Starting phenix.real_space_refine on Fri Feb 6 16:46:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nbt_49236/02_2026/9nbt_49236.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nbt_49236/02_2026/9nbt_49236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nbt_49236/02_2026/9nbt_49236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nbt_49236/02_2026/9nbt_49236.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nbt_49236/02_2026/9nbt_49236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nbt_49236/02_2026/9nbt_49236.map" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.054 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 168 5.16 5 C 16488 2.51 5 N 4335 2.21 5 O 5346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26337 Number of models: 1 Model: "" Number of chains: 63 Chain: "A" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3613 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 22, 'TRANS': 434} Chain breaks: 1 Chain: "B" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1022 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "C" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "D" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 759 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 91} Chain: "H" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1009 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 98} Chain: "E" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "F" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 759 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 91} Chain: "G" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1009 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "I" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 98} Chain: "J" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3613 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 22, 'TRANS': 434} Chain breaks: 1 Chain: "K" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1022 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "M" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "N" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 759 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 91} Chain: "O" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1009 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "P" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 98} Chain: "Q" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3613 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 22, 'TRANS': 434} Chain breaks: 1 Chain: "R" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1022 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "l" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 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: "2" 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: "3" 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: "4" 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "N" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.06, per 1000 atoms: 0.23 Number of scatterers: 26337 At special positions: 0 Unit cell: (160.208, 148.614, 141.236, 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 168 16.00 O 5346 8.00 N 4335 7.00 C 16488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.17 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.17 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.06 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.02 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 98 " distance=2.10 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.12 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.17 Simple disulfide: pdb=" SG CYS L 27C" - pdb=" SG CYS L 28 " distance=2.11 Simple disulfide: pdb=" SG CYS L 89 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.02 Simple disulfide: pdb=" SG CYS E 32 " - pdb=" SG CYS E 98 " distance=2.09 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.13 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.06 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.15 Simple disulfide: pdb=" SG CYS I 27C" - pdb=" SG CYS I 28 " distance=2.09 Simple disulfide: pdb=" SG CYS I 89 " - pdb=" SG CYS I 96 " distance=2.02 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.02 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.18 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.18 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.03 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.02 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.04 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS K 605 " distance=2.04 Simple disulfide: pdb=" SG CYS K 598 " - pdb=" SG CYS K 604 " distance=2.06 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.02 Simple disulfide: pdb=" SG CYS M 32 " - pdb=" SG CYS M 98 " distance=2.09 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.12 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.16 Simple disulfide: pdb=" SG CYS P 27C" - pdb=" SG CYS P 28 " distance=2.11 Simple disulfide: pdb=" SG CYS P 89 " - pdb=" SG CYS P 96 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 54 " - pdb=" SG CYS Q 74 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 119 " - pdb=" SG CYS Q 205 " distance=2.13 Simple disulfide: pdb=" SG CYS Q 126 " - pdb=" SG CYS Q 196 " distance=2.18 Simple disulfide: pdb=" SG CYS Q 131 " - pdb=" SG CYS Q 157 " distance=2.10 Simple disulfide: pdb=" SG CYS Q 218 " - pdb=" SG CYS Q 247 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 228 " - pdb=" SG CYS Q 239 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 296 " - pdb=" SG CYS Q 331 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 378 " - pdb=" SG CYS Q 445 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 385 " - pdb=" SG CYS Q 418 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 501 " - pdb=" SG CYS R 605 " distance=2.03 Simple disulfide: pdb=" SG CYS R 598 " - pdb=" SG CYS R 604 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA X 3 " - " MAN X 4 " " MAN Y 4 " - " MAN Y 5 " " BMA f 3 " - " MAN f 4 " " BMA k 3 " - " MAN k 4 " " MAN l 4 " - " MAN l 5 " " BMA s 3 " - " MAN s 4 " " BMA x 3 " - " MAN x 4 " " MAN y 4 " - " MAN y 5 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA X 3 " - " MAN X 5 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 4 " - " MAN Y 6 " " BMA f 3 " - " MAN f 5 " " BMA k 3 " - " MAN k 5 " " BMA l 3 " - " MAN l 4 " " MAN l 4 " - " MAN l 6 " " BMA s 3 " - " MAN s 5 " " BMA x 3 " - " MAN x 5 " " BMA y 3 " - " MAN y 4 " " MAN y 4 " - " MAN y 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " 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 h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " 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 x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN Q 301 " " NAG 1 1 " - " ASN Q 332 " " NAG 2 1 " - " ASN Q 386 " " NAG 3 1 " - " ASN Q 392 " " NAG 4 1 " - " ASN Q 448 " " NAG A 601 " - " ASN A 160 " " NAG A 602 " - " ASN A 295 " " NAG A 603 " - " ASN A 339 " " NAG A 604 " - " ASN A 356 " " NAG A 605 " - " ASN A 362 " " NAG A 606 " - " ASN A 396 " " NAG A 607 " - " ASN A 463 " " NAG D 301 " - " ASN D 72 " " NAG F 301 " - " ASN F 72 " " NAG J 601 " - " ASN J 160 " " NAG J 602 " - " ASN J 295 " " NAG J 603 " - " ASN J 339 " " NAG J 604 " - " ASN J 356 " " NAG J 605 " - " ASN J 362 " " NAG J 606 " - " ASN J 396 " " NAG J 607 " - " ASN J 463 " " NAG N 301 " - " ASN N 72 " " NAG Q 601 " - " ASN Q 160 " " NAG Q 602 " - " ASN Q 295 " " NAG Q 603 " - " ASN Q 339 " " NAG Q 604 " - " ASN Q 356 " " NAG Q 605 " - " ASN Q 362 " " NAG Q 606 " - " ASN Q 396 " " NAG Q 607 " - " ASN Q 463 " " NAG S 1 " - " ASN A 88 " " NAG T 1 " - " ASN A 130 " " NAG U 1 " - " ASN A 156 " " NAG V 1 " - " ASN A 197 " " NAG W 1 " - " ASN A 241 " " NAG X 1 " - " ASN A 262 " " NAG Y 1 " - " ASN A 276 " " NAG Z 1 " - " ASN A 289 " " NAG a 1 " - " ASN A 301 " " NAG b 1 " - " ASN A 332 " " NAG c 1 " - " ASN A 386 " " NAG d 1 " - " ASN A 392 " " NAG e 1 " - " ASN A 448 " " NAG f 1 " - " ASN J 88 " " NAG g 1 " - " ASN J 130 " " NAG h 1 " - " ASN J 156 " " NAG i 1 " - " ASN J 197 " " NAG j 1 " - " ASN J 241 " " NAG k 1 " - " ASN J 262 " " NAG l 1 " - " ASN J 276 " " NAG m 1 " - " ASN J 289 " " NAG n 1 " - " ASN J 301 " " NAG o 1 " - " ASN J 332 " " NAG p 1 " - " ASN J 386 " " NAG q 1 " - " ASN J 392 " " NAG r 1 " - " ASN J 448 " " NAG s 1 " - " ASN Q 88 " " NAG t 1 " - " ASN Q 130 " " NAG u 1 " - " ASN Q 156 " " NAG v 1 " - " ASN Q 197 " " NAG w 1 " - " ASN Q 241 " " NAG x 1 " - " ASN Q 262 " " NAG y 1 " - " ASN Q 276 " " NAG z 1 " - " ASN Q 289 " Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.0 seconds 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5736 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 48 sheets defined 19.0% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.056A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.527A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 520 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.521A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.716A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.521A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.914A pdb=" N PHE D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.529A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.612A pdb=" N PHE F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.524A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'J' and resid 70 through 74 Processing helix chain 'J' and resid 98 through 117 removed outlier: 4.058A pdb=" N GLU J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 126 Processing helix chain 'J' and resid 335 through 353 Processing helix chain 'J' and resid 368 through 373 Processing helix chain 'J' and resid 387 through 390 Processing helix chain 'J' and resid 396 through 401 Processing helix chain 'J' and resid 475 through 484 removed outlier: 3.672A pdb=" N TRP J 479 " --> pdb=" O MET J 475 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU J 482 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 516 through 520 Processing helix chain 'K' and resid 529 through 534 Processing helix chain 'K' and resid 536 through 543 removed outlier: 3.774A pdb=" N GLN K 540 " --> pdb=" O THR K 536 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN K 543 " --> pdb=" O VAL K 539 " (cutoff:3.500A) Processing helix chain 'K' and resid 569 through 596 Processing helix chain 'K' and resid 611 through 615 Processing helix chain 'K' and resid 618 through 626 removed outlier: 3.691A pdb=" N MET K 626 " --> pdb=" O ILE K 622 " (cutoff:3.500A) Processing helix chain 'K' and resid 627 through 635 Processing helix chain 'K' and resid 638 through 662 removed outlier: 3.541A pdb=" N ASN K 651 " --> pdb=" O GLU K 647 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.998A pdb=" N PHE N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'Q' and resid 70 through 74 Processing helix chain 'Q' and resid 98 through 117 removed outlier: 4.057A pdb=" N GLU Q 102 " --> pdb=" O ASN Q 98 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS Q 117 " --> pdb=" O ASP Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 122 through 126 Processing helix chain 'Q' and resid 335 through 353 Processing helix chain 'Q' and resid 368 through 373 Processing helix chain 'Q' and resid 396 through 401 Processing helix chain 'Q' and resid 475 through 484 removed outlier: 3.595A pdb=" N TRP Q 479 " --> pdb=" O MET Q 475 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU Q 482 " --> pdb=" O ASN Q 478 " (cutoff:3.500A) Processing helix chain 'R' and resid 516 through 520 Processing helix chain 'R' and resid 529 through 534 Processing helix chain 'R' and resid 536 through 543 removed outlier: 3.755A pdb=" N GLN R 540 " --> pdb=" O THR R 536 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN R 543 " --> pdb=" O VAL R 539 " (cutoff:3.500A) Processing helix chain 'R' and resid 569 through 596 Processing helix chain 'R' and resid 611 through 615 Processing helix chain 'R' and resid 618 through 625 Processing helix chain 'R' and resid 627 through 635 Processing helix chain 'R' and resid 638 through 662 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.286A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.899A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 67 removed outlier: 6.713A pdb=" N ARG A 66 " --> pdb=" O THR A 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.003A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.764A pdb=" N ASN A 301 " --> pdb=" O ILE A 322A" (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE A 322A" --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 10 through 12 current: chain 'C' and resid 46 through 52 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 59 current: chain 'C' and resid 102 through 103 Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 10 through 12 current: chain 'D' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 53 through 54 current: chain 'D' and resid 97 through 98 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 6 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 18 through 27 current: chain 'H' and resid 74 through 82 Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100F through 103 Processing sheet with id=AB6, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB7, first strand: chain 'L' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 12 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 Processing sheet with id=AB8, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 10 through 12 current: chain 'E' and resid 46 through 52 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 56 through 59 current: chain 'E' and resid 102 through 103 Processing sheet with id=AC1, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'F' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 10 through 12 current: chain 'F' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 53 through 54 current: chain 'F' and resid 97 through 98 Processing sheet with id=AC3, first strand: chain 'G' and resid 3 through 6 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 18 through 27 current: chain 'G' and resid 74 through 82 