Starting phenix.real_space_refine on Wed Apr 10 17:25:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3v_29710/04_2024/8g3v_29710.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3v_29710/04_2024/8g3v_29710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3v_29710/04_2024/8g3v_29710.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3v_29710/04_2024/8g3v_29710.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3v_29710/04_2024/8g3v_29710.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3v_29710/04_2024/8g3v_29710.pdb" } resolution = 2.2 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= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 116 5.16 5 C 12484 2.51 5 N 3416 2.21 5 O 4024 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 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 "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 "I ARG 85": "NH1" <-> "NH2" 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 "J ARG 85": "NH1" <-> "NH2" Residue "J ARG 107": "NH1" <-> "NH2" Residue "J ARG 118": "NH1" <-> "NH2" 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" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 87": "NH1" <-> "NH2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "O ARG 18": "NH1" <-> "NH2" Residue "O ARG 24": "NH1" <-> "NH2" Residue "O ARG 27": "NH1" <-> "NH2" Residue "O ARG 45": "NH1" <-> "NH2" Residue "O ARG 54": "NH1" <-> "NH2" Residue "O ARG 61": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 20045 Number of models: 1 Model: "" Number of chains: 28 Chain: "G" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 375} 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: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 375} 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: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 375} 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: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 375} Chain: "D" 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: "O" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.10, per 1000 atoms: 0.55 Number of scatterers: 20045 At special positions: 0 Unit cell: (131.97, 131.97, 102.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 116 16.00 O 4024 8.00 N 3416 7.00 C 12484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, 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=2.03 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=2.11 Simple disulfide: pdb=" SG CYS G 278 " - pdb=" SG CYS G 291 " distance=2.11 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 289 " distance=2.10 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.10 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 447 " distance=2.15 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.06 Simple disulfide: pdb=" SG CYS H 92 " - pdb=" SG CYS H 417 " distance=2.06 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=2.07 Simple disulfide: pdb=" SG CYS H 232 " - pdb=" SG CYS H 237 " distance=2.11 Simple disulfide: pdb=" SG CYS H 278 " - pdb=" SG CYS H 291 " distance=2.11 Simple disulfide: pdb=" SG CYS H 280 " - pdb=" SG CYS H 289 " distance=2.10 Simple disulfide: pdb=" SG CYS H 318 " - pdb=" SG CYS H 337 " distance=2.10 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=2.05 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.07 Simple disulfide: pdb=" SG CYS I 92 " - pdb=" SG CYS I 417 " distance=2.06 Simple disulfide: pdb=" SG CYS I 124 " - pdb=" SG CYS I 129 " distance=2.07 Simple disulfide: pdb=" SG CYS I 175 " - pdb=" SG CYS I 193 " distance=2.03 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=2.11 Simple disulfide: pdb=" SG CYS I 278 " - pdb=" SG CYS I 291 " distance=2.11 Simple disulfide: pdb=" SG CYS I 280 " - pdb=" SG CYS I 289 " distance=2.10 Simple disulfide: pdb=" SG CYS I 318 " - pdb=" SG CYS I 337 " distance=2.10 Simple disulfide: pdb=" SG CYS I 421 " - pdb=" SG CYS I 447 " distance=2.15 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=2.06 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=2.08 Simple disulfide: pdb=" SG CYS J 232 " - pdb=" SG CYS J 237 " distance=2.11 Simple disulfide: pdb=" SG CYS J 278 " - pdb=" SG CYS J 291 " distance=2.11 Simple disulfide: pdb=" SG CYS J 280 " - pdb=" SG CYS J 289 " distance=2.10 Simple disulfide: pdb=" SG CYS J 318 " - pdb=" SG CYS J 337 " distance=2.10 Simple disulfide: pdb=" SG CYS J 421 " - pdb=" SG CYS J 447 " distance=2.15 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.05 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.06 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 F 4 " - " MAN F 5 " " MAN Q 4 " - " MAN Q 5 " " MAN T 4 " - " MAN T 5 " " MAN W 4 " - " MAN W 5 " ALPHA1-3 " BMA F 3 " - " MAN F 4 " " MAN F 6 " - " MAN F 7 " " BMA Q 3 " - " MAN Q 4 " " MAN Q 6 " - " MAN Q 7 " " BMA T 3 " - " MAN T 4 " " MAN T 6 " - " MAN T 7 " " BMA W 3 " - " MAN W 4 " " MAN W 6 " - " MAN W 7 " ALPHA1-6 " BMA F 3 " - " MAN F 6 " " MAN F 6 " - " MAN F 8 " " BMA Q 3 " - " MAN Q 6 " " MAN Q 6 " - " MAN Q 8 " " BMA T 3 " - " MAN T 6 " " MAN T 6 " - " MAN T 8 " " BMA W 3 " - " MAN W 6 " " MAN W 6 " - " MAN W 8 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG K 1 " - " NAG K 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG E 1 " - " ASN G 86 " " NAG F 1 " - " ASN G 200 " " NAG G1101 " - " ASN G 146 " " NAG G1102 " - " ASN G 367 " " NAG H1101 " - " ASN H 146 " " NAG H1102 " - " ASN H 367 " " NAG I1101 " - " ASN I 146 " " NAG I1102 " - " ASN I 367 " " NAG J1101 " - " ASN J 146 " " NAG J1102 " - " ASN J 367 " " NAG K 1 " - " ASN G 234 " " NAG P 1 " - " ASN H 86 " " NAG Q 1 " - " ASN H 200 " " NAG R 1 " - " ASN H 234 " " NAG S 1 " - " ASN I 86 " " NAG T 1 " - " ASN I 200 " " NAG U 1 " - " ASN I 234 " " NAG V 1 " - " ASN J 86 " " NAG W 1 " - " ASN J 200 " " NAG X 1 " - " ASN J 234 " Time building additional restraints: 9.20 Conformation dependent library (CDL) restraints added in 3.3 seconds 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 48 sheets defined 5.1% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'G' and