Starting phenix.real_space_refine on Sat Feb 17 10:24:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq1_25376/02_2024/7sq1_25376.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq1_25376/02_2024/7sq1_25376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq1_25376/02_2024/7sq1_25376.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq1_25376/02_2024/7sq1_25376.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq1_25376/02_2024/7sq1_25376.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq1_25376/02_2024/7sq1_25376.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 121 5.16 5 C 11459 2.51 5 N 3049 2.21 5 O 3711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18340 Number of models: 1 Model: "" Number of chains: 42 Chain: "B" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 969 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3467 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "D" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 969 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "E" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3512 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "L" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 845 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 101} Chain: "H" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 958 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "F" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 969 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "G" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3497 Classifications: {'peptide': 444} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 3 Chain: "I" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 845 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 101} Chain: "A" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 958 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "O" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BMA': 1, 'MAN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 9.45, per 1000 atoms: 0.52 Number of scatterers: 18340 At special positions: 0 Unit cell: (189, 152.88, 123.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 121 16.00 O 3711 8.00 N 3049 7.00 C 11459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS C 501 " distance=2.05 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.16 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.14 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.06 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.22 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.18 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.12 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.05 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.26 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.06 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.08 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.08 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.15 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.10 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.04 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.05 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.19 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.07 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 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!! Possible link ignored !!! !!! HETATM18122 C6 NAG E 608 45.489 78.875 67.940 1.00 90.40 C !!! !!! HETATM17308 C6 NAG V 1 46.816 79.842 68.554 1.00 85.00 C !!! !!! N-linked glycan : False !!! !!! O-linked glycan : False !!! !!! Glycan-glycan : True !!! !!! No oxygen atom found !!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Atom "HETATM17708 O5 NAG h 2 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA O 1 " - " MAN O 2 " " BMA V 3 " - " MAN V 4 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA O 1 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 137 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 160 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 295 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 355 " " NAG C 609 " - " ASN C 392 " " NAG C 610 " - " ASN C 448 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 625 " " NAG D 704 " - " ASN D 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 137 " " NAG E 604 " - " ASN E 160 " " NAG E 605 " - " ASN E 276 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 448 " " NAG E 609 " - " ASN E 462 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 137 " " NAG G 603 " - " ASN G 197 " " NAG G 604 " - " ASN G 276 " " NAG G 605 " - " ASN G 295 " " NAG G 606 " - " ASN G 301 " " NAG G 607 " - " ASN G 332 " " NAG G 608 " - " ASN G 339 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 398 " " NAG G 611 " - " ASN G 462 " " NAG J 1 " - " ASN C 133 " " NAG K 1 " - " ASN C 197 " " NAG M 1 " - " ASN C 234 " " NAG N 1 " - " ASN C 262 " " NAG P 1 " - " ASN C 301 " " NAG Q 1 " - " ASN C 332 " " NAG R 1 " - " ASN C 386 " " NAG S 1 " - " ASN E 156 " " NAG T 1 " - " ASN E 197 " " NAG U 1 " - " ASN E 234 " " NAG V 1 " - " ASN E 262 " " NAG W 1 " - " ASN