Processing sheet with id=AC4, first strand: chain 'G' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 10 through 12 current: chain 'G' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 57 through 59 current: chain 'G' and resid 100F through 103 Processing sheet with id=AC5, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AC6, first strand: chain 'I' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 9 through 12 current: chain 'I' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 53 through 54 current: chain 'I' and resid 95 through 98 Processing sheet with id=AC7, first strand: chain 'J' and resid 494 through 499 removed outlier: 5.282A pdb=" N VAL K 608 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N VAL J 38 " --> pdb=" O THR K 606 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N THR K 606 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N TYR J 40 " --> pdb=" O CYS K 604 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N CYS K 604 " --> pdb=" O TYR J 40 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 45 through 47 removed outlier: 3.902A pdb=" N ILE J 225 " --> pdb=" O VAL J 245 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 75 through 76 Processing sheet with id=AD1, first strand: chain 'J' and resid 66 through 67 removed outlier: 6.679A pdb=" N ARG J 66 " --> pdb=" O THR J 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'J' and resid 91 through 94 Processing sheet with id=AD3, first strand: chain 'J' and resid 169 through 177 Processing sheet with id=AD4, first strand: chain 'J' and resid 200 through 203 removed outlier: 6.008A pdb=" N VAL J 200 " --> pdb=" O ALA J 433 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TYR J 435 " --> pdb=" O VAL J 200 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR J 202 " --> pdb=" O TYR J 435 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 259 through 261 current: chain 'J' and resid 284 through 312 removed outlier: 6.790A pdb=" N ASN J 301 " --> pdb=" O ILE J 322A" (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE J 322A" --> pdb=" O ASN J 301 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR J 303 " --> pdb=" O GLY J 321 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ARG J 315 " --> pdb=" O ILE J 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 315 through 323 current: chain 'J' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 381 through 385 current: chain 'J' and resid 465 through 470 Processing sheet with id=AD6, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AD7, first strand: chain 'M' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 10 through 12 current: chain 'M' and resid 46 through 52 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 56 through 59 current: chain 'M' and resid 102 through 103 Processing sheet with id=AD8, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AD9, first strand: chain 'N' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 10 through 12 current: chain 'N' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 53 through 54 current: chain 'N' and resid 97 through 98 Processing sheet with id=AE1, first strand: chain 'O' and resid 3 through 6 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 18 through 27 current: chain 'O' and resid 74 through 82 Processing sheet with id=AE2, first strand: chain 'O' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 10 through 12 current: chain 'O' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 57 through 58 current: chain 'O' and resid 100F through 103 Processing sheet with id=AE3, first strand: chain 'P' and resid 5 through 6 Processing sheet with id=AE4, first strand: chain 'P' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 9 through 12 current: chain 'P' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 53 through 54 current: chain 'P' and resid 95 through 98 Processing sheet with id=AE5, first strand: chain 'Q' and resid 494 through 499 removed outlier: 5.279A pdb=" N VAL R 608 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL Q 38 " --> pdb=" O THR R 606 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N THR R 606 " --> pdb=" O VAL Q 38 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N TYR Q 40 " --> pdb=" O CYS R 604 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N CYS R 604 " --> pdb=" O TYR Q 40 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 45 through 47 removed outlier: 3.917A pdb=" N ILE Q 225 " --> pdb=" O VAL Q 245 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 75 through 76 Processing sheet with id=AE8, first strand: chain 'Q' and resid 66 through 67 removed outlier: 6.706A pdb=" N ARG Q 66 " --> pdb=" O THR Q 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'Q' and resid 91 through 94 Processing sheet with id=AF1, first strand: chain 'Q' and resid 169 through 177 Processing sheet with id=AF2, first strand: chain 'Q' and resid 200 through 203 removed outlier: 6.028A pdb=" N VAL Q 200 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TYR Q 435 " --> pdb=" O VAL Q 200 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR Q 202 " --> pdb=" O TYR Q 435 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 259 through 261 current: chain 'Q' and resid 284 through 312 removed outlier: 6.759A pdb=" N ASN Q 301 " --> pdb=" O ILE Q 322A" (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE Q 322A" --> pdb=" O ASN Q 301 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N THR Q 303 " --> pdb=" O GLY Q 321 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG Q 315 " --> pdb=" O ILE Q 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 315 through 323 current: chain 'Q' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 381 through 385 current: chain 'Q' and resid 465 through 470 669 hydrogen bonds defined for protein. 1683 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: 5.55 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6514 1.33 - 1.46: 8621 1.46 - 1.60: 11538 1.60 - 1.73: 0 1.73 - 1.87: 228 Bond restraints: 26901 Sorted by residual: bond pdb=" CG ASP Q 167 " pdb=" OD1 ASP Q 167 " ideal model delta sigma weight residual 1.249 1.196 0.053 1.90e-02 2.77e+03 7.78e+00 bond pdb=" CG ASP J 167 " pdb=" OD1 ASP J 167 " ideal model delta sigma weight residual 1.249 1.196 0.053 1.90e-02 2.77e+03 7.78e+00 bond pdb=" CG ASP A 167 " pdb=" OD1 ASP A 167 " ideal model delta sigma weight residual 1.249 1.196 0.053 1.90e-02 2.77e+03 7.67e+00 bond pdb=" CG ASP L 51 " pdb=" OD1 ASP L 51 " ideal model delta sigma weight residual 1.249 1.197 0.052 1.90e-02 2.77e+03 7.62e+00 bond pdb=" CD GLU B 654 " pdb=" OE1 GLU B 654 " ideal model delta sigma weight residual 1.249 1.197 0.052 1.90e-02 2.77e+03 7.44e+00 ... (remaining 26896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 32475 1.84 - 3.68: 3376 3.68 - 5.52: 538 5.52 - 7.36: 142 7.36 - 9.20: 18 Bond angle restraints: 36549 Sorted by residual: angle pdb=" C GLY D 68 " pdb=" N PRO D 69 " pdb=" CA PRO D 69 " ideal model delta sigma weight residual 119.56 128.76 -9.20 1.02e+00 9.61e-01 8.14e+01 angle pdb=" C GLY N 68 " pdb=" N PRO N 69 " pdb=" CA