resid 104 through 110 Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.690A pdb=" N ASN G 146 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 32 removed outlier: 3.560A pdb=" N LYS A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.658A 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: 3.691A pdb=" N ASN H 146 " --> pdb=" O VAL H 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.558A 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: 3.659A 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 142 through 146 removed outlier: 3.689A pdb=" N ASN I 146 " --> pdb=" O VAL I 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.561A 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: 3.658A 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: 3.679A pdb=" N ASN J 146 " --> pdb=" O VAL J 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.561A pdb=" N LYS D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.658A pdb=" N PHE O 83 " --> pdb=" O SER O 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 96 through 102 removed outlier: 3.802A pdb=" N GLY G 96 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL G 445 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS G 102 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE G 443 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 5.881A 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: 4.796A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 3.985A 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: 4.116A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP G 213 " --> pdb=" O PHE G 205 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR G 207 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 5.327A 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: 6.527A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.417A 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: 5.381A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 353 through 356 removed outlier: 7.082A pdb=" N ASP G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.439A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.497A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.487A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.241A 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: 6.249A pdb=" N LEU A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY A 50 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A 40 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.391A pdb=" N PHE A 117 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.849A pdb=" N GLN L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER L 67 " --> pdb=" O GLN L 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.474A pdb=" N LEU L 33 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 96 through 102 removed outlier: 3.804A pdb=" N GLY H 96 " --> pdb=" O THR H 449 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL H 445 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS H 102 " --> pdb=" O ILE H 443 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE H 443 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG H 420 " --> pdb=" O GLY H 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 115 through 124 removed outlier: 4.797A pdb=" N TRP H 115 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR H 138 " --> pdb=" O TRP H 115 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N THR H 117 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN H 136 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU H 119 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU H 134 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR H 157 " --> pdb=" O GLY H 135 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU H 158 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS H 172 " --> pdb=" O MET H 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 179 through 184 removed outlier: 4.121A pdb=" N ASP H 197 " --> pdb=" O ASN H 200 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP H 213 " --> pdb=" O PHE H 205 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TYR H 207 " --> pdb=" O LEU H 211 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU H 211 " --> pdb=" O TYR H 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 231 through 233 removed outlier: 6.524A pdb=" N GLU H 258 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE H 262 " --> pdb=" O GLU H 258 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 276 through 283 removed outlier: 5.381A pdb=" N GLU H 277 " --> pdb=" O ARG H 292 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG H 292 " --> pdb=" O GLU H 277 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 353 through 356 removed outlier: 7.085A pdb=" N ASP H 402 " --> pdb=" O GLY H 373 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N GLU H 375 " --> pdb=" O ARG H 400 " (cutoff:3.500A) removed outlier: 10.428A pdb=" N ARG H 400 " --> pdb=" O GLU H 375 " (cutoff:3.500A) removed outlier: 11.418A pdb=" N PHE H 377 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 13.500A pdb=" N VAL H 398 " --> pdb=" O PHE H 377 " (cutoff:3.500A) removed outlier: 15.525A pdb=" N VAL H 379 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 16.245A pdb=" N VAL H 396 " --> pdb=" O VAL H 379 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AC2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.252A pdb=" N LEU B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA B 40 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.391A pdb=" N PHE B 117 " --> pdb=" O THR B 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AC5, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.849A pdb=" N GLN M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER M 67 " --> pdb=" O GLN M 70 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.475A pdb=" N LEU M 33 " --> pdb=" O PHE M 49 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 96 through 102 removed outlier: 3.801A pdb=" N GLY I 96 " --> pdb=" O THR I 449 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL I 445 " --> pdb=" O PHE I 100 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS I 102 " --> pdb=" O ILE I 443 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE I 443 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG I 420 " --> pdb=" O GLY I 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 115 through 124 removed outlier: 4.795A pdb=" N TRP I 115 " --> pdb=" O THR I 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR I 138 " --> pdb=" O TRP I 115 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR I 117 " --> pdb=" O GLN I 136 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN I 136 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU I 119 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU I 134 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR I 157 " --> pdb=" O GLY I 135 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU I 158 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS I 172 " --> pdb=" O MET I 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 179 through 184 removed outlier: 4.114A pdb=" N ASP I 197 " --> pdb=" O ASN I 200 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP I 213 " --> pdb=" O PHE I 205 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR I 207 " --> pdb=" O LEU I 211 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU I 211 " --> pdb=" O TYR I 207 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 231 through 233 removed outlier: 6.524A pdb=" N GLU I 258 " --> pdb=" O ILE I 262 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE I 262 " --> pdb=" O GLU I 258 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 276 through 283 removed outlier: 5.384A pdb=" N GLU I 277 " --> pdb=" O ARG I 292 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG I 292 " --> pdb=" O GLU I 277 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 353 through 356 removed outlier: 7.093A pdb=" N ASP I 402 " --> pdb=" O GLY I 373 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N GLU I 375 " --> pdb=" O ARG I 400 " (cutoff:3.500A) removed outlier: 10.448A pdb=" N ARG I 400 " --> pdb=" O GLU I 375 " (cutoff:3.500A) removed outlier: 11.415A pdb=" N PHE I 377 " --> pdb=" O VAL I 398 " (cutoff:3.500A) removed outlier: 13.491A pdb=" N VAL I 398 " --> pdb=" O PHE I 377 " (cutoff:3.500A) removed outlier: 15.522A pdb=" N VAL I 379 " --> pdb=" O VAL I 396 " (cutoff:3.500A) removed outlier: 16.245A pdb=" N VAL I 396 " --> pdb=" O VAL I 379 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AD5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.261A pdb=" N LEU C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA C 40 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.394A pdb=" N PHE C 117 " --> pdb=" O THR C 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AD8, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.849A pdb=" N GLN N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER N 67 " --> pdb=" O GLN N 70 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.476A pdb=" N LEU N 33 " --> pdb=" O PHE N 49 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 96 through 102 removed outlier: 3.801A pdb=" N GLY J 96 " --> pdb=" O THR J 449 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL J 445 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LYS J 102 " --> pdb=" O ILE J 443 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE J 443 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ARG J 420 " --> pdb=" O GLY J 448 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 115 through 124 removed outlier: 4.798A pdb=" N TRP J 115 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR J 138 " --> pdb=" O TRP J 115 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR J 117 " --> pdb=" O GLN J 136 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN J 136 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLU J 119 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU J 134 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR J 157 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU J 158 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS J 172 " --> pdb=" O MET J 160 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 179 through 184 removed outlier: 4.119A pdb=" N ASP J 197 " --> pdb=" O ASN J 200 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP J 213 " --> pdb=" O PHE J 205 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TYR J 207 " --> pdb=" O LEU J 211 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU J 211 " --> pdb=" O TYR J 207 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 231 through 233 removed outlier: 6.525A pdb=" N GLU J 258 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE J 262 " --> pdb=" O GLU J 258 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 276 through 283 removed outlier: 5.383A pdb=" N GLU J 277 " --> pdb=" O ARG J 292 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG J 292 " --> pdb=" O GLU J 277 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 353 through 356 removed outlier: 7.092A pdb=" N ASP J 402 " --> pdb=" O GLY J 373 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N GLU J 375 " --> pdb=" O ARG J 400 " (cutoff:3.500A) removed outlier: 10.449A pdb=" N ARG J 400 " --> pdb=" O GLU J 375 " (cutoff:3.500A) removed outlier: 11.414A pdb=" N PHE J 377 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 13.493A pdb=" N VAL J 398 " --> pdb=" O PHE J 377 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N VAL J 379 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 16.245A pdb=" N VAL J 396 " --> pdb=" O VAL J 379 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AE8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.259A pdb=" N LEU D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA D 40 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.394A pdb=" N PHE D 117 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 104 through 105 Processing sheet with id=AF2, first strand: chain 'O' and resid 4 through 7 removed outlier: 3.850A pdb=" N GLN O 70 " --> pdb=" O SER O 67 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER O 67 " --> pdb=" O GLN O 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.477A pdb=" N LEU O 33 " --> pdb=" O PHE O 49 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) 684 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.75 Time building geometry restraints manager: 9.