E 295 " " NAG X 1 " - " ASN E 332 " " NAG Y 1 " - " ASN E 355 " " NAG Z 1 " - " ASN E 386 " " NAG a 1 " - " ASN E 392 " " NAG b 1 " - " ASN E 398 " " NAG c 1 " - " ASN G 133 " " NAG d 1 " - " ASN G 156 " " NAG e 1 " - " ASN G 160 " " NAG f 1 " - " ASN G 234 " " NAG g 1 " - " ASN G 262 " " NAG h 1 " - " ASN G 355 " " NAG i 1 " - " ASN G 386 " " NAG j 1 " - " ASN G 448 " Time building additional restraints: 7.63 Conformation dependent library (CDL) restraints added in 3.1 seconds 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4002 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 42 sheets defined 24.5% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.234A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.629A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.941A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 597 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.801A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 650 removed outlier: 3.611A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 664 removed outlier: 3.800A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 removed outlier: 3.544A pdb=" N HIS C 72 " --> pdb=" O TRP C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.813A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.648A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.690A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 571 through 597 Processing helix chain 'D' and resid 611 through 615 removed outlier: 3.743A pdb=" N SER D 615 " --> pdb=" O SER D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.634A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.701A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 650 removed outlier: 3.858A pdb=" N GLN D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 664 removed outlier: 4.092A pdb=" N ASN D 656 " --> pdb=" O GLN D 652 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 73 removed outlier: 3.692A pdb=" N HIS E 72 " --> pdb=" O TRP E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 115 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.717A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 52A through 54 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.236A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.750A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.799A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 597 Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.666A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 650 Processing helix chain 'F' and resid 650 through 664 removed outlier: 3.941A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 73 removed outlier: 3.615A pdb=" N HIS G 72 " --> pdb=" O TRP G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 99 through 115 Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 335 through 354 removed outlier: 3.674A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 475 through 484 removed outlier: 3.532A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.668A pdb=" N TYR A 32 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 52A through 54 Processing helix chain 'A' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 8.546A pdb=" N CYS B 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N TYR C 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR B 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL C 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL B 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.691A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.721A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 92 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 131 through 133 Processing sheet with id=AA6, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.360A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.586A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.316A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.871A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.862A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.981A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 274 removed outlier: 10.939A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.981A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.862A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.871A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.316A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 302 through 309 removed outlier: 4.730A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 603 through 609 removed outlier: 8.301A pdb=" N CYS D 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR E 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N THR D 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL E 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL D 