PRO N 69 " ideal model delta sigma weight residual 119.56 128.75 -9.19 1.02e+00 9.61e-01 8.12e+01 angle pdb=" C GLY F 68 " pdb=" N PRO F 69 " pdb=" CA PRO F 69 " ideal model delta sigma weight residual 119.56 128.45 -8.89 1.02e+00 9.61e-01 7.59e+01 angle pdb=" C ALA J 436 " pdb=" N PRO J 437 " pdb=" CA PRO J 437 " ideal model delta sigma weight residual 119.66 125.22 -5.56 7.20e-01 1.93e+00 5.96e+01 angle pdb=" C GLY A 237 " pdb=" N PRO A 238 " pdb=" CA PRO A 238 " ideal model delta sigma weight residual 119.76 127.63 -7.87 1.03e+00 9.43e-01 5.84e+01 ... (remaining 36544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.02: 17085 21.02 - 42.05: 427 42.05 - 63.07: 106 63.07 - 84.10: 109 84.10 - 105.12: 57 Dihedral angle restraints: 17784 sinusoidal: 8835 harmonic: 8949 Sorted by residual: dihedral pdb=" CB CYS L 89 " pdb=" SG CYS L 89 " pdb=" SG CYS L 96 " pdb=" CB CYS L 96 " ideal model delta sinusoidal sigma weight residual 93.00 174.20 -81.20 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" CB CYS I 89 " pdb=" SG CYS I 89 " pdb=" SG CYS I 96 " pdb=" CB CYS I 96 " ideal model delta sinusoidal sigma weight residual 93.00 169.36 -76.36 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS P 89 " pdb=" SG CYS P 89 " pdb=" SG CYS P 96 " pdb=" CB CYS P 96 " ideal model delta sinusoidal sigma weight residual 93.00 166.91 -73.91 1 1.00e+01 1.00e-02 6.94e+01 ... (remaining 17781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 3915 0.114 - 0.228: 459 0.228 - 0.342: 36 0.342 - 0.455: 15 0.455 - 0.569: 6 Chirality restraints: 4431 Sorted by residual: chirality pdb=" C1 BMA Y 3 " pdb=" O4 NAG Y 2 " pdb=" C2 BMA Y 3 " pdb=" O5 BMA Y 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-02 2.50e+03 8.10e+02 chirality pdb=" C1 BMA y 3 " pdb=" O4 NAG y 2 " pdb=" C2 BMA y 3 " pdb=" O5 BMA y 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-02 2.50e+03 8.08e+02 chirality pdb=" C1 BMA l 3 " pdb=" O4 NAG l 2 " pdb=" C2 BMA l 3 " pdb=" O5 BMA l 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-02 2.50e+03 8.07e+02 ... (remaining 4428 not shown) Planarity restraints: 4539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 72 " -0.057 2.00e-02 2.50e+03 5.94e-02 4.41e+01 pdb=" CG ASN D 72 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN D 72 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN D 72 " 0.093 2.00e-02 2.50e+03 pdb=" C1 NAG D 301 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN N 72 " -0.056 2.00e-02 2.50e+03 5.86e-02 4.30e+01 pdb=" CG ASN N 72 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN N 72 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN N 72 " 0.092 2.00e-02 2.50e+03 pdb=" C1 NAG N 301 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 197 " 0.036 2.00e-02 2.50e+03 3.71e-02 1.72e+01 pdb=" CG ASN J 197 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN J 197 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN J 197 " -0.057 2.00e-02 2.50e+03 pdb=" C1 NAG i 1 " 0.044 2.00e-02 2.50e+03 ... (remaining 4536 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 9060 2.86 - 3.37: 22343 3.37 - 3.88: 44812 3.88 - 4.39: 51117 4.39 - 4.90: 85410 Nonbonded interactions: 212742 Sorted by model distance: nonbonded pdb=" OG SER B 607 " pdb=" OG SER B 649 " model vdw 2.348 3.040 nonbonded pdb=" OG SER R 607 " pdb=" OG SER R 649 " model vdw 2.350 3.040 nonbonded pdb=" O TYR N 49 " pdb=" OG1 THR N 53 " model vdw 2.410 3.040 nonbonded pdb=" O TYR D 49 " pdb=" OG1 THR D 53 " model vdw 2.411 3.040 nonbonded pdb=" O TYR F 49 " pdb=" OG1 THR F 53 " model vdw 2.431 3.040 ... (remaining 212737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'u' selection = chain 'w' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'J' selection = chain 'Q' } ncs_group { reference = chain 'B' selection = chain 'K' selection = chain 'R' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'O' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'P' } ncs_group { reference = chain 'S' selection = chain 'X' selection = chain 'f' selection = chain 'k' selection = chain 's' selection = chain 'x' } ncs_group { reference = chain 'V' selection = chain 'i' selection = chain 'v' } ncs_group { reference = chain 'Y' selection = chain 'l' selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.420 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 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 : 0.013 0.153 27090 Z= 0.678 Angle : 1.440 20.716 37062 Z= 0.853 Chirality : 0.076 0.569 4431 Planarity : 0.005 0.022 4476 Dihedral : 13.457 105.120 11886 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 0.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.15), residues: 3069 helix: -0.12 (0.20), residues: 447 sheet: 1.89 (0.15), residues: 996 loop : 2.96 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 61 TYR 0.041 0.004 TYR A 40 PHE 0.024 0.004 PHE L 98 TRP 0.031 0.006 TRP J 479 HIS 0.004 0.001 HIS Q 330 Details of bonding type rmsd covalent geometry : bond 0.01179 (26901) covalent geometry : angle 1.26942 (36549) SS BOND : bond 0.06581 ( 54) SS BOND : angle 4.04043 ( 108) hydrogen bonds : bond 0.20147 ( 669) hydrogen bonds : angle 6.80854 ( 1683) link_ALPHA1-3 : bond 0.04827 ( 9) link_ALPHA1-3 : angle 3.35789 ( 27) link_ALPHA1-6 : bond 0.03872 ( 12) link_ALPHA1-6 : angle 4.40274 ( 36) link_BETA1-4 : bond 0.04748 ( 51) link_BETA1-4 : angle 8.28680 ( 153) link_NAG-ASN : bond 0.07111 ( 63) link_NAG-ASN : angle 4.99856 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 590 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 GLN cc_start: 0.7368 (tt0) cc_final: 0.7129 (mm-40) REVERT: A 264 SER cc_start: 0.8303 (p) cc_final: 0.7657 (m) REVERT: C 69 MET cc_start: 0.8577 (mtt) cc_final: 0.8311 (mtt) REVERT: D 37 GLN cc_start: 0.7946 (tt0) cc_final: 0.7693 (tt0) REVERT: H 29 PHE cc_start: 0.6255 (t80) cc_final: 0.6033 (t80) REVERT: H 100 THR cc_start: 0.6905 (p) cc_final: 0.6583 (t) REVERT: E 31 ASP cc_start: 0.7329 (m-30) cc_final: 0.7025 (m-30) REVERT: E 69 MET cc_start: 0.8661 (mtt) cc_final: 0.8378 (mtm) REVERT: J 264 SER cc_start: 0.8182 (p) cc_final: 0.7510 (m) REVERT: M 31 ASP cc_start: 0.7319 (m-30) cc_final: 0.7008 (m-30) REVERT: O 69 MET cc_start: 0.2171 (mtt) cc_final: 0.1618 (ptt) REVERT: Q 190 ASN cc_start: 0.8293 (m-40) cc_final: 0.8090 (m-40) outliers start: 0 outliers final: 1 residues processed: 590 average time/residue: 0.6227 time to fit residues: 423.6901 Evaluate side-chains 399 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 398 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 412 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 249 HIS A 308 ASN B 543 ASN B 591 GLN D 27 GLN F 27 GLN J 300 ASN J 374 HIS K 543 ASN N 27 GLN N 42 GLN N 89 GLN Q 170 GLN Q 300 ASN Q 374 HIS Q 442 GLN R 543 ASN ** R 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 651 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.222829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.177317 restraints weight = 29140.318| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 4.54 r_work: 0.3605 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27090 