdb=" O GLY G 363 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY G 363 " --> pdb=" O TRP G 352 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ASP G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.538A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.517A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.631A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.269A pdb=" N VAL G 396 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY A 50 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.281A pdb=" N PHE A 117 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.763A pdb=" N GLN L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.415A pdb=" N LEU L 33 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 96 through 102 removed outlier: 5.385A pdb=" N PHE H 97 " --> pdb=" O THR H 449 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR H 449 " --> pdb=" O PHE H 97 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N CYS H 447 " --> pdb=" O PRO H 99 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ARG H 420 " --> pdb=" O GLY H 448 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 115 through 124 removed outlier: 4.809A pdb=" N TRP H 115 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR H 138 " --> pdb=" O TRP H 115 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR H 117 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN H 136 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLU H 119 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU H 134 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR H 157 " --> pdb=" O GLY H 135 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU H 158 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS H 172 " --> pdb=" O MET H 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 179 through 184 removed outlier: 4.166A pdb=" N ASP H 197 " --> pdb=" O ASN H 200 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR H 207 " --> pdb=" O LEU H 211 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU H 211 " --> pdb=" O TYR H 207 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 231 through 233 removed outlier: 6.518A pdb=" N GLU H 258 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE H 262 " --> pdb=" O GLU H 258 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 276 through 283 removed outlier: 5.406A pdb=" N GLU H 277 " --> pdb=" O ARG H 292 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ARG H 292 " --> pdb=" O GLU H 277 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 352 through 356 removed outlier: 4.548A pdb=" N TRP H 352 " --> pdb=" O GLY H 363 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY H 363 " --> pdb=" O TRP H 352 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASP H 402 " --> pdb=" O GLY H 373 " (cutoff:3.500A) removed outlier: 9.573A pdb=" N GLU H 375 " --> pdb=" O ARG H 400 " (cutoff:3.500A) removed outlier: 10.453A pdb=" N ARG H 400 " --> pdb=" O GLU H 375 " (cutoff:3.500A) removed outlier: 11.522A pdb=" N PHE H 377 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 13.472A pdb=" N VAL H 398 " --> pdb=" O PHE H 377 " (cutoff:3.500A) removed outlier: 15.564A pdb=" N VAL H 379 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 16.280A pdb=" N VAL H 396 " --> pdb=" O VAL H 379 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AC1, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.313A pdb=" N LEU B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.311A pdb=" N PHE B 117 " --> pdb=" O THR B 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AC4, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.895A pdb=" N GLN M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER M 67 " --> pdb=" O GLN M 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.381A pdb=" N LEU M 33 " --> pdb=" O PHE M 49 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 96 through 102 removed outlier: 5.403A pdb=" N PHE I 97 " --> pdb=" O THR I 449 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR I 449 " --> pdb=" O PHE I 97 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N CYS I 447 " --> pdb=" O PRO I 99 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ARG I 420 " --> pdb=" O GLY I 448 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 115 through 124 removed outlier: 4.818A pdb=" N TRP I 115 " --> pdb=" O THR I 138 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR I 138 " --> pdb=" O TRP I 115 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N THR I 117 " --> pdb=" O GLN I 136 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLN I 136 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLU I 119 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU I 134 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR I 157 " --> pdb=" O GLY I 135 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU I 158 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS I 172 " --> pdb=" O MET I 160 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 179 through 184 removed outlier: 4.108A pdb=" N ASP I 197 " --> pdb=" O ASN I 