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.656A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB5, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AB6, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AB7, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AB8, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.300A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.446A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.697A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.458A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.967A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.458A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.697A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 302 through 309 removed outlier: 4.736A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.686A pdb=" N MET L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N TYR L 49 " --> pdb=" O MET L 33 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.560A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.113A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.611A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 603 through 609 removed outlier: 8.345A pdb=" N CYS F 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N TYR G 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N THR F 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL G 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL F 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.241A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.675A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 92 through 94 Processing sheet with id=AD5, first strand: chain 'G' and resid 130 through 133 removed outlier: 3.544A pdb=" N GLN G 130 " --> pdb=" O SER G 158 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AD7, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.387A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.383A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.344A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.982A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.878A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 271 through 274 removed outlier: 6.933A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.878A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.982A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.344A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 304 through 309 removed outlier: 3.555A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AE3, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.146A pdb=" N PHE I 98 " --> pdb=" O GLN I 90 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLN I 90 " --> pdb=" O PHE I 98 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY I 100 " --> pdb=" O CYS I 88 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS I 88 " --> pdb=" O GLY I 100 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA I 84 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N MET I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TYR I 49 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'A' and resid 10 through 12 removed outlier: 7.100A pdb=" N MET A 34 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.593A pdb=" N TYR A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.63 Time building geometry restraints manager: 8.18 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: 3190 1.32 - 1.44: 5014 1.44 - 1.57: 10329 1.57 - 1.70: 2 1.70 - 1.82: 168 Bond restraints: 18703 Sorted by residual: bond pdb=" C1 NAG B 701 " pdb=" C2 NAG B 701 " ideal model delta sigma weight residual 1.532 1.603 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" CB HIS G 374 " pdb=" CG HIS G 374 " ideal model delta sigma weight residual 1.497 1.449 0.048 1.40e-02 5.10e+03 1.19e+01 bond pdb=" CB TYR A 32 " pdb=" CG TYR A 32 " ideal model delta sigma weight residual 1.512 1.444 0.068 2.20e-02 2.07e+03 9.65e+00 bond pdb=" CG ASP H 101 " pdb=" OD1 ASP H 101 " ideal model delta sigma weight residual 1.249 1.191 0.058 1.90e-02 2.77e+03 9.29e+00 bond pdb=" CB LEU C 111 " pdb=" CG LEU C 111 " ideal model delta sigma weight residual 1.530 1.470 0.060 2.00e-02 2.50e+03 9.08e+00 ... (remaining 18698 not shown) Histogram of bond angle deviations from ideal: 79.72 - 95.73: 4 95.73 - 111.74: 9486 111.74 - 127.75: 15709 127.75 - 143.76: 182 143.76 - 159.76: 2 Bond angle restraints: 25383 Sorted by residual: angle pdb=" C8 NAG G 610 " pdb=" C7 NAG G 610 " pdb=" N2 NAG G 610 " ideal model delta sigma weight residual 115.06 159.76 -44.70 3.00e+00 1.11e-01 2.22e+02 angle pdb=" C8 NAG F 701 " pdb=" C7 NAG F 701 " pdb=" N2 NAG F 701 " ideal model delta sigma weight residual 115.06 159.74 -44.68 3.00e+00 1.11e-01 2.22e+02 angle pdb=" N2 NAG G 610 " pdb=" C7 NAG G 610 " pdb=" O7 NAG G 610 " ideal model delta sigma weight residual 123.46 80.00 43.46 3.00e+00 1.11e-01 2.10e+02 angle pdb=" N2 NAG F 701 " pdb=" C7 NAG F 701 " pdb=" O7 NAG F 701 " ideal model delta sigma weight residual 123.46 80.02 43.44 3.00e+00 1.11e-01 2.10e+02 angle pdb=" C8 NAG F 701 " pdb=" C7 NAG F 701 " pdb=" O7 NAG F 701 " ideal model delta sigma weight residual 121.48 79.72 41.76 3.00e+00 1.11e-01 1.94e+02 ... (remaining 25378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.90: 12100 21.90 - 43.79: 227 43.79 - 65.69: 93 65.69 - 87.59: 58 87.59 - 109.48: 21 Dihedral angle restraints: 12499 sinusoidal: 6289 harmonic: 6210 Sorted by