Z= 0.149 Angle : 0.658 8.984 37062 Z= 0.319 Chirality : 0.046 0.205 4431 Planarity : 0.004 0.047 4476 Dihedral : 10.060 88.311 6146 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.90 % Allowed : 8.11 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.15), residues: 3069 helix: 1.59 (0.25), residues: 438 sheet: 1.57 (0.15), residues: 1077 loop : 2.20 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 504 TYR 0.023 0.001 TYR F 49 PHE 0.029 0.002 PHE O 29 TRP 0.017 0.002 TRP C 50 HIS 0.006 0.001 HIS Q 105 Details of bonding type rmsd covalent geometry : bond 0.00339 (26901) covalent geometry : angle 0.60870 (36549) SS BOND : bond 0.00385 ( 54) SS BOND : angle 1.19209 ( 108) hydrogen bonds : bond 0.05823 ( 669) hydrogen bonds : angle 5.35197 ( 1683) link_ALPHA1-3 : bond 0.00998 ( 9) link_ALPHA1-3 : angle 2.36853 ( 27) link_ALPHA1-6 : bond 0.00512 ( 12) link_ALPHA1-6 : angle 1.64179 ( 36) link_BETA1-4 : bond 0.00437 ( 51) link_BETA1-4 : angle 2.28085 ( 153) link_NAG-ASN : bond 0.00426 ( 63) link_NAG-ASN : angle 2.61270 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 430 time to evaluate : 0.973 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: A 66 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6865 (ptt90) REVERT: A 264 SER cc_start: 0.8797 (p) cc_final: 0.8159 (m) REVERT: A 267 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6038 (mp0) REVERT: A 429 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7892 (mm-30) REVERT: A 504 ARG cc_start: 0.7876 (mtt90) cc_final: 0.7602 (mpt90) REVERT: B 538 THR cc_start: 0.8464 (m) cc_final: 0.8228 (p) REVERT: C 31 ASP cc_start: 0.7714 (m-30) cc_final: 0.7453 (m-30) REVERT: E 23 ARG cc_start: 0.7552 (ttt180) cc_final: 0.7323 (ttp80) REVERT: E 28 GLU cc_start: 0.7169 (tt0) cc_final: 0.6954 (tt0) REVERT: E 32 CYS cc_start: 0.7348 (m) cc_final: 0.7147 (m) REVERT: E 84 VAL cc_start: 0.8064 (m) cc_final: 0.7733 (p) REVERT: E 92 CYS cc_start: 0.7131 (m) cc_final: 0.6914 (m) REVERT: E 105 ARG cc_start: 0.7480 (ptt180) cc_final: 0.6996 (mpp-170) REVERT: J 102 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7501 (mm-30) REVERT: J 264 SER cc_start: 0.8613 (p) cc_final: 0.7918 (m) REVERT: J 271 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8363 (tp) REVERT: J 319 THR cc_start: 0.7625 (t) cc_final: 0.7328 (t) REVERT: K 588 ARG cc_start: 0.7174 (mtt180) cc_final: 0.6806 (mtp180) REVERT: K 601 LYS cc_start: 0.8316 (mtmm) cc_final: 0.8114 (mtmt) REVERT: M 32 CYS cc_start: 0.7377 (m) cc_final: 0.7098 (m) REVERT: O 69 MET cc_start: 0.3156 (mtt) cc_final: 0.1797 (ptt) REVERT: Q 39 TYR cc_start: 0.8667 (m-80) cc_final: 0.8461 (m-80) REVERT: Q 102 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7563 (mm-30) REVERT: Q 264 SER cc_start: 0.8648 (p) cc_final: 0.7875 (m) REVERT: Q 373 MET cc_start: 0.8762 (mtp) cc_final: 0.8467 (OUTLIER) REVERT: R 518 MET cc_start: 0.6531 (OUTLIER) cc_final: 0.6144 (mmt) outliers start: 79 outliers final: 25 residues processed: 461 average time/residue: 0.6893 time to fit residues: 362.3686 Evaluate side-chains 392 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 361 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 96 LYS Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 271 ILE Chi-restraints excluded: chain J residue 365 SER Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 163 THR Chi-restraints excluded: chain Q residue 365 SER Chi-restraints excluded: chain Q residue 414 ILE Chi-restraints excluded: chain Q residue 505 VAL Chi-restraints excluded: chain R residue 518 MET Chi-restraints excluded: chain R residue 595 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 284 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 242 optimal weight: 0.1980 chunk 137 optimal weight: 0.0770 chunk 61 optimal weight: 0.8980 chunk 219 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 256 optimal weight: 1.9990 chunk 228 optimal weight: 0.0370 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN D 27 GLN D 37 GLN J 344 GLN J 377 ASN K 653 GLN N 27 GLN N 90 GLN R 591 GLN R 651 ASN R 653 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.222927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.176736 restraints weight = 28991.127| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 4.46 r_work: 0.3608 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 27090 Z= 0.114 Angle : 0.590 11.632 37062 Z= 0.285 Chirality : 0.044 0.204 4431 Planarity : 0.004 0.030 4476 Dihedral : 8.750 81.054 6144 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.72 % Allowed : 11.01 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.10 % Twisted Proline : 0.69 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.15), residues: 3069 helix: 1.82 (0.25), residues: 438 sheet: 1.38 (0.15), residues: 1062 loop : 1.79 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 633 TYR 0.017 0.001 TYR J 191 PHE 0.028 0.001 PHE O 29 TRP 0.016 0.001 TRP C 50 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00258 (26901) covalent geometry : angle 0.54578 (36549) SS BOND : bond 0.00388 ( 54) SS BOND : angle 1.51375 ( 108) hydrogen bonds : bond 0.04720 ( 669) hydrogen bonds : angle 4.93671 ( 1683) link_ALPHA1-3 : bond 0.01052 ( 9) link_ALPHA1-3 : angle 2.01436 ( 27) link_ALPHA1-6 : bond 0.00614 ( 12) link_ALPHA1-6 : angle 1.64478 ( 36) link_BETA1-4 : bond 0.00406 ( 51) link_BETA1-4 : angle 2.09847 ( 153) link_NAG-ASN : bond 0.00316 ( 63) link_NAG-ASN : angle 2.19020 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 380 time to evaluate : 1.008 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: A 66 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6940 (ptm160) REVERT: A 264 SER cc_start: 0.8832 (p) cc_final: 0.8187 (m) REVERT: A 267 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6008 (mp0) REVERT: A 429 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7875 (mm-30) REVERT: A 504 ARG cc_start: 0.7721 (mtt90) cc_final: 0.7409 (mpt90) REVERT: B 634 GLU cc_start: 0.7440 (tt0) cc_final: 0.7204 (tt0) REVERT: C 46 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8495 (tt0) REVERT: D 37 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.6990 (tt0) REVERT: D 42 GLN cc_start: 0.8165 (mt0) cc_final: 0.7904 (mt0) REVERT: E 23 ARG cc_start: 0.7548 (ttt180) cc_final: 0.7260 (ttp80) REVERT: E 31 ASP cc_start: 0.7742 (m-30) cc_final: 0.7542 (m-30) REVERT: E 84 VAL cc_start: 0.8031 (m) cc_final: 0.7679 (p) REVERT: E 105 ARG cc_start: 0.7507 (ptt180) cc_final: 0.6903 (mpp-170) REVERT: G 28 ARG cc_start: 0.6542 (ttt180) cc_final: 0.5947 (tpp80) REVERT: J 102 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7351 (mm-30) REVERT: J 264 SER cc_start: 0.8589 (p) cc_final: 0.7922 (m) REVERT: J 271 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8388 (tp) REVERT: J 319 THR cc_start: 0.7600 (t) cc_final: 0.7334 (t) REVERT: J 344 GLN cc_start: 0.8419 (mm110) cc_final: 0.8207 (mt0) REVERT: K 577 GLN cc_start: 0.6304 (mm-40) cc_final: 0.5778 (mt0) REVERT: K 588 ARG cc_start: 0.7046 (mtt180) cc_final: 0.6657 (mtt-85) REVERT: K 659 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: N 