200 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR I 207 " --> pdb=" O LEU I 211 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LEU I 211 " --> pdb=" O TYR I 207 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 231 through 233 removed outlier: 6.537A pdb=" N GLU I 258 " --> pdb=" O ILE I 262 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ILE I 262 " --> pdb=" O GLU I 258 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 276 through 283 removed outlier: 5.425A pdb=" N GLU I 277 " --> pdb=" O ARG I 292 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ARG I 292 " --> pdb=" O GLU I 277 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 352 through 356 removed outlier: 4.649A pdb=" N TRP I 352 " --> pdb=" O GLY I 363 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY I 363 " --> pdb=" O TRP I 352 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASP I 402 " --> pdb=" O GLY I 373 " (cutoff:3.500A) removed outlier: 9.638A pdb=" N GLU I 375 " --> pdb=" O ARG I 400 " (cutoff:3.500A) removed outlier: 10.472A pdb=" N ARG I 400 " --> pdb=" O GLU I 375 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N PHE I 377 " --> pdb=" O VAL I 398 " (cutoff:3.500A) removed outlier: 13.494A pdb=" N VAL I 398 " --> pdb=" O PHE I 377 " (cutoff:3.500A) removed outlier: 15.354A pdb=" N VAL I 379 " --> pdb=" O VAL I 396 " (cutoff:3.500A) removed outlier: 16.233A pdb=" N VAL I 396 " --> pdb=" O VAL I 379 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AD4, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.332A pdb=" N LEU C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA C 40 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.307A pdb=" N PHE C 117 " --> pdb=" O THR C 98 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AD7, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.685A pdb=" N GLN N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.407A pdb=" N LEU N 33 " --> pdb=" O PHE N 49 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 96 through 102 removed outlier: 5.437A pdb=" N PHE J 97 " --> pdb=" O THR J 449 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N THR J 449 " --> pdb=" O PHE J 97 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N CYS J 447 " --> pdb=" O PRO J 99 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG J 420 " --> pdb=" O GLY J 448 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 115 through 124 removed outlier: 4.779A pdb=" N TRP J 115 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N THR J 138 " --> pdb=" O TRP J 115 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR J 117 " --> pdb=" O GLN J 136 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLN J 136 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLU J 119 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU J 134 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR J 157 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU J 158 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS J 172 " --> pdb=" O MET J 160 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 179 through 184 removed outlier: 4.284A pdb=" N ASP J 197 " --> pdb=" O ASN J 200 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR J 207 " --> pdb=" O LEU J 211 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU J 211 " --> pdb=" O TYR J 207 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 231 through 233 removed outlier: 3.500A pdb=" N VAL J 231 " --> pdb=" O THR J 238 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLU J 258 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ILE J 262 " --> pdb=" O GLU J 258 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 276 through 283 removed outlier: 5.396A pdb=" N GLU J 277 " --> pdb=" O ARG J 292 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ARG J 292 " --> pdb=" O GLU J 277 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 352 through 356 removed outlier: 4.623A pdb=" N TRP J 352 " --> pdb=" O GLY J 363 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY J 363 " --> pdb=" O TRP J 352 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP J 402 " --> pdb=" O GLY J 373 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N GLU J 375 " --> pdb=" O ARG J 400 " (cutoff:3.500A) removed outlier: 10.427A pdb=" N ARG J 400 " --> pdb=" O GLU J 375 " (cutoff:3.500A) removed outlier: 11.500A pdb=" N PHE J 377 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 13.507A pdb=" N VAL J 398 " --> pdb=" O PHE J 377 " (cutoff:3.500A) removed outlier: 15.839A pdb=" N VAL J 379 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 16.338A pdb=" N VAL J 396 " --> pdb=" O VAL J 379 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1542 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: 6.24 Time building geometry restraints manager: 9.