residual: dihedral pdb=" CB CYS B 605 " pdb=" SG CYS B 605 " pdb=" SG CYS C 501 " pdb=" CB CYS C 501 " ideal model delta sinusoidal sigma weight residual -86.00 -137.19 51.19 1 1.00e+01 1.00e-02 3.58e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -128.76 42.76 1 1.00e+01 1.00e-02 2.55e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -128.23 42.23 1 1.00e+01 1.00e-02 2.49e+01 ... (remaining 12496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.263: 3068 0.263 - 0.527: 29 0.527 - 0.790: 5 0.790 - 1.053: 1 1.053 - 1.317: 1 Chirality restraints: 3104 Sorted by residual: chirality pdb=" C1 MAN O 2 " pdb=" O3 BMA O 1 " pdb=" C2 MAN O 2 " pdb=" O5 MAN O 2 " both_signs ideal model delta sigma weight residual False 2.40 1.08 1.32 2.00e-02 2.50e+03 4.34e+03 chirality pdb=" C1 BMA O 1 " pdb=" O4 NAG N 2 " pdb=" C2 BMA O 1 " pdb=" O5 BMA O 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.15 0.75 2.00e-02 2.50e+03 1.40e+03 chirality pdb=" C1 NAG h 2 " pdb=" O4 NAG h 1 " pdb=" C2 NAG h 2 " pdb=" O5 NAG h 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-02 2.50e+03 9.30e+02 ... (remaining 3101 not shown) Planarity restraints: 3188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " 0.094 2.00e-02 2.50e+03 9.45e-02 1.12e+02 pdb=" CG ASN B 611 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " -0.142 2.00e-02 2.50e+03 pdb=" C1 NAG B 701 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 448 " 0.072 2.00e-02 2.50e+03 7.52e-02 7.06e+01 pdb=" CG ASN G 448 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN G 448 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN G 448 " -0.118 2.00e-02 2.50e+03 pdb=" C1 NAG j 1 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 301 " 0.070 2.00e-02 2.50e+03 7.10e-02 6.31e+01 pdb=" CG ASN G 301 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN G 301 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN G 301 " -0.109 2.00e-02 2.50e+03 pdb=" C1 NAG G 606 " 0.085 2.00e-02 2.50e+03 ... (remaining 3185 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 43 2.38 - 3.01: 10585 3.01 - 3.64: 24239 3.64 - 4.27: 40449 4.27 - 4.90: 65636 Nonbonded interactions: 140952 Sorted by model distance: nonbonded pdb=" C6 NAG V 1 " pdb=" C6 NAG E 608 " model vdw 1.753 3.840 nonbonded pdb=" C8 NAG R 2 " pdb=" O3 NAG R 2 " model vdw 1.873 3.460 nonbonded pdb=" O3 NAG E 609 " pdb=" O7 NAG E 609 " model vdw 1.887 2.440 nonbonded pdb=" C8 NAG j 1 " pdb=" O3 NAG j 1 " model vdw 1.887 3.460 nonbonded pdb=" C8 NAG G 606 " pdb=" O3 NAG G 606 " model vdw 1.892 3.460 ... (remaining 140947 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 'H' } ncs_group { reference = (chain 'B' and (resid 520 through 664 or resid 701 through 703)) selection = (chain 'D' and (resid 520 through 664 or resid 701 through 703)) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 32 through 57 or resid 66 through 504 or resid 602 through \ 610)) selection = (chain 'E' and (resid 32 through 57 or resid 66 through 397 or resid 412 through \ 504 or resid 601 through 609)) selection = (chain 'G' and (resid 32 through 184 or resid 189 through 397 or resid 412 throu \ gh 504 or resid 603 through 611)) } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'h' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'U' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.820 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: 29.800 Check model and map are aligned: 0.270 Set scattering table: 0.150 Process input model: 49.610 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 0.012 0.074 18703 Z= 0.771 Angle : 1.484 44.703 25383 Z= 0.891 Chirality : 0.083 1.317 3104 Planarity : 0.005 0.034 3122 Dihedral : 12.392 109.482 8386 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.18 % Favored : 98.77 % Rotamer: Outliers : 0.74 % Allowed : 0.74 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.40 (0.18), residues: 2113 helix: 0.36 (0.22), residues: 373 sheet: 1.35 (0.19), residues: 605 loop : 2.51 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.005 TRP G 479 HIS 0.003 0.001 HIS G 374 PHE 0.025 0.004 PHE I 98 TYR 0.030 0.004 TYR C 191 ARG 0.002 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 364 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 656 ASN cc_start: 0.5924 (m-40) cc_final: 0.5666 (p0) REVERT: C 180 ASP cc_start: 0.8615 (m-30) cc_final: 0.8251 (m-30) REVERT: E 161 MET cc_start: 0.8557 (tpt) cc_final: 0.8274 (tpt) REVERT: E 377 ASN cc_start: 0.8798 (t0) cc_final: 0.8493 (t0) REVERT: L 6 GLN cc_start: 0.6429 (tt0) cc_final: 0.6097 (tt0) REVERT: L 29 VAL cc_start: 0.8189 (m) cc_final: 0.7978 (p) REVERT: L 87 PHE cc_start: 0.8325 (m-80) cc_final: 0.8060 (m-80) REVERT: F 574 LYS cc_start: 0.9062 (mttt) cc_final: 0.8688 (mmtt) REVERT: G 504 ARG cc_start: 0.5583 (mtt180) cc_final: 0.4479 (mmt180) REVERT: A 79 TYR cc_start: 0.7226 (m-80) cc_final: 0.6938 (m-80) outliers start: 14 outliers final: 8 residues processed: 376 average time/residue: 0.3235 time to fit residues: 178.3809 Evaluate side-chains 171 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 163 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 137 