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3703 1.32 - 1.45: 5439 1.45 - 1.57: 11206 1.57 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 20492 Sorted by residual: bond pdb=" N VAL O 58 " pdb=" CA VAL O 58 " ideal model delta sigma weight residual 1.460 1.493 -0.034 7.50e-03 1.78e+04 2.00e+01 bond pdb=" CA SER J 457 " pdb=" CB SER J 457 " ideal model delta sigma weight residual 1.534 1.460 0.074 1.72e-02 3.38e+03 1.85e+01 bond pdb=" CA SER H 457 " pdb=" CB SER H 457 " ideal model delta sigma weight residual 1.534 1.463 0.070 1.72e-02 3.38e+03 1.67e+01 bond pdb=" N VAL G 165 " pdb=" CA VAL G 165 " ideal model delta sigma weight residual 1.460 1.490 -0.029 7.30e-03 1.88e+04 1.61e+01 bond pdb=" N VAL I 165 " pdb=" CA VAL I 165 " ideal model delta sigma weight residual 1.460 1.490 -0.029 7.30e-03 1.88e+04 1.61e+01 ... (remaining 20487 not shown) Histogram of bond angle deviations from ideal: 97.77 - 105.27: 396 105.27 - 112.76: 9945 112.76 - 120.25: 9451 120.25 - 127.75: 7792 127.75 - 135.24: 240 Bond angle restraints: 27824 Sorted by residual: angle pdb=" C ARG I 430 " pdb=" N LYS I 431 " pdb=" CA LYS I 431 " ideal model delta sigma weight residual 121.54 133.45 -11.91 1.91e+00 2.74e-01 3.89e+01 angle pdb=" C ARG G 430 " pdb=" N LYS G 431 " pdb=" CA LYS G 431 " ideal model delta sigma weight residual 121.54 133.42 -11.88 1.91e+00 2.74e-01 3.87e+01 angle pdb=" C ARG J 430 " pdb=" N LYS J 431 " pdb=" CA LYS J 431 " ideal model delta sigma weight residual 121.54 133.41 -11.87 1.91e+00 2.74e-01 3.86e+01 angle pdb=" C ARG H 430 " pdb=" N LYS H 431 " pdb=" CA LYS H 431 " ideal model delta sigma weight residual 121.54 133.40 -11.86 1.91e+00 2.74e-01 3.86e+01 angle pdb=" N ILE J 397 " pdb=" CA ILE J 397 " pdb=" C ILE J 397 " ideal model delta sigma weight residual 111.67 106.00 5.67 9.50e-01 1.11e+00 3.56e+01 ... (remaining 27819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.51: 12055 20.51 - 41.03: 576 41.03 - 61.54: 102 61.54 - 82.05: 63 82.05 - 102.56: 24 Dihedral angle restraints: 12820 sinusoidal: 5708 harmonic: 7112 Sorted by residual: dihedral pdb=" CA ARG G 430 " pdb=" C ARG G 430 " pdb=" N LYS G 431 " pdb=" CA LYS G 431 " ideal model delta harmonic sigma weight residual -180.00 -143.33 -36.67 0 5.00e+00 4.00e-02 5.38e+01 dihedral pdb=" CA ARG H 430 " pdb=" C ARG H 430 " pdb=" N LYS H 431 " pdb=" CA LYS H 431 " ideal model delta harmonic sigma weight residual -180.00 -143.45 -36.55 0 5.00e+00 4.00e-02 5.34e+01 dihedral pdb=" CA ARG J 430 " pdb=" C ARG J 430 " pdb=" N LYS J 431 " pdb=" CA LYS J 431 " ideal model delta harmonic sigma weight residual -180.00 -143.50 -36.50 0 5.00e+00 4.00e-02 5.33e+01 ... (remaining 12817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1388 0.056 - 0.113: 1105 0.113 - 0.169: 483 0.169 - 0.225: 185 0.225 - 0.282: 35 Chirality restraints: 3196 Sorted by residual: chirality pdb=" C1 MAN Q 4 " pdb=" O3 BMA Q 3 " pdb=" C2 MAN Q 4 " pdb=" O5 MAN Q 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.93e+01 chirality pdb=" C1 MAN W 4 " pdb=" O3 BMA W 3 " pdb=" C2 MAN W 4 " pdb=" O5 MAN W 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.67e+01 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.11e+01 ... (remaining 3193 not shown) Planarity restraints: 3520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 1 " -0.088 2.00e-02 2.50e+03 7.60e-02 7.21e+01 pdb=" C7 NAG Q 1 " 0.061 2.00e-02 2.50e+03 pdb=" C8 NAG Q 1 " -0.078 2.00e-02 2.50e+03 pdb=" N2 NAG Q 1 " 0.107 2.00e-02 2.50e+03 pdb=" O7 NAG Q 1 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.087 2.00e-02 2.50e+03 7.54e-02 7.11e+01 pdb=" C7 NAG F 1 " -0.059 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.077 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.107 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 1 " 0.087 2.00e-02 2.50e+03 7.48e-02 7.00e+01 pdb=" C7 NAG W 1 " -0.058 2.00e-02 2.50e+03 pdb=" C8 NAG W 1 " 0.076 2.00e-02 2.50e+03 pdb=" N2 NAG W 1 " -0.107 2.00e-02 2.50e+03 pdb=" O7 NAG W 1 " 0.001 2.00e-02 2.50e+03 ... (remaining 3517 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2596 2.79 - 3.31: 19147 3.31 - 3.84: 35950 3.84 - 4.37: 46110 4.37 - 4.90: 73522 Nonbonded interactions: 177325 Sorted by model distance: nonbonded pdb=" O ASP G 293 " pdb="CA CA G1103 " model vdw 2.257 2.510 nonbonded pdb=" O ASP I 293 " pdb="CA CA I1103 " model vdw 2.257 2.510 nonbonded pdb=" O ASP H 293 " pdb="CA CA H1103 " model vdw 2.257 2.510 nonbonded pdb=" O ASP J 293 " pdb="CA CA J1103 " model vdw 2.265 2.510 nonbonded pdb=" O GLY J 345 " pdb="CA CA J1103 " model vdw 2.323 2.510 ... (remaining 177320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'F' selection = chain 'Q' selection = chain 'T' selection = chain 'W' } ncs_group { reference = (chain 'G' and (resid 82 through 469 or resid 1101 through 1103)) selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.170 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 56.740 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 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 : 0.014 0.079 20492 Z= 0.916 Angle : 1.611 11.913 27824 Z= 1.043 Chirality : 0.092 0.282 3196 Planarity : 0.010 0.076 3500 Dihedral : 14.337 102.563 8160 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.88 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.74 (0.16), residues: 2476 helix: 0.14 (0.94), residues: 24 sheet: 0.03 (0.16), residues: 1012 loop : -0.88 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.016 TRP H 458 HIS 0.024 0.006 HIS H 168 PHE 0.066 0.012 PHE G 205 TYR 0.060 0.013 TYR H 281 ARG 0.020 0.003 ARG G 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 2.278 Fit side-chains REVERT: G 400 ARG cc_start: 0.8987 (ptm-80) cc_final: 0.8568 (ptm160) REVERT: G 467 MET cc_start: 0.9081 (ptm) cc_final: 0.8878 (ptm) REVERT: A 10 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8503 (mt-10) REVERT: A 62 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8282 (tp-100) REVERT: L 61 ARG cc_start: 0.9078 (ptt-90) cc_final: 0.8828 (ptt-90) REVERT: L 82 ASP cc_start: 0.9266 (m-30) cc_final: 0.9047 (m-30) REVERT: H 400 ARG cc_start: 0.8991 (ptm-80) cc_final: 0.8573 (ptm160) REVERT: B 10 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8498 (mt-10) REVERT: B 62 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8268 (tp-100) REVERT: M 61 ARG cc_start: 0.9084 (ptt-90) cc_final: 0.8832 (ptt-90) REVERT: M 82 ASP cc_start: 0.9269 (m-30) cc_final: 0.9049 (m-30) REVERT: I 400 ARG cc_start: 0.8955 (ptm-80) cc_final: 0.8558 (ptm160) REVERT: C 10 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8497 (mt-10) REVERT: C 62 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8283 (tp-100) REVERT: N 61 ARG cc_start: 0.9081 (ptt-90) cc_final: 0.8831 (ptt-90) REVERT: N 82 ASP cc_start: 0.9267 (m-30) cc_final: 0.9046 (m-30) REVERT: J 247 THR cc_start: 0.7304 (m) cc_final: 0.6837 (p) REVERT: J 400 ARG cc_start: 0.8955 (ptm-80) cc_final: 0.8559 (ptm160) REVERT: D 10 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8501 (mt-10) REVERT: D 62 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8331 (tp-100) REVERT: O 61 ARG cc_start: 0.9085 (ptt-90) cc_final: 0.8826 (ptt-90) REVERT: O 82 ASP cc_start: 0.9270 (m-30) cc_final: 0.9045 (m-30) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 1.5645 time to fit residues: 579.3934 Evaluate side-chains 277 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 188 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 347 HIS A 65 GLN L 6 GLN H 347 HIS B 65 GLN M 6 GLN I 347 HIS C 65 GLN N 6 GLN J 347 HIS O 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20492 Z= 0.190 Angle : 0.638 6.014 27824 Z= 0.350 Chirality : 0.047 0.153 3196 Planarity : 0.003 0.033 3500 Dihedral : 9.336 79.283 3848 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.54 % Favored : 97.13 % Rotamer: Outliers : 1.27 % Allowed : 8.92 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2476 helix: 0.19 (0.91), residues: 24 sheet: 0.26 (0.15), residues: 1080 loop : -0.16 (0.16), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 178 HIS 0.005 0.001 HIS H 274 PHE 0.013 0.002 PHE J 410 TYR 0.014 0.002 TYR J 121 ARG 0.003 0.001 ARG J 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 277 time to evaluate : 2.700 Fit side-chains REVERT: G 400 ARG cc_start: 0.8834 (ptm-80) cc_final: 0.8479 (ptm160) REVERT: A 62 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8192 (tp-100) REVERT: L 61 ARG cc_start: 0.9090 (ptt-90) cc_final: 0.8776 (ptt-90) REVERT: L 101 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8578 (mm110) REVERT: H 400 ARG cc_start: 0.8836 (ptm-80) cc_final: 0.8479 (ptm160) REVERT: B 62 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8214 (tp-100) REVERT: M 61 ARG cc_start: 0.9097 (ptt-90) cc_final: 0.8782 (ptt-90) REVERT: M 101 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8578 (mm110) REVERT: I 400 ARG cc_start: 0.8804 (ptm-80) cc_final: 0.8471 (ptm160) REVERT: C 62 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8193 (tp-100) REVERT: N 61 ARG cc_start: 0.9096 (ptt-90) cc_final: 0.8783 (ptt-90) REVERT: N 101 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8595 (mm110) REVERT: J 400 ARG cc_start: 0.8803 (ptm-80) cc_final: 0.8469 (ptm160) REVERT: D 62 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8302 (mm-40) REVERT: O 61 ARG cc_start: 0.9089 (ptt-90) cc_final: 0.8775 (ptt-90) REVERT: O 101 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8596 (mm110) outliers start: 27 outliers final: 10 residues processed: 283 average time/residue: 1.3766 time to fit residues: 440.0070 Evaluate side-chains 259 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 249 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 218 optimal weight: 0.0030 chunk 235 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 216 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 175 optimal weight: 0.2980 overall best weight: 1.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 141 ASN A 65 GLN L 6 GLN H 141 ASN B 65 GLN M 6 GLN I 141 ASN C 65 GLN N 6 GLN J 141 ASN O 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20492 Z= 0.239 Angle : 0.590 7.709 27824 Z= 0.318 Chirality : 0.046 0.175 3196 Planarity : 0.003 0.040 3500 Dihedral : 8.268 68.424 3848 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.75 % Favored : 96.93 % Rotamer: Outliers : 1.93 % Allowed : 10.19 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.17), residues: 2476 helix: 0.66 (0.96), residues: 24 sheet: 0.46 (0.15), residues: 1064 loop : -0.04 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 178 HIS 0.004 0.001 HIS H 274 PHE 0.012 0.002 PHE G 410 TYR 0.014 0.001 TYR H 121 ARG 0.003 0.000 ARG G 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 268 time to evaluate : 2.325 Fit side-chains REVERT: G 400 ARG cc_start: 0.8924 (ptm-80) cc_final: 0.8490 (ptm160) REVERT: A 62 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8198 (tp-100) REVERT: L 61 ARG cc_start: 0.9045 (ptt-90) cc_final: 0.8818 (ptt-90) REVERT: H 400 ARG cc_start: 0.8917 (ptm-80) cc_final: 0.8487 (ptm160) REVERT: B 62 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8197 (tp-100) REVERT: M 61 ARG cc_start: 0.9047 (ptt-90) cc_final: 0.8817 (ptt-90) REVERT: I 400 ARG cc_start: 0.8899 (ptm-80) cc_final: 0.8489 (ptm160) REVERT: C 62 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8187 (tp-100) REVERT: N 61 ARG cc_start: 0.9041 (ptt-90) cc_final: 0.8825 (ptt-90) REVERT: J 400 ARG cc_start: 0.8904 (ptm-80) cc_final: 0.8494 (ptm160) REVERT: D 62 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8314 (tp-100) REVERT: O 61 ARG cc_start: 0.9057 (ptt-90) cc_final: 0.8826 (ptt-90) outliers start: 41 outliers final: 24 residues processed: 285 average