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2965 1.30 - 1.44: 5354 1.44 - 1.57: 10597 1.57 - 1.71: 0 1.71 - 1.84: 134 Bond restraints: 19050 Sorted by residual: bond pdb=" C SER G 88 " pdb=" O SER G 88 " ideal model delta sigma weight residual 1.235 1.302 -0.067 1.26e-02 6.30e+03 2.79e+01 bond pdb=" C PRO I 166 " pdb=" O PRO I 166 " ideal model delta sigma weight residual 1.232 1.170 0.062 1.27e-02 6.20e+03 2.40e+01 bond pdb=" C LYS J 249 " pdb=" O LYS J 249 " ideal model delta sigma weight residual 1.233 1.284 -0.050 1.06e-02 8.90e+03 2.24e+01 bond pdb=" N GLY J 286 " pdb=" CA GLY J 286 " ideal model delta sigma weight residual 1.442 1.476 -0.034 7.70e-03 1.69e+04 1.99e+01 bond pdb=" C GLY G 93 " pdb=" O GLY G 93 " ideal model delta sigma weight residual 1.235 1.175 0.060 1.35e-02 5.49e+03 1.99e+01 ... (remaining 19045 not shown) Histogram of bond angle deviations from ideal: 97.73 - 105.25: 343 105.25 - 112.77: 9761 112.77 - 120.29: 8628 120.29 - 127.82: 6921 127.82 - 135.34: 212 Bond angle restraints: 25865 Sorted by residual: angle pdb=" N LYS J 128 " pdb=" CA LYS J 128 " pdb=" CB LYS J 128 " ideal model delta sigma weight residual 111.52 99.83 11.69 1.86e+00 2.89e-01 3.95e+01 angle pdb=" CA ASP G 125 " pdb=" CB ASP G 125 " pdb=" CG ASP G 125 " ideal model delta sigma weight residual 112.60 117.90 -5.30 1.00e+00 1.00e+00 2.81e+01 angle pdb=" N ILE H 397 " pdb=" CA ILE H 397 " pdb=" C ILE H 397 " ideal model delta sigma weight residual 111.81 107.35 4.46 8.60e-01 1.35e+00 2.69e+01 angle pdb=" N ILE I 397 " pdb=" CA ILE I 397 " pdb=" C ILE I 397 " ideal model delta sigma weight residual 111.81 107.37 4.44 8.60e-01 1.35e+00 2.67e+01 angle pdb=" CA ASP J 243 " pdb=" CB ASP J 243 " pdb=" CG ASP J 243 " ideal model delta sigma weight residual 112.60 117.74 -5.14 1.00e+00 1.00e+00 2.64e+01 ... (remaining 25860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.36: 11670 22.36 - 44.72: 496 44.72 - 67.07: 88 67.07 - 89.43: 105 89.43 - 111.79: 65 Dihedral angle restraints: 12424 sinusoidal: 5991 harmonic: 6433 Sorted by residual: dihedral pdb=" CA GLY G 297 " pdb=" C GLY G 297 " pdb=" N SER G 298 " pdb=" CA SER G 298 " ideal model delta harmonic sigma weight residual 180.00 147.27 32.73 0 5.00e+00 4.00e-02 4.29e+01 dihedral pdb=" CA ALA C 40 " pdb=" C ALA C 40 " pdb=" N PRO C 41 " pdb=" CA PRO C 41 " ideal model delta harmonic sigma weight residual -180.00 -147.75 -32.25 0 5.00e+00 4.00e-02 4.16e+01 dihedral pdb=" CA GLY J 297 " pdb=" C GLY J 297 " pdb=" N SER J 298 " pdb=" CA SER J 298 " ideal model delta harmonic sigma weight residual 180.00 148.23 31.77 0 5.00e+00 4.00e-02 4.04e+01 ... (remaining 12421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1860 0.083 - 0.165: 1028 0.165 - 0.248: 200 0.248 - 0.331: 8 0.331 - 0.414: 3 Chirality restraints: 3099 Sorted by residual: chirality pdb=" C1 MAN k 4 " pdb=" O3 BMA k 3 " pdb=" C2 MAN k 4 " pdb=" O5 MAN k 4 " both_signs ideal model delta sigma weight residual False 2.40 2.21 0.19 2.00e-02 2.50e+03 8.56e+01 chirality pdb=" C1 MAN 3 4 " pdb=" O3 BMA 3 3 " pdb=" C2 MAN 3 4 " pdb=" O5 MAN 3 4 " both_signs ideal model delta sigma weight residual False 2.40 2.22 0.18 2.00e-02 2.50e+03 8.38e+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 5.26e+01 ... (remaining 3096 not shown) Planarity restraints: 3213 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG 3 1 " 0.129 2.00e-02 2.50e+03 1.07e-01 1.43e+02 pdb=" C7 NAG 3 1 " -0.059 2.00e-02 2.50e+03 pdb=" C8 NAG 3 1 " 0.105 2.00e-02 2.50e+03 pdb=" N2 NAG 3 1 " -0.161 2.00e-02 2.50e+03 pdb=" O7 NAG 3 1 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG m 2 " 0.104 2.00e-02 2.50e+03 8.57e-02 9.18e+01 pdb=" C7 NAG m 2 " -0.035 2.00e-02 2.50e+03 pdb=" C8 NAG m 2 " 0.081 2.00e-02 2.50e+03 pdb=" N2 NAG m 2 " -0.134 2.00e-02 2.50e+03 pdb=" O7 NAG m 2 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG s 1 " -0.087 2.00e-02 2.50e+03 7.36e-02 6.77e+01 pdb=" C7 NAG s 1 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG s 1 " -0.077 2.00e-02 2.50e+03 pdb=" N2 NAG s 1 " 0.102 2.00e-02 2.50e+03 pdb=" O7 NAG s 1 " 0.006 2.00e-02 2.50e+03 ... (remaining 3210 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1034 2.74 - 3.28: 18576 3.28 - 3.82: 31170 3.82 - 4.36: 43610 4.36 - 4.90: 69557 Nonbonded interactions: 163947 Sorted by model distance: nonbonded pdb=" O HIS I 347 " pdb="CA CA I2000 " model vdw 2.196 2.510 nonbonded pdb=" OD2 ASP J 324 " pdb="CA CA J2000 " model vdw 2.230 2.510 nonbonded pdb=" O HIS H 347 " pdb="CA CA H2000 " model vdw 2.242 2.510 nonbonded pdb=" O HIS J 347 " pdb="CA CA J2000 " model vdw 2.272 2.510 nonbonded pdb=" OD2 ASP G 324 " pdb="CA CA G 501 " model vdw 2.291 2.510 ... (remaining 163942 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 '1' and resid 1 through 2) selection = (chain '2' and resid 1 through 2) selection = (chain '5' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'q' and resid 1 through 2) selection = (chain 'r' and resid 1 through 2) selection = (chain 'u' and resid 1 through 2) } ncs_group { reference = (chain '3' and (resid 2 or resid 5 through 8)) selection = (chain 'c' and (resid 2 or resid 5 through 8)) selection = (chain 'k' and (resid 2 or resid 5 through 8)) selection = (chain 's' and (resid 1 or resid 4 through 7)) } ncs_group { reference = (chain '4' and resid 1 through 