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS C 195 ASN C 374 HIS C 422 GLN C 425 ASN D 540 GLN D 543 ASN D 590 GLN E 136 ASN E 195 ASN L 38 GLN L 89 GLN H 13 GLN H 39 GLN H 100 HIS G 377 ASN ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18703 Z= 0.255 Angle : 1.029 43.609 25383 Z= 0.446 Chirality : 0.052 0.705 3104 Planarity : 0.005 0.067 3122 Dihedral : 9.110 82.235 4369 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.66 % Favored : 98.30 % Rotamer: Outliers : 2.27 % Allowed : 6.13 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.70 (0.18), residues: 2113 helix: 1.60 (0.26), residues: 386 sheet: 0.77 (0.19), residues: 594 loop : 1.39 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 479 HIS 0.005 0.001 HIS C 374 PHE 0.040 0.002 PHE E 53 TYR 0.016 0.002 TYR A 32 ARG 0.006 0.001 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 188 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 647 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7947 (mt-10) REVERT: B 656 ASN cc_start: 0.6094 (m-40) cc_final: 0.5566 (p0) REVERT: C 180 ASP cc_start: 0.8625 (m-30) cc_final: 0.8272 (m-30) REVERT: E 377 ASN cc_start: 0.8732 (t0) cc_final: 0.8356 (t0) REVERT: E 424 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9035 (mt) REVERT: L 82 ASP cc_start: 0.8132 (m-30) cc_final: 0.7881 (m-30) REVERT: F 648 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8217 (tm-30) REVERT: G 504 ARG cc_start: 0.5685 (mtt180) cc_final: 0.4412 (mmt180) outliers start: 43 outliers final: 32 residues processed: 216 average time/residue: 0.2876 time to fit residues: 96.4663 Evaluate side-chains 187 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 154 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 358 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain A residue 73 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 161 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN H 13 GLN H 100 HIS ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18703 Z= 0.235 Angle : 0.953 43.475 25383 Z= 0.403 Chirality : 0.049 0.621 3104 Planarity : 0.004 0.070 3122 Dihedral : 7.713 73.665 4365 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.74 % Favored : 97.21 % Rotamer: Outliers : 2.80 % Allowed : 7.08 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.30 (0.18), residues: 2113 helix: 1.73 (0.27), residues: 387 sheet: 0.64 (0.20), residues: 587 loop : 0.85 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 623 HIS 0.033 0.001 HIS C 66 PHE 0.031 0.002 PHE E 53 TYR 0.017 0.001 TYR F 586 ARG 0.006 0.000 ARG A 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 166 time to evaluate : 2.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 656 ASN cc_start: 0.6285 (m-40) cc_final: 0.5673 (p0) REVERT: C 180 ASP cc_start: 0.8624 (m-30) cc_final: 0.8337 (m-30) REVERT: E 377 ASN cc_start: 0.8743 (t0) cc_final: 0.8382 (t0) REVERT: E 424 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9075 (mt) REVERT: L 6 GLN cc_start: 0.6672 (tt0) cc_final: 0.6336 (tt0) REVERT: F 633 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8489 (mttp) REVERT: F 648 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8228 (tm-30) REVERT: G 125 LEU cc_start: 0.9009 (tp) cc_final: 0.8478 (tp) REVERT: G 504 ARG cc_start: 0.5758 (mtt180) cc_final: 0.4512 (mmt180) outliers start: 53 outliers final: 44 residues processed: 202 average time/residue: 0.2898 time to fit residues: 91.8374 Evaluate side-chains 196 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 150 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 93 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 185 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN H 13 GLN G 258 GLN G 330 HIS ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18703 Z= 0.303 Angle : 0.969 43.760 25383 Z= 0.413 Chirality : 0.050 0.482 3104 Planarity : 0.005 0.060 3122 Dihedral : 7.613 76.006 4363 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.22 % Favored : 96.73 % Rotamer: Outliers : 2.96 % Allowed : 8.45 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.79 (0.17), residues: 2113 helix: 1.38 (0.26), residues: 398 sheet: 0.52 (0.20), residues: 596 loop : 0.33 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 631 HIS 0.014 0.002 HIS C 66 PHE 0.028 0.002 PHE E 53 TYR 0.018 0.002 TYR H 98 ARG 0.009 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 155 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 180 ASP cc_start: 0.8690 (m-30) cc_final: 0.8448 (m-30) REVERT: D 535 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7036 (tmm) REVERT: D 540 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.6167 (mp-120) REVERT: E 377 ASN cc_start: 0.8791 (t0) cc_final: 0.8489 (t0) REVERT: E 424 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9126 (mt) REVERT: E 475 MET cc_start: 0.8567 (mmp) cc_final: 0.7989 (mmt) REVERT: L 6 GLN cc_start: 0.6818 (tt0) cc_final: 0.6520 (tt0) REVERT: H 32 TYR cc_start: 0.5915 (OUTLIER) cc_final: 0.4926 (t80) REVERT: G 125 LEU cc_start: 0.9045 (tp) cc_final: 0.8452 (tp) REVERT: G 129 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8737 (tp) REVERT: G 504 