time/residue: 1.4206 time to fit residues: 461.4287 Evaluate side-chains 276 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 252 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 104 optimal weight: 0.0970 chunk 146 optimal weight: 4.9990 chunk 219 optimal weight: 7.9990 chunk 231 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 141 ASN A 65 GLN L 6 GLN L 70 GLN H 141 ASN B 65 GLN M 6 GLN M 70 GLN I 141 ASN C 65 GLN N 6 GLN N 70 GLN J 141 ASN O 6 GLN O 70 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20492 Z= 0.246 Angle : 0.580 8.643 27824 Z= 0.310 Chirality : 0.046 0.188 3196 Planarity : 0.003 0.043 3500 Dihedral : 7.935 65.049 3848 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.63 % Favored : 97.05 % Rotamer: Outliers : 1.70 % Allowed : 10.28 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2476 helix: -0.22 (0.91), residues: 28 sheet: 0.42 (0.15), residues: 1056 loop : -0.05 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 178 HIS 0.003 0.001 HIS H 168 PHE 0.013 0.002 PHE J 410 TYR 0.013 0.001 TYR H 121 ARG 0.002 0.000 ARG J 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 259 time to evaluate : 2.328 Fit side-chains REVERT: G 400 ARG cc_start: 0.8941 (ptm-80) cc_final: 0.8498 (ptm160) REVERT: A 62 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8162 (tp-100) REVERT: L 61 ARG cc_start: 0.9037 (ptt-90) cc_final: 0.8785 (ptt-90) REVERT: H 400 ARG cc_start: 0.8942 (ptm-80) cc_final: 0.8503 (ptm160) REVERT: B 62 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8161 (tp-100) REVERT: M 61 ARG cc_start: 0.9037 (ptt-90) cc_final: 0.8784 (ptt-90) REVERT: I 400 ARG cc_start: 0.8926 (ptm-80) cc_final: 0.8492 (ptm160) REVERT: C 62 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8161 (tp-100) REVERT: N 61 ARG cc_start: 0.9036 (ptt-90) cc_final: 0.8777 (ptt-90) REVERT: J 400 ARG cc_start: 0.8922 (ptm-80) cc_final: 0.8490 (ptm160) REVERT: D 62 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8306 (tp-100) REVERT: O 61 ARG cc_start: 0.9040 (ptt-90) cc_final: 0.8791 (ptt-90) outliers start: 36 outliers final: 30 residues processed: 275 average time/residue: 1.3594 time to fit residues: 422.5719 Evaluate side-chains 283 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 253 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.0980 chunk 131 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 95 optimal weight: 0.0670 chunk 197 optimal weight: 0.6980 chunk 160 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.2320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 70 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN M 6 GLN M 70 GLN ** M 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN N 6 GLN N 70 GLN ** N 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN O 6 GLN O 70 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20492 Z= 0.229 Angle : 0.569 9.716 27824 Z= 0.303 Chirality : 0.045 0.191 3196 Planarity : 0.003 0.044 3500 Dihedral : 7.650 62.048 3848 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.42 % Favored : 97.25 % Rotamer: Outliers : 1.89 % Allowed : 10.33 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 2476 helix: -1.61 (0.65), residues: 52 sheet: 0.47 (0.15), residues: 1048 loop : -0.04 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 178 HIS 0.002 0.001 HIS H 274 PHE 0.013 0.002 PHE J 410 TYR 0.013 0.001 TYR H 121 ARG 0.002 0.000 ARG J 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 255 time to evaluate : 2.424 Fit side-chains REVERT: G 400 ARG cc_start: 0.8942 (ptm-80) cc_final: 0.8483 (ptm160) REVERT: A 62 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8187 (tp-100) REVERT: L 61 ARG cc_start: 0.9005 (ptt-90) cc_final: 0.8755 (ptt-90) REVERT: H 400 ARG cc_start: 0.8946 (ptm-80) cc_final: 0.8492 (ptm160) REVERT: B 62 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8189 (tp-100) REVERT: M 61 ARG cc_start: 0.9004 (ptt-90) cc_final: 0.8754 (ptt-90) REVERT: I 400 ARG cc_start: 0.8938 (ptm-80) cc_final: 0.8483 (ptm160) REVERT: C 62 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8187 (tp-100) REVERT: N 61 ARG cc_start: 0.9006 (ptt-90) cc_final: 0.8765 (ptt-90) REVERT: J 400 ARG cc_start: 0.8939 (ptm-80) cc_final: 0.8485 (ptm160) REVERT: D 62 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8295 (tp-100) REVERT: O 61 ARG cc_start: 0.9008 (ptt-90) cc_final: 0.8756 (ptt-90) outliers start: 40 outliers final: 32 residues processed: 271 average time/residue: 1.4173 time to fit residues: 432.5688 Evaluate side-chains 280 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 248 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 70 GLN B 65 GLN M 6 GLN M 70 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 20492 Z= 0.395 Angle : 0.629 9.664 27824 Z= 0.335 Chirality : 0.048 0.190 3196 Planarity : 0.004 0.046 3500 Dihedral : 8.208 67.830 3848 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.58 % Favored : 97.09 % Rotamer: Outliers : 2.03 % Allowed : 10.33 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2476 helix: 0.46 (0.94), residues: 24 sheet: 0.32 (0.15), residues: 1076 loop : -0.07 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 115 HIS 0.003 0.001 HIS J 168 PHE 0.015 0.002 PHE J 410 TYR 0.015 0.002 TYR H 121 ARG 0.003 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 248 time to evaluate : 2.449 Fit side-chains REVERT: G 400 ARG cc_start: 0.8969 (ptm-80) cc_final: 0.8491 (ptm160) REVERT: A 10 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8553 (mt-10) REVERT: A 19 ARG cc_start: 0.9434 (ttt-90) cc_final: 0.9181 (ttt-90) REVERT: A 62 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8238 (tp-100) REVERT: A 82 GLU cc_start: 0.8729 (tt0) cc_final: 0.8353 (mm-30) REVERT: L 33 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9039 (tm) REVERT: L 61 ARG cc_start: 0.8995 (ptt-90) cc_final: 0.8688 (ptt-90) REVERT: H 400 ARG cc_start: 0.8986 (ptm-80) cc_final: 0.8507 (ptm160) REVERT: B 10 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8552 (mt-10) REVERT: B 62 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8237 (tp-100) REVERT: M 33 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9048 (tm) REVERT: M 61 ARG cc_start: 0.8994 (ptt-90) cc_final: 0.8687 (ptt-90) REVERT: I 400 ARG cc_start: 0.8995 (ptm-80) cc_final: 0.8508 (ptm160) REVERT: C 10 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8554 (mt-10) REVERT: C 62 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8236 (tp-100) REVERT: N 33 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9045 (tm) REVERT: N 61 ARG cc_start: 0.8981 (ptt-90) cc_final: 0.8677 (ptt-90) REVERT: J 400 ARG cc_start: 0.8994 (ptm-80) cc_final: 0.8508 (ptm160) REVERT: D 10 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8552 (mt-10) REVERT: D 62 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8313 (tp-100) REVERT: O 33 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9040 (tm) REVERT: O 61 ARG cc_start: 0.8988 (ptt-90) cc_final: 0.8670 (ptt-90) outliers start: 43 outliers final: 31 residues processed: 272 average time/residue: 1.4805 time to fit residues: 452.3745 Evaluate side-chains 277 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 242 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 169 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 231 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 70 GLN B 65 GLN M 6 GLN M 70 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20492 Z= 0.192 Angle : 0.561 10.771 27824 Z= 0.297 Chirality : 0.045 0.183 3196 Planarity : 0.003 0.045 3500 Dihedral : 7.490 60.109 3848 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.42 % Favored : 97.42 % Rotamer: Outliers : 1.08 % Allowed : 11.56 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.17), residues: 2476 helix: -1.65 (0.65), residues: 52 sheet: 0.52 (0.16), residues: 964 loop : 0.03 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 178 HIS 0.002 0.001 HIS J 184 PHE 0.013 0.002 PHE I 410 TYR 0.012 0.001 TYR G 121 ARG 0.004 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 248 time to evaluate : 2.411 Fit side-chains REVERT: G 400 ARG cc_start: 0.8933 (ptm-80) cc_final: 0.8460 (ptm160) REVERT: A 19 ARG cc_start: 0.9408 (ttt-90) cc_final: 0.9206 (ttt-90) REVERT: A 62 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8171 (tp-100) REVERT: A 82 GLU cc_start: 0.8720 (tt0) cc_final: 0.8331 (mm-30) REVERT: L 33 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9027 (tm) REVERT: L 61 ARG cc_start: 0.8972 (ptt-90) cc_final: 0.8663 (ptt-90) REVERT: H 230 CYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8868 (p) REVERT: H 400 ARG cc_start: 0.8956 (ptm-80) cc_final: 0.8485 (ptm160) REVERT: B 62 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8207 (tp-100) REVERT: B 82 GLU cc_start: 0.8682 (tt0) cc_final: 0.8412 (mm-30) REVERT: M 61 ARG cc_start: 0.8971 (ptt-90) cc_final: 0.8662 (ptt-90) REVERT: I 400 ARG cc_start: 0.8954 (ptm-80) cc_final: 0.8472 (ptm160) REVERT: C 62 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8174 (tp-100) REVERT: C 82 GLU cc_start: 0.8678 (tt0) cc_final: 0.8393 (mm-30) REVERT: N 33 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9024 (tm) REVERT: N 61 ARG cc_start: 0.8967 (ptt-90) cc_final: 0.8660 (ptt-90) REVERT: J 400 ARG cc_start: 0.8953 (ptm-80) cc_final: 0.8472 (ptm160) REVERT: D 62 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8281 (tp-100) REVERT: D 82 GLU cc_start: 0.8675 (tt0) cc_final: 0.8383 (mm-30) REVERT: O 33 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8996 (tm) REVERT: O 61 ARG cc_start: 0.8989 (ptt-90) cc_final: 0.8670 (ptt-90) outliers start: 23 outliers final: 11 residues processed: 262 average time/residue: 1.4941 time to fit residues: 440.0901 Evaluate side-chains 255 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 240 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 33 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 181 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 70 GLN B 65 GLN M 6 GLN M 70 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20492 Z= 0.170 Angle : 0.546 10.822 27824 Z= 0.287 Chirality : 0.044 0.198 3196 Planarity : 0.003 0.044 3500 Dihedral : 7.016 54.454 3848 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.58 % Favored : 97.25 % Rotamer: Outliers : 1.04 % Allowed : 12.08 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2476 helix: -1.60 (0.65), residues: 52 sheet: 0.59 (0.16), residues: 972 loop : 0.04 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 178 HIS 0.002 0.001 HIS H 274 PHE 0.013 0.002 PHE J 410 TYR 0.012 0.001 TYR H 121 ARG 0.004 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 247 time to evaluate : 2.472 Fit side-chains REVERT: G 400 ARG cc_start: 0.8930 (ptm-80) cc_final: 0.8466 (ptm160) REVERT: A 62 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8190 (tp-100) REVERT: A 82 GLU cc_start: 0.8730 (tt0) cc_final: 0.8360 (mm-30) REVERT: L 61 ARG cc_start: 0.8973 (ptt-90) cc_final: 0.8669 (ptt-90) REVERT: H 230 CYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8857 (p) REVERT: H 400 ARG cc_start: 0.8951 (ptm-80) cc_final: 0.8489 (ptm160) REVERT: B 62 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8207 (tp-100) REVERT: B 82 GLU cc_start: 0.8681 (tt0) cc_final: 0.8381 (mm-30) REVERT: M 61 ARG cc_start: 0.8973 (ptt-90) cc_final: 0.8670 (ptt-90) REVERT: I 400 ARG cc_start: 0.8930 (ptm-80) cc_final: 0.8457 (ptm160) REVERT: C 62 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8189 (tp-100) REVERT: C 82 GLU cc_start: 0.8673 (tt0) cc_final: 0.8399 (mm-30) REVERT: N 61 ARG cc_start: 0.8973 (ptt-90) cc_final: 0.8673 (ptt-90) REVERT: J 400 ARG cc_start: 0.8929 (ptm-80) cc_final: 0.8455 (ptm160) REVERT: D 62 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8264 (tp-100) REVERT: D 82 GLU cc_start: 0.8673 (tt0) cc_final: 0.8392 (mm-30) REVERT: O 61 ARG cc_start: 0.8978 (ptt-90) cc_final: 0.8666 (ptt-90) outliers start: 22 outliers final: 17 residues processed: 264 average time/residue: 1.4272 time to fit residues: 426.3343 Evaluate side-chains 265 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 247 