3) selection = (chain 'd' and resid 1 through 3) selection = (chain 'j' and resid 1 through 3) selection = (chain 'l' and resid 1 through 3) selection = (chain 't' and resid 1 through 3) } ncs_group { reference = chain '7' selection = chain 'g' selection = chain 'o' selection = chain 'w' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'G' and (resid 82 through 469 or resid 501)) selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 14.310 Check model and map are aligned: 0.240 Set scattering table: 0.170 Process input model: 52.430 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 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 0.069 19050 Z= 0.955 Angle : 1.658 11.686 25865 Z= 1.064 Chirality : 0.093 0.414 3099 Planarity : 0.011 0.107 3189 Dihedral : 17.440 111.790 8202 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.37 % Favored : 95.32 % Rotamer: Outliers : 0.42 % Allowed : 3.01 % Favored : 96.57 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 1.23 % Twisted General : 0.18 % 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 (0.17), residues: 2243 helix: -1.44 (0.89), residues: 24 sheet: 0.23 (0.17), residues: 893 loop : -1.01 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.014 TRP G 115 HIS 0.040 0.008 HIS J 336 PHE 0.073 0.012 PHE I 205 TYR 0.076 0.014 TYR I 281 ARG 0.028 0.004 ARG H 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 261 time to evaluate : 2.174 Fit side-chains REVERT: G 400 ARG cc_start: 0.8857 (ptm-80) cc_final: 0.8517 (ptm-80) REVERT: L 75 ILE cc_start: 0.9297 (mt) cc_final: 0.8991 (mt) REVERT: L 101 GLN cc_start: 0.9163 (mm110) cc_final: 0.8800 (pm20) REVERT: H 356 ASP cc_start: 0.8842 (t0) cc_final: 0.8520 (t0) REVERT: H 400 ARG cc_start: 0.8699 (ptm-80) cc_final: 0.8127 (ptp90) REVERT: B 62 GLN cc_start: 0.8814 (mp10) cc_final: 0.8548 (mp10) REVERT: B 63 LYS cc_start: 0.9152 (ptmt) cc_final: 0.8947 (ptpp) REVERT: B 65 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8027 (mt0) REVERT: M 69 THR cc_start: 0.9249 (p) cc_final: 0.8991 (p) REVERT: M 74 THR cc_start: 0.9097 (m) cc_final: 0.8820 (t) REVERT: M 80 SER cc_start: 0.8998 (m) cc_final: 0.8744 (p) REVERT: M 82 ASP cc_start: 0.8971 (m-30) cc_final: 0.8736 (m-30) REVERT: I 465 ASN cc_start: 0.8976 (m-40) cc_final: 0.8542 (t0) REVERT: J 83 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8366 (tt0) REVERT: J 249 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8077 (tmmt) REVERT: J 400 ARG cc_start: 0.8960 (ptm-80) cc_final: 0.8594 (ptm160) outliers start: 8 outliers final: 5 residues processed: 267 average time/residue: 1.2806 time to fit residues: 386.8017 Evaluate side-chains 218 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 213 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 178 TRP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain H residue 178 TRP Chi-restraints excluded: chain I residue 178 TRP Chi-restraints excluded: chain J residue 178 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 0.2980 chunk 127 optimal weight: 0.8980 chunk 197 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 141 ASN B 6 GLN M 32 ASN M 79 GLN M 92 ASN I 274 HIS I 468 HIS J 465 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19050 Z= 0.187 Angle : 0.685 7.373 25865 Z= 0.349 Chirality : 0.049 0.299 3099 Planarity : 0.004 0.037 3189 Dihedral : 12.521 75.328 4297 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.90 % Favored : 96.92 % Rotamer: Outliers : 1.35 % Allowed : 8.46 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % 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: -0.13 (0.17), residues: 2243 helix: -0.41 (0.84), residues: 24 sheet: 0.33 (0.17), residues: 889 loop : -0.33 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 115 HIS 0.007 0.001 HIS I 336 PHE 0.015 0.002 PHE H 410 TYR 0.016 0.002 TYR L 91 ARG 0.010 0.001 ARG M 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 246 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8790 (ptm-80) cc_final: 0.8512 (ptm160) REVERT: L 75 ILE cc_start: 0.9146 (mt) cc_final: 0.8873 (mt) REVERT: L 101 GLN cc_start: 0.9206 (mm110) cc_final: 0.8797 (pm20) REVERT: H 356 ASP cc_start: 0.8837 (t0) cc_final: 0.8612 (t0) REVERT: H 400 ARG cc_start: 0.8654 (ptm-80) cc_final: 0.8063 (ptp90) REVERT: B 63 LYS cc_start: 0.9092 (ptmt) cc_final: 0.8881 (ptpp) REVERT: M 18 ARG cc_start: 0.8838 (mtp-110) cc_final: 0.8379 (ttm170) REVERT: M 20 THR cc_start: 0.8860 (p) cc_final: 0.8477 (t) REVERT: M 61 ARG cc_start: 0.8533 (ptt90) cc_final: 0.8213 (ptt90) REVERT: M 82 ASP cc_start: 0.8786 (m-30) cc_final: 0.8284 (m-30) REVERT: I 465 ASN cc_start: 0.8939 (m-40) cc_final: 0.8569 (t0) REVERT: J 227 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8355 (mp0) REVERT: J 249 LYS cc_start: 0.8484 (ttpt) cc_final: 0.7937 (tmmt) REVERT: J 400 ARG cc_start: 0.8887 (ptm-80) cc_final: 0.8477 (ptm160) outliers start: 26 outliers final: 9 residues processed: 255 average time/residue: 1.3068 time to fit residues: 374.9917 Evaluate side-chains 216 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 