89 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: O 31 PHE cc_start: 0.5916 (m-10) cc_final: 0.5669 (m-10) REVERT: O 69 MET cc_start: 0.3067 (mtt) cc_final: 0.1664 (ptt) REVERT: Q 102 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7451 (mm-30) REVERT: Q 264 SER cc_start: 0.8683 (p) cc_final: 0.7954 (m) REVERT: Q 373 MET cc_start: 0.8805 (mtp) cc_final: 0.8549 (OUTLIER) REVERT: R 518 MET cc_start: 0.6303 (OUTLIER) cc_final: 0.5935 (mmt) REVERT: R 595 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8126 (mm) outliers start: 74 outliers final: 30 residues processed: 409 average time/residue: 0.7067 time to fit residues: 331.8431 Evaluate side-chains 383 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 342 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 96 LYS Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 205 CYS Chi-restraints excluded: chain J residue 267 GLU Chi-restraints excluded: chain J residue 271 ILE Chi-restraints excluded: chain K residue 659 GLU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 163 THR Chi-restraints excluded: chain Q residue 267 GLU Chi-restraints excluded: chain Q residue 414 ILE Chi-restraints excluded: chain Q residue 505 VAL Chi-restraints excluded: chain R residue 518 MET Chi-restraints excluded: chain R residue 595 ILE Chi-restraints excluded: chain R residue 660 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 65 optimal weight: 1.9990 chunk 294 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 229 optimal weight: 7.9990 chunk 279 optimal weight: 0.7980 chunk 275 optimal weight: 0.0370 chunk 167 optimal weight: 1.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN A 344 GLN B 651 ASN D 27 GLN L 6 GLN F 89 GLN K 651 ASN N 27 GLN R 651 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.219089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.172793 restraints weight = 28830.065| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 4.76 r_work: 0.3538 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27090 Z= 0.155 Angle : 0.606 12.397 37062 Z= 0.291 Chirality : 0.046 0.227 4431 Planarity : 0.004 0.051 4476 Dihedral : 8.097 73.967 6144 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.27 % Allowed : 11.78 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.15), residues: 3069 helix: 1.72 (0.24), residues: 438 sheet: 1.26 (0.15), residues: 1068 loop : 1.53 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 633 TYR 0.016 0.001 TYR J 191 PHE 0.025 0.002 PHE O 29 TRP 0.015 0.001 TRP C 50 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00368 (26901) covalent geometry : angle 0.56641 (36549) SS BOND : bond 0.00351 ( 54) SS BOND : angle 1.34057 ( 108) hydrogen bonds : bond 0.04627 ( 669) hydrogen bonds : angle 4.88673 ( 1683) link_ALPHA1-3 : bond 0.00986 ( 9) link_ALPHA1-3 : angle 2.30870 ( 27) link_ALPHA1-6 : bond 0.00603 ( 12) link_ALPHA1-6 : angle 1.64891 ( 36) link_BETA1-4 : bond 0.00423 ( 51) link_BETA1-4 : angle 1.95372 ( 153) link_NAG-ASN : bond 0.00361 ( 63) link_NAG-ASN : angle 2.12984 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 372 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6947 (ptt90) REVERT: A 264 SER cc_start: 0.8887 (p) cc_final: 0.8260 (m) REVERT: A 267 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6129 (mp0) REVERT: A 373 MET cc_start: 0.8689 (mtp) cc_final: 0.8470 (mmm) REVERT: A 504 ARG cc_start: 0.7827 (mtt90) cc_final: 0.7578 (mpt90) REVERT: B 634 GLU cc_start: 0.7556 (tt0) cc_final: 0.7216 (tt0) REVERT: B 652 GLN cc_start: 0.7506 (mt0) cc_final: 0.7133 (tp40) REVERT: C 46 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8560 (tt0) REVERT: D 42 GLN cc_start: 0.8185 (mt0) cc_final: 0.7960 (mt0) REVERT: E 23 ARG cc_start: 0.7676 (ttt180) cc_final: 0.7376 (ttp80) REVERT: E 46 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8861 (tt0) REVERT: E 92 CYS cc_start: 0.7400 (m) cc_final: 0.7165 (m) REVERT: E 105 ARG cc_start: 0.7622 (ptt180) cc_final: 0.7067 (tpp-160) REVERT: F 6 GLN cc_start: 0.7741 (tt0) cc_final: 0.7475 (mt0) REVERT: F 48 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7584 (mp) REVERT: F 102 THR cc_start: 0.8331 (m) cc_final: 0.8013 (p) REVERT: G 28 ARG cc_start: 0.6632 (ttt180) cc_final: 0.6147 (tpp80) REVERT: J 102 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7595 (mm-30) REVERT: J 164 SER cc_start: 0.8936 (p) cc_final: 0.8702 (p) REVERT: J 264 SER cc_start: 0.8728 (p) cc_final: 0.7993 (m) REVERT: J 271 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8403 (tp) REVERT: J 308 ASN cc_start: 0.8734 (t0) cc_final: 0.8467 (t0) REVERT: K 588 ARG cc_start: 0.7225 (mtt180) cc_final: 0.6850 (mmm160) REVERT: K 632 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7629 (mm-30) REVERT: K 652 GLN cc_start: 0.7579 (mt0) cc_final: 0.7172 (tp-100) REVERT: M 23 ARG cc_start: 0.7549 (ttm110) cc_final: 0.7166 (ttt180) REVERT: M 46 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8763 (tt0) REVERT: M 73 VAL cc_start: 0.8320 (OUTLIER) cc_final: 0.8007 (t) REVERT: O 69 MET cc_start: 0.3142 (mtt) cc_final: 0.1627 (ptt) REVERT: R 518 MET cc_start: 0.6454 (OUTLIER) cc_final: 0.6047 (mmt) REVERT: R 595 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8110 (mm) REVERT: R 634 GLU cc_start: 0.7452 (tt0) cc_final: 0.7116 (mt-10) outliers start: 89 outliers final: 41 residues processed: 409 average time/residue: 0.6396 time to fit residues: 300.3327 Evaluate side-chains 390 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 338 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 267 GLU Chi-restraints excluded: chain J residue 271 ILE Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 640 SER Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 66 ARG Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 163 THR Chi-restraints excluded: chain Q residue 165 ILE Chi-restraints excluded: chain Q residue 267 GLU Chi-restraints excluded: chain Q residue 365 SER Chi-restraints excluded: chain Q residue 373 MET Chi-restraints excluded: chain Q residue 414 ILE Chi-restraints excluded: chain Q residue 505 VAL Chi-restraints excluded: chain R residue 518 MET Chi-restraints excluded: chain R residue 595 ILE Chi-restraints excluded: chain R residue 660 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 213 optimal weight: 7.9990 chunk 201 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 261 optimal weight: 0.0470 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN D 27 GLN J 234 ASN N 27 GLN N 89 GLN Q 190 ASN Q 377 ASN R 651 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.217758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.171119 restraints weight = 28759.855| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 5.26 r_work: 0.3528 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27090 Z= 0.158 Angle : 0.598 10.441 37062 Z= 0.287 Chirality : 0.045 0.225 4431 Planarity : 0.004 0.048 4476 Dihedral : 7.820 69.027 6144 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.56 % Allowed : 12.44 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.15), residues: 3069 helix: 1.60 (0.24), residues: 438 