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.0000 chunk 221 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 169 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 70 GLN B 65 GLN M 6 GLN M 70 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20492 Z= 0.180 Angle : 0.546 10.704 27824 Z= 0.288 Chirality : 0.045 0.204 3196 Planarity : 0.003 0.045 3500 Dihedral : 6.908 52.884 3848 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.42 % Favored : 97.42 % Rotamer: Outliers : 1.32 % Allowed : 11.93 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2476 helix: -1.61 (0.65), residues: 52 sheet: 0.58 (0.16), residues: 980 loop : 0.01 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 178 HIS 0.002 0.001 HIS H 274 PHE 0.013 0.001 PHE J 410 TYR 0.012 0.001 TYR H 121 ARG 0.005 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 249 time to evaluate : 2.305 Fit side-chains REVERT: G 400 ARG cc_start: 0.8932 (ptm-80) cc_final: 0.8465 (ptm160) REVERT: A 62 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8179 (tp-100) REVERT: A 82 GLU cc_start: 0.8715 (tt0) cc_final: 0.8381 (mm-30) REVERT: L 61 ARG cc_start: 0.8979 (ptt-90) cc_final: 0.8671 (ptt-90) REVERT: H 230 CYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8857 (p) REVERT: H 400 ARG cc_start: 0.8943 (ptm-80) cc_final: 0.8477 (ptm160) REVERT: B 62 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8261 (tp-100) REVERT: B 82 GLU cc_start: 0.8678 (tt0) cc_final: 0.8401 (mm-30) REVERT: M 61 ARG cc_start: 0.8979 (ptt-90) cc_final: 0.8672 (ptt-90) REVERT: I 400 ARG cc_start: 0.8932 (ptm-80) cc_final: 0.8455 (ptm160) REVERT: C 62 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8259 (tp-100) REVERT: C 82 GLU cc_start: 0.8649 (tt0) cc_final: 0.8393 (mm-30) REVERT: N 61 ARG cc_start: 0.8976 (ptt-90) cc_final: 0.8669 (ptt-90) REVERT: J 400 ARG cc_start: 0.8930 (ptm-80) cc_final: 0.8455 (ptm160) REVERT: D 62 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8270 (tp-100) REVERT: D 82 GLU cc_start: 0.8652 (tt0) cc_final: 0.8391 (mm-30) REVERT: O 61 ARG cc_start: 0.8982 (ptt-90) cc_final: 0.8664 (ptt-90) outliers start: 28 outliers final: 20 residues processed: 270 average time/residue: 1.4227 time to fit residues: 431.7065 Evaluate side-chains 266 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 245 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 4.9990 chunk 227 optimal weight: 7.9990 chunk 139 optimal weight: 0.4980 chunk 108 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 32 ASN L 70 GLN L 92 ASN B 65 GLN M 6 GLN M 32 ASN M 70 GLN M 92 ASN C 65 GLN N 6 GLN N 70 GLN J 220 ASN O 6 GLN O 32 ASN ** O 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20492 Z= 0.341 Angle : 0.614 10.019 27824 Z= 0.324 Chirality : 0.047 0.203 3196 Planarity : 0.004 0.046 3500 Dihedral : 7.599 60.343 3848 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.07 % Favored : 96.77 % Rotamer: Outliers : 1.27 % Allowed : 12.36 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.17), residues: 2476 helix: -1.32 (0.68), residues: 48 sheet: 0.43 (0.15), residues: 1084 loop : 0.04 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 115 HIS 0.003 0.001 HIS J 184 PHE 0.015 0.002 PHE H 410 TYR 0.015 0.002 TYR H 121 ARG 0.005 0.000 ARG A 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 247 time to evaluate : 2.424 Fit side-chains REVERT: G 400 ARG cc_start: 0.8973 (ptm-80) cc_final: 0.8486 (ptm160) REVERT: A 10 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8540 (mt-10) REVERT: A 62 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8271 (tp-100) REVERT: L 61 ARG cc_start: 0.8982 (ptt-90) cc_final: 0.8648 (ptt-90) REVERT: H 400 ARG cc_start: 0.8975 (ptm-80) cc_final: 0.8489 (ptm160) REVERT: B 10 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8397 (tt0) REVERT: B 62 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8268 (tp-100) REVERT: B 82 GLU cc_start: 0.8783 (tt0) cc_final: 0.8397 (mm-30) REVERT: M 61 ARG cc_start: 0.8981 (ptt-90) cc_final: 0.8648 (ptt-90) REVERT: I 400 ARG cc_start: 0.8966 (ptm-80) cc_final: 0.8476 (ptm160) REVERT: C 10 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8396 (tt0) REVERT: C 62 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8270 (tp-100) REVERT: C 82 GLU cc_start: 0.8788 (tt0) cc_final: 0.8405 (mm-30) REVERT: N 61 ARG cc_start: 0.8973 (ptt-90) cc_final: 0.8642 (ptt-90) REVERT: J 400 ARG cc_start: 0.8972 (ptm-80) cc_final: 0.8484 (ptm160) REVERT: D 10 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8401 (tt0) REVERT: D 62 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8328 (tp-100) REVERT: D 82 GLU cc_start: 0.8786 (tt0) cc_final: 0.8402 (mm-30) REVERT: O 61 ARG cc_start: 0.8982 (ptt-90) cc_final: 0.8647 (ptt-90) outliers start: 27 outliers final: 26 residues processed: 262 average time/residue: 1.4129 time to fit residues: 417.2412 Evaluate side-chains 271 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 245 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 175 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 220 ASN A 65 GLN L 6 GLN L 70 GLN B 65 GLN M 6 GLN M 70 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.099393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.071372 restraints weight = 28062.645| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.18 r_work: 0.2744 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20492 Z= 0.157 Angle : 0.552 11.013 27824 Z= 0.288 Chirality : 0.044 0.190 3196 Planarity : 0.003 0.044 3500 Dihedral : 6.951 52.989 3848 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.30 % Favored : 97.54 % Rotamer: Outliers : 0.75 % Allowed : 12.78 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2476 helix: -1.65 (0.64), residues: 52 sheet: 0.58 (0.16), residues: 968 loop : 0.02 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 178 HIS 0.005 0.001 HIS H 184 PHE 0.012 0.001 PHE H 410 TYR 0.011 0.001 TYR H 121 ARG 0.005 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7828.29 seconds wall clock time: 141 minutes 35.78 seconds (8495.78 seconds total)