207 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain J residue 230 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 110 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 196 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 347 HIS A 3 GLN H 141 ASN ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN M 38 GLN M 42 GLN I 142 ASN I 347 HIS I 468 HIS N 38 GLN J 465 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 19050 Z= 0.286 Angle : 0.676 14.031 25865 Z= 0.339 Chirality : 0.049 0.292 3099 Planarity : 0.004 0.038 3189 Dihedral : 9.556 66.802 4288 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.34 % Favored : 96.48 % Rotamer: Outliers : 2.49 % Allowed : 10.28 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % 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: -0.13 (0.17), residues: 2243 helix: 0.71 (1.02), residues: 24 sheet: 0.21 (0.17), residues: 895 loop : -0.24 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 115 HIS 0.007 0.001 HIS J 336 PHE 0.015 0.002 PHE G 410 TYR 0.022 0.002 TYR G 121 ARG 0.006 0.000 ARG J 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 211 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8816 (ptm-80) cc_final: 0.8530 (ptm160) REVERT: G 432 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8960 (mp0) REVERT: L 27 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7568 (mtp85) REVERT: L 101 GLN cc_start: 0.9234 (mm110) cc_final: 0.8792 (pm20) REVERT: H 230 CYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8129 (p) REVERT: H 400 ARG cc_start: 0.8678 (ptm-80) cc_final: 0.8077 (ptp90) REVERT: B 3 GLN cc_start: 0.8750 (mm110) cc_final: 0.8356 (mm110) REVERT: B 62 GLN cc_start: 0.8501 (mp10) cc_final: 0.7769 (tp-100) REVERT: B 65 GLN cc_start: 0.8869 (tp40) cc_final: 0.8639 (tp40) REVERT: M 61 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8088 (ptt90) REVERT: M 82 ASP cc_start: 0.8833 (m-30) cc_final: 0.8357 (m-30) REVERT: I 141 ASN cc_start: 0.8988 (OUTLIER) cc_final: 0.8733 (t0) REVERT: I 465 ASN cc_start: 0.8958 (m-40) cc_final: 0.8605 (t0) REVERT: J 141 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8587 (t0) REVERT: J 227 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8380 (mp0) REVERT: J 249 LYS cc_start: 0.8532 (ttpt) cc_final: 0.7953 (tmmt) REVERT: J 400 ARG cc_start: 0.8912 (ptm-80) cc_final: 0.8507 (ptm160) outliers start: 48 outliers final: 18 residues processed: 230 average time/residue: 1.3051 time to fit residues: 338.4125 Evaluate side-chains 218 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 196 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 319 SER Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain I residue 442 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain J residue 141 ASN Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 465 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 195 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 210 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 188 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 274 HIS A 3 GLN L 90 HIS H 142 ASN I 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19050 Z= 0.204 Angle : 0.612 10.987 25865 Z= 0.308 Chirality : 0.046 0.281 3099 Planarity : 0.003 0.040 3189 Dihedral : 8.011 60.461 4288 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.85 % Favored : 96.97 % Rotamer: Outliers : 1.87 % Allowed : 11.31 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % 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: 2243 helix: -0.30 (0.93), residues: 28 sheet: 0.23 (0.17), residues: 895 loop : -0.22 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 178 HIS 0.005 0.001 HIS J 336 PHE 0.014 0.002 PHE H 410 TYR 0.015 0.001 TYR C 32 ARG 0.009 0.000 ARG M 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 206 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8793 (ptm-80) cc_final: 0.8521 (ptm160) REVERT: G 431 LYS cc_start: 0.9287 (tppt) cc_final: 0.8935 (ptpt) REVERT: G 432 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8897 (mp0) REVERT: L 27 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7607 (mtp85) REVERT: L 101 GLN cc_start: 0.9242 (mm110) cc_final: 0.8765 (pm20) REVERT: H 400 ARG cc_start: 0.8593 (ptm-80) cc_final: 0.8017 (ptp90) REVERT: B 3 GLN cc_start: 0.8754 (mm110) cc_final: 0.8363 (mm110) REVERT: M 18 ARG cc_start: 0.8622 (mtp-110) cc_final: 0.8123 (ttm170) REVERT: M 61 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8238 (ptt90) REVERT: M 82 ASP cc_start: 0.8810 (m-30) cc_final: 0.8373 (m-30) REVERT: I 141 ASN cc_start: 0.9032 (OUTLIER) cc_final: 0.8778 (t0) REVERT: I 465 ASN cc_start: 0.8942 (m-40) cc_final: 0.8599 (t0) REVERT: J 249 LYS cc_start: 0.8584 (ttpt) cc_final: 0.7999 (tmmt) REVERT: J 400 ARG cc_start: 0.8890 (ptm-80) cc_final: 0.8504 (ptm160) outliers start: 36 outliers final: 17 residues processed: 224 average time/residue: 1.2988 time to fit residues: 327.7824 Evaluate side-chains 213 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 194 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain J residue 230 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 175 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 189 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN L 90 HIS H 273 GLN M 70 GLN I 142 ASN N 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 19050 Z= 0.365 Angle : 0.660 12.517 25865 Z= 0.332 Chirality : 0.048 0.254 3099 Planarity : 0.004 0.043 3189 Dihedral : 7.952 64.710 4288 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.48 % Favored : 96.34 % Rotamer: Outliers : 2.75 % Allowed : 11.31 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.18 (0.17), residues: 2243 helix: 0.84 (1.04), residues: 24 sheet: 0.16 (0.18), residues: 855 loop : -0.26 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 178 HIS 0.004 0.001 HIS G 191 PHE 0.016 0.002 PHE G 410 TYR 0.022 0.002 TYR G 121 ARG 0.011 0.000 ARG J 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 193 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8883 (ptm-80) cc_final: 0.8601 (ptm-80) REVERT: G 431 LYS cc_start: 0.9250 (tppt) cc_final: 0.8919 (ptpt) REVERT: G 432 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8910 (mp0) REVERT: L 101 GLN cc_start: 0.9302 (mm110) cc_final: 0.8778 (pm20) REVERT: H 400 ARG cc_start: 0.8587 (ptm-80) cc_final: 0.7974 (ptp90) REVERT: B 3 GLN cc_start: 0.8796 (mm110) cc_final: 0.8395 (mm110) REVERT: M 18 ARG cc_start: 0.8576 (mtp-110) cc_final: 0.8192 (ttm170) REVERT: M 61 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8155 (ptt90) REVERT: M 82 ASP cc_start: 0.8683 (m-30) cc_final: 0.8250 (m-30) REVERT: I 141 ASN cc_start: 0.9004 (OUTLIER) cc_final: 0.8772 (t0) REVERT: I 465 ASN cc_start: 0.8958 (m-40) cc_final: 0.8584 (t0) REVERT: C 62 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8260 (tp-100) REVERT: N 106 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7917 (tp30) REVERT: J 141 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8673 (t0) REVERT: J 249 LYS cc_start: 0.8582 (ttpt) cc_final: 0.7984 (tmmt) REVERT: J 400 ARG cc_start: 0.8933 (ptm-80) cc_final: 0.8530 (ptm160) outliers start: 53 outliers final: 31 residues processed: 218 average time/residue: 1.3107 time to fit residues: 323.4921 Evaluate side-chains 224 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 189 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 362 MET Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain J residue 141 ASN Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 465 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 70 optimal weight: 1.9990 chunk 189 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 110 optimal weight: 0.0870 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN L 90 HIS M 70 GLN I 468 HIS ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19050 Z= 0.217 Angle : 0.598 12.625 25865 Z= 0.301 Chirality : 0.045 0.268 3099 Planarity : 0.003 0.043 3189 Dihedral : 7.330 58.245 4288 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.99 % Favored : 96.83 % Rotamer: Outliers : 2.54 % Allowed : 12.09 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % 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: -0.16 (0.17), residues: 2243 helix: -0.17 (0.97), residues: 28 sheet: 0.14 (0.17), residues: 907 loop : -0.21 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 178 HIS 0.004 0.001 HIS I 274 PHE 0.014 0.002 PHE H 410 TYR 0.016 0.001 TYR C 32 ARG 0.012 0.000 ARG J 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 198 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8824 (ptm-80) cc_final: 0.8549 (ptm-80) REVERT: G 431 LYS cc_start: 0.9258 (tppt) cc_final: 0.8938 (ptpt) REVERT: G 432 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8918 (mp0) REVERT: L 101 GLN cc_start: 0.9283 (mm110) cc_final: 0.8774 (pm20) REVERT: H 400 ARG cc_start: 0.8573 (ptm-80) cc_final: 0.7963 (ptp90) REVERT: B 3 GLN cc_start: 0.8816 (mm110) cc_final: 0.8557 (mm110) REVERT: B 65 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8489 (tt0) REVERT: M 18 ARG cc_start: 0.8519 (mtp-110) cc_final: 0.8108 (ttm170) REVERT: M 61 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8126 (ptt-90) REVERT: I 465 ASN cc_start: 0.8940 (m-40) cc_final: 0.8580 (t0) REVERT: N 81 GLU cc_start: 0.8909 (pt0) cc_final: 0.8400 (pm20) REVERT: N 106 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7953 (tp30) REVERT: J 249 LYS cc_start: 0.8569 (ttpt) cc_final: 0.7983 (tmmt) REVERT: J 400 ARG cc_start: 0.8897 (ptm-80) cc_final: 0.8511 (ptm160) outliers start: 49 outliers final: 28 residues processed: 222 average time/residue: 1.2642 time to fit residues: 316.9464 Evaluate side-chains 219 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 190 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 337 CYS Chi-restraints excluded: chain H residue 362 MET Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain J residue 230 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 210 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN L 90 HIS H 142 ASN M 6 GLN M 70 GLN I 142 ASN I 274 HIS J 465 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19050 