ARG cc_start: 0.5697 (mtt180) cc_final: 0.4546 (mmt180) REVERT: I 30 ASP cc_start: 0.7195 (m-30) cc_final: 0.6962 (p0) outliers start: 56 outliers final: 44 residues processed: 196 average time/residue: 0.2820 time to fit residues: 87.6525 Evaluate side-chains 193 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 144 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 73 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 154 optimal weight: 0.0980 chunk 85 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS C 425 ASN E 195 ASN L 76 HIS H 13 GLN ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 18703 Z= 0.162 Angle : 0.900 43.488 25383 Z= 0.372 Chirality : 0.047 0.452 3104 Planarity : 0.004 0.059 3122 Dihedral : 7.207 75.690 4361 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.97 % Rotamer: Outliers : 2.38 % Allowed : 8.93 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.91 (0.18), residues: 2113 helix: 1.73 (0.27), residues: 393 sheet: 0.56 (0.20), residues: 589 loop : 0.34 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 610 HIS 0.007 0.001 HIS G 374 PHE 0.027 0.001 PHE E 53 TYR 0.013 0.001 TYR F 586 ARG 0.005 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 158 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 125 LEU cc_start: 0.9240 (tp) cc_final: 0.8924 (tp) REVERT: D 535 MET cc_start: 0.7727 (mpp) cc_final: 0.6918 (tmm) REVERT: E 290 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8691 (t) REVERT: E 377 ASN cc_start: 0.8726 (t0) cc_final: 0.8481 (t0) REVERT: E 424 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9115 (mt) REVERT: E 475 MET cc_start: 0.8596 (mmp) cc_final: 0.7992 (mmt) REVERT: L 6 GLN cc_start: 0.6938 (tt0) cc_final: 0.6555 (tt0) REVERT: L 97 THR cc_start: 0.8412 (m) cc_final: 0.8207 (m) REVERT: F 633 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8237 (mttt) REVERT: G 125 LEU cc_start: 0.8985 (tp) cc_final: 0.8430 (tp) REVERT: G 504 ARG cc_start: 0.5791 (mtt180) cc_final: 0.4627 (mmt180) REVERT: I 3 VAL cc_start: 0.8496 (t) cc_final: 0.8274 (m) outliers start: 45 outliers final: 32 residues processed: 190 average time/residue: 0.2948 time to fit residues: 88.5562 Evaluate side-chains 181 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 73 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 0.5980 chunk 186 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 207 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN C 66 HIS H 13 GLN ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18703 Z= 0.203 Angle : 0.906 43.459 25383 Z= 0.374 Chirality : 0.048 0.412 3104 Planarity : 0.004 0.103 3122 Dihedral : 7.337 76.356 4361 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.69 % Favored : 96.26 % Rotamer: Outliers : 2.69 % Allowed : 8.77 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.85 (0.18), residues: 2113 helix: 1.72 (0.27), residues: 399 sheet: 0.58 (0.20), residues: 583 loop : 0.24 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 338 HIS 0.016 0.001 HIS C 66 PHE 0.024 0.002 PHE E 53 TYR 0.011 0.001 TYR A 91 ARG 0.011 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 151 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 125 LEU cc_start: 0.9279 (tp) cc_final: 0.9020 (tp) REVERT: D 535 MET cc_start: 0.7839 (mpp) cc_final: 0.7003 (tmm) REVERT: E 290 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8689 (t) REVERT: E 377 ASN cc_start: 0.8734 (t0) cc_final: 0.8499 (t0) REVERT: E 424 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9108 (mt) REVERT: L 6 GLN cc_start: 0.7008 (tt0) cc_final: 0.6550 (tt0) REVERT: L 97 THR cc_start: 0.8444 (m) cc_final: 0.8221 (m) REVERT: H 3 LYS cc_start: 0.7942 (mmmt) cc_final: 0.7421 (pptt) REVERT: F 633 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8207 (mttt) REVERT: G 125 LEU cc_start: 0.8966 (tp) cc_final: 0.8467 (tp) REVERT: G 504 ARG cc_start: 0.5854 (mtt180) cc_final: 0.4628 (mmt180) REVERT: I 24 ARG cc_start: 0.8572 (ptm-80) cc_final: 0.8126 (ptm-80) outliers start: 51 outliers final: 39 residues processed: 191 average time/residue: 0.2893 time to fit residues: 86.8704 Evaluate side-chains 186 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 144 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 73 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 151 optimal weight: 0.1980 chunk 174 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 206 optimal weight: 0.0370 chunk 129 optimal weight: 0.2980 chunk 125 optimal weight: 7.9990 chunk 95 optimal weight: 0.0870 chunk 127 optimal weight: 0.8980 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN H 31 ASN ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18703 Z= 0.131 Angle : 0.883 43.940 25383 Z= 0.359 Chirality : 0.046 0.395 3104 Planarity : 0.004 0.065 3122 Dihedral : 7.089 74.209 4361 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.74 % Favored : 97.21 % Rotamer: Outliers : 2.01 % Allowed : 9.51 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.96 (0.18), residues: 2113 helix: 1.98 (0.27), residues: 396 sheet: 0.58 (0.21), residues: 578 loop : 0.29 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 47 HIS 0.024 0.001 HIS C 66 PHE 0.024 0.001 PHE E 53 TYR 0.011 0.001 TYR F 586 ARG 0.007 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 165 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 651 ASN cc_start: 0.6352 (t0) cc_final: 0.6095 (t0) REVERT: C 142 MET cc_start: 0.2514 (mmm) cc_final: 0.0763 (ttt) REVERT: D 535 MET cc_start: 0.7806 (mpp) cc_final: 0.6950 (tmm) REVERT: E 377 ASN cc_start: 0.8630 (t0) cc_final: 0.8397 (t0) REVERT: E 424 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.9050 (mt) REVERT: E 475 MET cc_start: 0.8527 (mmp) cc_final: 0.7889 (mmt) REVERT: L 6 GLN cc_start: 0.7081 (tt0) cc_final: 0.6558 (tt0) REVERT: L 97 THR cc_start: 0.8328 (m) cc_final: 0.8095 (m) REVERT: H 3 LYS cc_start: 0.7910 (mmmt) cc_final: 0.7432 (pptt) REVERT: H 32 TYR cc_start: 0.5165 (OUTLIER) cc_final: 0.4599 (t80) REVERT: H 75 ARG cc_start: 0.8964 (ttm-80) cc_final: 0.8528 (mtt180) REVERT: F 633 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8173 (mttt) REVERT: G 125 LEU cc_start: 0.8991 (tp) cc_final: 0.8381 (tp) REVERT: G 504 ARG cc_start: 0.5923 (mtt180) cc_final: 0.4645 (mmt180) REVERT: I 3 VAL cc_start: 0.8483 (t) cc_final: 0.8237 (m) REVERT: I 24 ARG cc_start: 0.8519 (ptm-80) cc_final: 0.8233 (ptm160) REVERT: A 77 THR cc_start: 0.7496 (p) cc_final: 0.7066 (p) REVERT: A 82 ASN cc_start: 0.8505 (t0) cc_final: 0.8259 (t0) outliers start: 38 outliers final: 33 residues processed: 190 average time/residue: 0.2755 time to fit residues: 84.0666 Evaluate side-chains 190 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 154 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 73 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 39 optimal weight: 0.1980 chunk 131 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18703 Z= 0.156 Angle : 0.883 43.412 25383 Z= 0.360 Chirality : 0.046 0.377 3104 Planarity : 0.004 0.050 3122 Dihedral : 7.105 73.636 4359 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.41 % Favored : 96.55 % Rotamer: Outliers : 2.38 % Allowed : 9.51 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.95 (0.18), residues: 2113 helix: 1.98 (0.27), residues: 396 sheet: 0.61 (0.21), residues: 578 loop : 0.25 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 610 HIS 0.014 0.001 HIS C 66 PHE 0.022 0.001 PHE E 53 TYR 0.016 0.001 TYR B 643 ARG 0.005 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 150 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 535 MET cc_start: 0.7869 (mpp) cc_final: 0.7035 (tmm) REVERT: D 633 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8803 (pptt) REVERT: E 290 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8602 (t) REVERT: E 377 ASN cc_start: 0.8666 (t0) cc_final: 0.8418 (t0) REVERT: E 424 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.9037 (mt) REVERT: E 475 MET cc_start: 0.8558 (mmp) cc_final: 0.7937 (mmt) REVERT: L 6 GLN cc_start: 0.7120 (tt0) cc_final: 0.6606 (tt0) REVERT: L 97 THR cc_start: 0.8330 (m) cc_final: 0.8102 (m) REVERT: H 3 LYS cc_start: 0.7942 (mmmt) cc_final: 0.7445 (pptt) REVERT: H 32 TYR cc_start: 0.5407 (OUTLIER) cc_final: 0.4666 (t80) REVERT: H 75 ARG cc_start: 0.8973 (ttm-80) cc_final: 0.8545 (mtt180) REVERT: F 633 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8209 (mttt) REVERT: G 125 LEU cc_start: 0.8944 (tp) cc_final: 0.8412 (tp) REVERT: G 504 ARG cc_start: 0.5933 (mtt180) cc_final: 0.4681 (mmt180) REVERT: I 24 ARG cc_start: 0.8487 (ptm-80) cc_final: 0.8225 (ptm160) REVERT: A 77 THR cc_start: 0.7455 (p) cc_final: 0.7037 (p) REVERT: A 82 ASN cc_start: 0.8557 (t0) cc_final: 0.8290 (t0) outliers start: 45 outliers final: 35 residues processed: 181 average time/residue: 0.2713 time to fit residues: 78.6388 Evaluate side-chains 183 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 143 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 73 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 58 optimal weight: 0.0870 chunk 173 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 191 optimal weight: 0.5980 chunk 126 optimal weight: 0.8980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN C 66 HIS ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18703 Z= 0.160 Angle : 0.889 43.423 25383 Z= 0.361 Chirality : 0.046 0.363 3104 Planarity : 0.004 0.048 3122 Dihedral : 7.032 73.096 4359 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.41 % Favored : 96.55 % Rotamer: Outliers : 2.27 % Allowed : 9.98 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.92 (0.18), residues: 2113 helix: 1.99 (0.27), residues: 396 sheet: 0.62 (0.21), residues: 578 loop : 0.20 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.014 0.001 HIS C 66 PHE 0.021 0.001 PHE E 53 TYR 0.013 0.001 TYR B 643 ARG 0.004 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 145 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 656 ASN cc_start: 0.6051 (m-40) cc_final: 0.5216 (p0) REVERT: C 142 MET cc_start: 0.2564 (mmm) cc_final: 0.0798 (ttt) REVERT: D 535 MET cc_start: 0.7884 (mpp) cc_final: 0.6955 (tmm) REVERT: D 633 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8807 (pptt) REVERT: E 290 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8609 (t) REVERT: E 377 ASN cc_start: 0.8670 (t0) cc_final: 0.8436 (t0) REVERT: E 424 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9040 (mt) REVERT: E 475 MET cc_start: 0.8591 (mmp) cc_final: 0.7974 (mmt) REVERT: L 6 GLN cc_start: 0.7123 (tt0) cc_final: 0.6597 (tt0) REVERT: L 97 THR cc_start: 0.8275 (m) cc_final: 0.8044 (m) REVERT: H 3 LYS cc_start: 0.7980 (mmmt) cc_final: 0.7471 (pptt) REVERT: H 32 TYR cc_start: 0.5578 (OUTLIER) cc_final: 0.4566 (t80) REVERT: H 75 ARG cc_start: 0.8970 (ttm-80) cc_final: 0.8553 (mtt180) REVERT: F 574 LYS cc_start: 0.9005 (mttt) cc_final: 0.8558 (mmtt) REVERT: F 633 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8184 (mttt) REVERT: G 125 LEU cc_start: 0.8935 (tp) cc_final: 0.8410 (tp) REVERT: G 504 ARG cc_start: 0.5952 (mtt180) cc_final: 0.4688 (mmt180) REVERT: I 3 VAL cc_start: 0.8542 (t) cc_final: 0.8261 (m) REVERT: I 24 ARG cc_start: 0.8460 (ptm-80) cc_final: 0.8242 (ptm160) REVERT: A 77 THR cc_start: 0.7430 (p) cc_final: 0.7032 (p) REVERT: A 82 ASN cc_start: 0.8613 (t0) cc_final: 0.8353 (t0) outliers start: 43 outliers final: 36 residues processed: 175 average time/residue: 0.2889 time to fit residues: 79.8025 Evaluate side-chains 183 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 142 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 141 optimal weight: 0.3980 chunk 213 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 104 optimal weight: 0.0370 chunk 134 optimal weight: 0.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN C 66 HIS ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18703 Z= 0.140 Angle : 0.884 43.394 25383 Z= 0.359 Chirality : 0.046 0.352 3104 Planarity : 0.004 0.047 3122 Dihedral : 6.875 71.662 4359 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.36 % Favored : 96.59 % Rotamer: Outliers : 2.11 % Allowed : 10.04 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.93 (0.18), residues: 2113 helix: 2.03 (0.27), residues: 396 sheet: 0.67 (0.21), residues: 566 loop : 0.17 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 47 HIS 0.011 0.001 HIS C 66 PHE 0.021 0.001 PHE E 53 TYR 0.011 0.001 TYR B 643 ARG 0.005 0.000 ARG C 308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 147 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 656 ASN cc_start: 0.6028 (m-40) cc_final: 0.5238 (p0) REVERT: C 142 MET cc_start: 0.2604 (mmm) cc_final: 0.0784 (ttt) REVERT: D 535 MET cc_start: 0.7929 (mpp) cc_final: 0.7021 (tmm) REVERT: D 633 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8814 (pptt) REVERT: E 207 LYS cc_start: 0.8869 (mmtt) cc_final: 0.8597 (pttt) REVERT: E 290 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8596 (t) REVERT: E 377 ASN cc_start: 0.8634 (t0) cc_final: 0.8412 (t0) REVERT: E 424 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.9022 (mt) REVERT: E 475 MET cc_start: 0.8556 (mmp) cc_final: 0.7941 (mmt) REVERT: L 6 GLN cc_start: 0.7124 (tt0) cc_final: 0.6581 (tt0) REVERT: L 97 THR cc_start: 0.8249 (m) cc_final: 0.8008 (m) REVERT: H 3 LYS cc_start: 0.7970 (mmmt) cc_final: 0.7502 (pptt) REVERT: H 32 TYR cc_start: 0.5575 (OUTLIER) cc_final: 0.4555 (t80) REVERT: H 75 ARG cc_start: 0.8963 (ttm-80) cc_final: 0.8591 (mtm180) REVERT: F 574 LYS cc_start: 0.8952 (mttt) cc_final: 0.8508 (mmtt) REVERT: F 624 ASP cc_start: 0.8524 (m-30) cc_final: 0.8260 (m-30) REVERT: F 633 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8179 (mttt) REVERT: G 125 LEU cc_start: 0.8944 (tp) cc_final: 0.8397 (tp) REVERT: G 504 ARG cc_start: 0.5940 (mtt180) cc_final: 0.4680 (mmt180) REVERT: I 3 VAL cc_start: 0.8563 (t) cc_final: 0.8344 (m) REVERT: A 77 THR cc_start: 0.7424 (p) cc_final: 0.7024 (p) REVERT: A 82 ASN cc_start: 0.8621 (t0) cc_final: 0.8391 (t0) outliers start: 40 outliers final: 34 residues processed: 175 average time/residue: 0.2850 time to fit residues: 78.9692 Evaluate side-chains 183 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 144 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.9980 chunk 52 optimal weight: 0.0970 chunk 156 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 170 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.083432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.069132 restraints weight = 57107.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.070988 restraints weight = 35325.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.072226 restraints weight = 25543.641| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18703 Z= 0.190 Angle : 0.899 43.442 25383 Z= 0.368 Chirality : 0.047 0.337 3104 Planarity : 0.004 0.047 3122 Dihedral : 7.006 71.699 4359 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.07 % Favored : 95.88 % Rotamer: Outliers : 2.27 % Allowed : 9.98 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.83 (0.18), residues: 2113 helix: 1.84 (0.28), residues: 402 sheet: 0.75 (0.22), residues: 557 loop : 0.06 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.010 0.001 HIS G 374 PHE 0.020 0.001 PHE E 53 TYR 0.011 0.001 TYR B 643 ARG 0.004 0.000 ARG A 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3493.10 seconds wall clock time: 66 minutes 56.52 seconds (4016.52 seconds total)