Z= 0.255 Angle : 0.613 12.676 25865 Z= 0.306 Chirality : 0.046 0.257 3099 Planarity : 0.003 0.044 3189 Dihedral : 7.204 57.578 4288 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.30 % Favored : 96.52 % Rotamer: Outliers : 2.65 % Allowed : 12.51 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % 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: -0.16 (0.17), residues: 2243 helix: -0.10 (0.98), residues: 28 sheet: 0.11 (0.17), residues: 881 loop : -0.16 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 178 HIS 0.004 0.001 HIS H 336 PHE 0.014 0.002 PHE H 410 TYR 0.017 0.001 TYR G 121 ARG 0.012 0.000 ARG J 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 191 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8843 (ptm-80) cc_final: 0.8567 (ptm-80) REVERT: G 431 LYS cc_start: 0.9254 (tppt) cc_final: 0.8930 (ptpt) REVERT: G 432 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8880 (mp0) REVERT: L 101 GLN cc_start: 0.9255 (mm110) cc_final: 0.8763 (pm20) REVERT: H 400 ARG cc_start: 0.8560 (ptm-80) cc_final: 0.7943 (ptp90) REVERT: B 3 GLN cc_start: 0.8816 (mm110) cc_final: 0.8555 (mm110) REVERT: B 65 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8450 (tt0) REVERT: M 61 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8299 (ptt90) REVERT: M 82 ASP cc_start: 0.8508 (m-30) cc_final: 0.8100 (m-30) REVERT: I 465 ASN cc_start: 0.8944 (m-40) cc_final: 0.8587 (t0) REVERT: N 81 GLU cc_start: 0.8949 (pt0) cc_final: 0.8505 (pm20) REVERT: N 106 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7865 (tp30) REVERT: J 141 ASN cc_start: 0.8886 (OUTLIER) cc_final: 0.8650 (t0) REVERT: J 249 LYS cc_start: 0.8579 (ttpt) cc_final: 0.7987 (tmmt) REVERT: J 400 ARG cc_start: 0.8913 (ptm-80) cc_final: 0.8527 (ptm160) outliers start: 51 outliers final: 27 residues processed: 219 average time/residue: 1.2723 time to fit residues: 314.7710 Evaluate side-chains 217 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 188 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 362 MET Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain J residue 141 ASN Chi-restraints excluded: chain J residue 230 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 3.9990 chunk 83 optimal weight: 0.0050 chunk 125 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN L 90 HIS C 62 GLN J 465 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19050 Z= 0.169 Angle : 0.584 12.655 25865 Z= 0.292 Chirality : 0.045 0.263 3099 Planarity : 0.003 0.047 3189 Dihedral : 6.714 50.878 4288 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.81 % Favored : 96.97 % Rotamer: Outliers : 1.82 % Allowed : 13.60 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.10 (0.17), residues: 2243 helix: -0.10 (0.96), residues: 28 sheet: 0.13 (0.17), residues: 909 loop : -0.11 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 178 HIS 0.002 0.001 HIS I 274 PHE 0.013 0.001 PHE H 410 TYR 0.016 0.001 TYR C 32 ARG 0.014 0.000 ARG M 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 207 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8809 (ptm-80) cc_final: 0.8479 (ptm160) REVERT: G 431 LYS cc_start: 0.9248 (tppt) cc_final: 0.8932 (ptpt) REVERT: G 432 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8874 (mp0) REVERT: G 467 MET cc_start: 0.8933 (ptm) cc_final: 0.8529 (ptm) REVERT: L 27 ARG cc_start: 0.7942 (ttp80) cc_final: 0.7578 (mtp85) REVERT: L 101 GLN cc_start: 0.9227 (mm110) cc_final: 0.8738 (pm20) REVERT: H 400 ARG cc_start: 0.8486 (ptm-80) cc_final: 0.7879 (ptp90) REVERT: B 3 GLN cc_start: 0.8829 (mm110) cc_final: 0.8576 (mm110) REVERT: M 18 ARG cc_start: 0.8457 (mtp-110) cc_final: 0.8000 (ttm170) REVERT: M 61 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8152 (ptt-90) REVERT: M 82 ASP cc_start: 0.8517 (m-30) cc_final: 0.8316 (m-30) REVERT: I 465 ASN cc_start: 0.8931 (m-40) cc_final: 0.8580 (t0) REVERT: N 81 GLU cc_start: 0.8982 (pt0) cc_final: 0.8539 (pm20) REVERT: N 106 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7832 (tp30) REVERT: J 249 LYS cc_start: 0.8565 (ttpt) cc_final: 0.7968 (tmmt) REVERT: J 400 ARG cc_start: 0.8901 (ptm-80) cc_final: 0.8516 (ptm160) outliers start: 35 outliers final: 25 residues processed: 229 average time/residue: 1.2660 time to fit residues: 328.2702 Evaluate side-chains 222 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 196 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain J residue 230 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 191 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 185 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN L 90 HIS H 141 ASN I 274 HIS C 62 GLN J 465 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19050 Z= 0.275 Angle : 0.617 12.521 25865 Z= 0.309 Chirality : 0.046 0.256 3099 Planarity : 0.004 0.051 3189 Dihedral : 6.921 53.990 4288 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.43 % Favored : 96.34 % Rotamer: Outliers : 1.76 % Allowed : 14.27 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % 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: -0.10 (0.18), residues: 2243 helix: -0.05 (0.99), residues: 28 sheet: 0.11 (0.17), residues: 881 loop : -0.10 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 178 HIS 0.003 0.001 HIS I 274 PHE 0.014 0.002 PHE H 410 TYR 0.018 0.001 TYR G 121 ARG 0.013 0.000 ARG J 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 195 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8845 (ptm-80) cc_final: 0.8512 (ptm160) REVERT: G 431 LYS cc_start: 0.9239 (tppt) cc_final: 0.8931 (ptpt) REVERT: G 432 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8870 (mp0) REVERT: G 467 MET cc_start: 0.8964 (ptm) cc_final: 0.8562 (ptm) REVERT: L 101 GLN cc_start: 0.9242 (mm110) cc_final: 0.8725 (pm20) REVERT: H 400 ARG cc_start: 0.8498 (ptm-80) cc_final: 0.7884 (ptp90) REVERT: B 3 GLN cc_start: 0.8838 (mm110) cc_final: 0.8583 (mm110) REVERT: M 18 ARG cc_start: 0.8464 (mtp-110) cc_final: 0.8048 (ttm170) REVERT: M 61 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8047 (ptt-90) REVERT: I 465 ASN cc_start: 0.8941 (m-40) cc_final: 0.8607 (t0) REVERT: N 106 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7817 (tp30) REVERT: J 249 LYS cc_start: 0.8571 (ttpt) cc_final: 0.7980 (tmmt) REVERT: J 400 ARG cc_start: 0.8915 (ptm-80) cc_final: 0.8533 (ptm160) outliers start: 34 outliers final: 27 residues processed: 215 average time/residue: 1.2819 time to fit residues: 311.6453 Evaluate side-chains 217 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 189 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 90 HIS Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain J residue 230 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 137 optimal weight: 0.6980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN L 90 HIS H 141 ASN H 142 ASN H 274 HIS I 274 HIS C 62 GLN J 465 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19050 Z= 0.310 Angle : 0.629 12.599 25865 Z= 0.316 Chirality : 0.046 0.263 3099 Planarity : 0.004 0.053 3189 Dihedral : 7.033 55.615 4288 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.48 % Favored : 96.30 % Rotamer: Outliers : 1.61 % Allowed : 14.48 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % 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: -0.16 (0.18), residues: 2243 helix: -0.04 (1.00), residues: 28 sheet: 0.08 (0.17), residues: 881 loop : -0.15 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 178 HIS 0.009 0.001 HIS L 90 PHE 0.015 0.002 PHE H 410 TYR 0.019 0.002 TYR C 32 ARG 0.013 0.000 ARG J 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 195 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8881 (ptm-80) cc_final: 0.8605 (ptm-80) REVERT: G 431 LYS cc_start: 0.9236 (tppt) cc_final: 0.8928 (ptpt) REVERT: G 432 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8887 (mp0) REVERT: G 467 MET cc_start: 0.8976 (ptm) cc_final: 0.8560 (ptm) REVERT: L 101 GLN cc_start: 0.9244 (mm110) cc_final: 0.8724 (pm20) REVERT: H 400 ARG cc_start: 0.8536 (ptm-80) cc_final: 0.7916 (ptp90) REVERT: B 3 GLN cc_start: 0.8830 (mm110) cc_final: 0.8572 (mm110) REVERT: B 62 GLN cc_start: 0.8267 (mp10) cc_final: 0.7665 (tp-100) REVERT: M 18 ARG cc_start: 0.8451 (mtp-110) cc_final: 0.8011 (ttm170) REVERT: M 61 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8033 (ptt-90) REVERT: I 465 ASN cc_start: 0.8934 (m-40) cc_final: 0.8584 (t0) REVERT: N 106 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7800 (tp30) REVERT: J 249 LYS cc_start: 0.8555 (ttpt) cc_final: 0.7974 (tmmt) REVERT: J 400 ARG cc_start: 0.8930 (ptm-80) cc_final: 0.8533 (ptm160) outliers start: 31 outliers final: 26 residues processed: 214 average time/residue: 1.3004 time to fit residues: 314.1813 Evaluate side-chains 218 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 191 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 441 ASN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain J residue 230 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 152 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN L 90 HIS H 141 ASN I 468 HIS C 62 GLN J 465 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.097308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.074484 restraints weight = 31660.519| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.52 r_work: 0.2802 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19050 Z= 0.182 Angle : 0.591 12.493 25865 Z= 0.294 Chirality : 0.045 0.240 3099 Planarity : 0.003 0.053 3189 Dihedral : 6.615 49.331 4288 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.03 % Favored : 96.75 % Rotamer: Outliers : 1.71 % Allowed : 14.48 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % 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: -0.07 (0.18), residues: 2243 helix: -0.10 (0.97), residues: 28 sheet: 0.13 (0.18), residues: 881 loop : -0.08 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 178 HIS 0.003 0.001 HIS I 468 PHE 0.012 0.001 PHE H 410 TYR 0.013 0.001 TYR G 121 ARG 0.013 0.000 ARG J 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6143.49 seconds wall clock time: 111 minutes 12.32 seconds (6672.32 seconds total)