sheet: 1.16 (0.15), residues: 1053 loop : 1.29 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 633 TYR 0.017 0.001 TYR J 191 PHE 0.027 0.002 PHE O 29 TRP 0.015 0.001 TRP C 50 HIS 0.004 0.001 HIS Q 374 Details of bonding type rmsd covalent geometry : bond 0.00377 (26901) covalent geometry : angle 0.56001 (36549) SS BOND : bond 0.00364 ( 54) SS BOND : angle 1.20748 ( 108) hydrogen bonds : bond 0.04480 ( 669) hydrogen bonds : angle 4.84310 ( 1683) link_ALPHA1-3 : bond 0.00991 ( 9) link_ALPHA1-3 : angle 2.29878 ( 27) link_ALPHA1-6 : bond 0.00614 ( 12) link_ALPHA1-6 : angle 1.67646 ( 36) link_BETA1-4 : bond 0.00398 ( 51) link_BETA1-4 : angle 1.86136 ( 153) link_NAG-ASN : bond 0.00382 ( 63) link_NAG-ASN : angle 2.12488 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 338 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6927 (ptt90) REVERT: A 264 SER cc_start: 0.8866 (p) cc_final: 0.8322 (m) REVERT: A 267 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6009 (mp0) REVERT: A 504 ARG cc_start: 0.7657 (mtt90) cc_final: 0.7358 (mpt90) REVERT: B 633 ARG cc_start: 0.6476 (mtm-85) cc_final: 0.6245 (mtm-85) REVERT: B 652 GLN cc_start: 0.7435 (mt0) cc_final: 0.7010 (tp40) REVERT: C 46 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8427 (tt0) REVERT: D 37 GLN cc_start: 0.8048 (tm-30) cc_final: 0.7581 (tp40) REVERT: D 42 GLN cc_start: 0.8198 (mt0) cc_final: 0.7953 (mt0) REVERT: E 23 ARG cc_start: 0.7660 (ttt180) cc_final: 0.7379 (ttp80) REVERT: E 46 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8837 (tt0) REVERT: E 92 CYS cc_start: 0.7164 (m) cc_final: 0.6936 (m) REVERT: F 6 GLN cc_start: 0.7585 (tt0) cc_final: 0.7359 (mt0) REVERT: F 48 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7560 (mp) REVERT: G 28 ARG cc_start: 0.6426 (ttt180) cc_final: 0.5910 (tpp80) REVERT: J 102 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7548 (mm-30) REVERT: J 164 SER cc_start: 0.8858 (p) cc_final: 0.8653 (p) REVERT: J 173 TYR cc_start: 0.7091 (m-80) cc_final: 0.6668 (p90) REVERT: J 264 SER cc_start: 0.8667 (p) cc_final: 0.7978 (m) REVERT: J 271 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8348 (tp) REVERT: J 308 ASN cc_start: 0.8699 (t0) cc_final: 0.8473 (t0) REVERT: K 577 GLN cc_start: 0.6189 (mm-40) cc_final: 0.5864 (mt0) REVERT: K 588 ARG cc_start: 0.7164 (mtt180) cc_final: 0.6694 (mmm160) REVERT: K 632 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7662 (mm-30) REVERT: K 652 GLN cc_start: 0.7411 (mt0) cc_final: 0.6977 (tp-100) REVERT: K 659 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: M 46 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8675 (tt0) REVERT: M 73 VAL cc_start: 0.8369 (OUTLIER) cc_final: 0.8156 (t) REVERT: M 105 ARG cc_start: 0.7225 (ptt180) cc_final: 0.6793 (tpp-160) REVERT: N 61 ARG cc_start: 0.6366 (OUTLIER) cc_final: 0.6128 (ptt-90) REVERT: O 69 MET cc_start: 0.3034 (mtt) cc_final: 0.1531 (ptt) REVERT: Q 205 CYS cc_start: 0.6585 (OUTLIER) cc_final: 0.6144 (m) REVERT: Q 322 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7411 (pm20) REVERT: R 595 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8091 (mm) REVERT: R 661 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7310 (tp) outliers start: 97 outliers final: 42 residues processed: 387 average time/residue: 0.6598 time to fit residues: 294.3271 Evaluate side-chains 390 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 333 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 267 GLU Chi-restraints excluded: chain J residue 271 ILE Chi-restraints excluded: chain J residue 365 SER Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain K residue 640 SER Chi-restraints excluded: chain K residue 659 GLU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 66 ARG Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 163 THR Chi-restraints excluded: chain Q residue 165 ILE Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 267 GLU Chi-restraints excluded: chain Q residue 322 GLU Chi-restraints excluded: chain Q residue 365 SER Chi-restraints excluded: chain Q residue 414 ILE Chi-restraints excluded: chain Q residue 505 VAL Chi-restraints excluded: chain R residue 595 ILE Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain R residue 661 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 248 optimal weight: 5.9990 chunk 243 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 228 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 246 optimal weight: 4.9990 chunk 194 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 89 GLN I 6 GLN J 234 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN R 651 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.216666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.171392 restraints weight = 28657.387| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 5.13 r_work: 0.3534 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27090 Z= 0.165 Angle : 0.601 7.947 37062 Z= 0.287 Chirality : 0.046 0.234 4431 Planarity : 0.004 0.054 4476 Dihedral : 7.693 63.471 6144 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.47 % Favored : 98.44 % Rotamer: Outliers : 3.30 % Allowed : 13.40 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.15), residues: 3069 helix: 1.52 (0.24), residues: 438 sheet: 1.11 (0.15), residues: 1047 loop : 1.03 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 633 TYR 0.014 0.001 TYR J 191 PHE 0.028 0.002 PHE O 29 TRP 0.018 0.001 TRP Q 479 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00397 (26901) covalent geometry : angle 0.56163 (36549) SS BOND : bond 0.00375 ( 54) SS BOND : angle 1.15145 ( 108) hydrogen bonds : bond 0.04449 ( 669) hydrogen bonds : angle 4.87240 ( 1683) link_ALPHA1-3 : bond 0.00977 ( 9) link_ALPHA1-3 : angle 2.38874 ( 27) link_ALPHA1-6 : bond 0.00640 ( 12) link_ALPHA1-6 : angle 1.66897 ( 36) link_BETA1-4 : bond 0.00389 ( 51) link_BETA1-4 : angle 1.82970 ( 153) link_NAG-ASN : bond 0.00439 ( 63) link_NAG-ASN : angle 2.25082 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 338 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6920 (ptt90) REVERT: A 205 CYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6432 (m) REVERT: A 264 SER cc_start: 0.8883 (p) cc_final: 0.8320 (m) REVERT: A 267 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6051 (mp0) REVERT: A 504 ARG cc_start: 0.7618 (mtt90) cc_final: 0.7318 (mpt90) REVERT: B 652 GLN cc_start: 0.7382 (mt0) cc_final: 0.7022 (tp-100) REVERT: B 654 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7277 (mt-10) REVERT: C 46 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8665 (tt0) REVERT: D 42 GLN cc_start: 0.8192 (mt0) cc_final: 0.7953 (mt0) REVERT: D 100 GLN cc_start: 0.7466 (mm-40) cc_final: 0.7106 (tp-100) REVERT: E 32 CYS cc_start: 0.6995 (m) cc_final: 0.6752 (m) REVERT: E 46 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8799 (tt0) REVERT: E 92 CYS cc_start: 0.7091 (m) cc_final: 0.6841 (m) REVERT: F 6 GLN cc_start: 0.7610 (tt0) cc_final: 0.7325 (mt0) REVERT: F 48 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7455 (mp) REVERT: G 28 ARG cc_start: 0.6328 (ttt180) cc_final: 0.6004 (tpp80) REVERT: J 102 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7494 (mm-30) REVERT: J 119 CYS cc_start: 0.5553 (OUTLIER) cc_final: 0.5265 (m) REVERT: J 164 SER cc_start: 0.8859 (p) cc_final: 0.8656 (p) REVERT: J 173 TYR cc_start: 0.7192 (m-80) cc_final: 0.6741 (p90) REVERT: J 264 SER cc_start: 0.8594 (p) cc_final: 0.7945 (m) REVERT: J 271 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8344 (tp) REVERT: J 308 ASN cc_start: 0.8663 (t0) cc_final: 0.8436 (t0) REVERT: K 577 GLN cc_start: 0.6243 (mm-40) cc_final: 0.5895 (mt0) REVERT: K 588 ARG cc_start: 0.7142 (mtt180) cc_final: 0.6693 (mmm160) REVERT: K 632 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7756 (mm-30) REVERT: K 652 GLN cc_start: 0.7340 (mt0) cc_final: 0.6950 (tp-100) REVERT: K 659 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7451 (mt-10) REVERT: M 11 MET cc_start: 0.6870 (tpt) cc_final: 0.6628 (mmm) REVERT: M 73 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8388 (t) REVERT: M 105 ARG cc_start: 0.7138 (ptt180) cc_final: 0.6797 (tpp-160) REVERT: O 69 MET cc_start: 0.3143 (mtt) cc_final: 0.1695 (ptt) REVERT: Q 205 CYS cc_start: 0.6637 (OUTLIER) cc_final: 0.6201 (m) REVERT: Q 322 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7377 (pm20) REVERT: R 595 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8077 (mm) outliers start: 90 outliers final: 45 residues processed: 380 average time/residue: 0.6665 time to fit residues: 291.1234 Evaluate side-chains 377 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 318 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 119 CYS Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 267 GLU Chi-restraints excluded: chain J residue 271 ILE Chi-restraints excluded: chain J residue 365 SER Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 640 SER Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain K residue 659 GLU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 66 ARG Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 163 THR Chi-restraints excluded: chain Q residue 165 ILE Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 267 GLU Chi-restraints excluded: chain Q residue 322 GLU Chi-restraints excluded: chain Q residue 365 SER Chi-restraints excluded: chain Q residue 414 ILE Chi-restraints excluded: chain Q residue 505 VAL Chi-restraints excluded: chain R residue 536 THR Chi-restraints excluded: chain R residue 595 ILE Chi-restraints excluded: chain R residue 660 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 101 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 236 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 136 optimal weight: 9.9990 chunk 184 optimal weight: 0.9990 chunk 287 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 257 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 37 GLN D 89 GLN J 234 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN N 89 GLN Q 190 ASN R 651 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.217097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.161481 restraints weight = 28668.742| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.65 r_work: 0.3530 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27090 Z= 0.148 Angle : 0.584 8.282 37062 Z= 0.279 Chirality : 0.045 0.232 4431 Planarity : 0.004 0.051 4476 Dihedral : 7.416 59.745 6144 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.66 % Favored : 98.27 % Rotamer: Outliers : 3.08 % Allowed : 14.21 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.15), residues: 3069 helix: 1.58 (0.24), residues: 438 sheet: 1.10 (0.15), residues: 1044 loop : 0.92 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 633 TYR 0.013 0.001 TYR J 191 PHE 0.027 0.002 PHE O 29 TRP 0.022 0.001 TRP Q 479 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00355 (26901) covalent geometry : angle 0.54674 (36549) SS BOND : bond 0.00339 ( 54) SS BOND : angle 1.05365 ( 108) hydrogen bonds : bond 0.04213 ( 669) hydrogen bonds : angle 4.79083 ( 1683) link_ALPHA1-3 : bond 0.00989 ( 9) link_ALPHA1-3 : angle 2.34368 ( 27) link_ALPHA1-6 : bond 0.00667 ( 12) link_ALPHA1-6 : angle 1.67067 ( 36) link_BETA1-4 : bond 0.00392 ( 51) link_BETA1-4 : angle 1.74484 ( 153) link_NAG-ASN : bond 0.00546 ( 63) link_NAG-ASN : angle 2.17574 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 335 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6885 (ptt90) REVERT: A 205 CYS cc_start: 0.6783 (OUTLIER) cc_final: 0.6383 (m) REVERT: A 264 SER cc_start: 0.8915 (p) cc_final: 0.8370 (m) REVERT: A 267 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.5969 (mp0) REVERT: A 504 ARG cc_start: 0.7605 (mtt90) cc_final: 0.7310 (mpt90) REVERT: B 652 GLN cc_start: 0.7513 (mt0) cc_final: 0.7131 (tp-100) REVERT: B 654 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7182 (mt-10) REVERT: C 46 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8570 (tt0) REVERT: C 84 VAL cc_start: 0.8004 (m) cc_final: 0.7784 (t) REVERT: D 37 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7691 (tp40) REVERT: D 42 GLN cc_start: 0.8197 (mt0) cc_final: 0.7949 (mt0) REVERT: D 100 GLN cc_start: 0.7475 (mm-40) cc_final: 0.7178 (tp-100) REVERT: E 32 CYS cc_start: 0.7023 (m) cc_final: 0.6722 (m) REVERT: E 46 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8769 (tt0) REVERT: E 92 CYS cc_start: 0.7111 (m) cc_final: 0.6869 (m) REVERT: F 6 GLN cc_start: 0.7614 (tt0) cc_final: 0.7362 (mt0) REVERT: F 48 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7441 (mp) REVERT: G 69 MET cc_start: 0.1474 (mtt) cc_final: 0.0665 (ptp) REVERT: J 102 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7478 (mm-30) REVERT: J 173 TYR cc_start: 0.7182 (m-80) cc_final: 0.6774 (p90) REVERT: J 264 SER cc_start: 0.8614 (p) cc_final: 0.7966 (m) REVERT: J 271 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8338 (tp) REVERT: J 308 ASN cc_start: 0.8620 (t0) cc_final: 0.8404 (t0) REVERT: J 319 THR cc_start: 0.7783 (t) cc_final: 0.7481 (t) REVERT: K 577 GLN cc_start: 0.6259 (mm-40) cc_final: 0.5940 (mt0) REVERT: K 588 ARG cc_start: 0.7111 (mtt180) cc_final: 0.6672 (mmm160) REVERT: K 632 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7694 (mm-30) REVERT: K 652 GLN cc_start: 0.7394 (mt0) cc_final: 0.6977 (tp-100) REVERT: M 73 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8390 (t) REVERT: M 105 ARG cc_start: 0.7136 (ptt180) cc_final: 0.6827 (tpp-160) REVERT: O 69 MET cc_start: 0.3128 (mtt) cc_final: 0.1721 (ptt) REVERT: Q 102 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7668 (mm-30) REVERT: Q 205 CYS cc_start: 0.6476 (OUTLIER) cc_final: 0.6030 (m) REVERT: Q 322 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7393 (pm20) REVERT: Q 434 MET cc_start: 0.9082 (ttp) cc_final: 0.8862 (ttp) REVERT: R 595 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8072 (mm) outliers start: 84 outliers final: 49 residues processed: 378 average time/residue: 0.6447 time to fit residues: 279.6439 Evaluate side-chains 381 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 318 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 267 GLU Chi-restraints excluded: chain J residue 271 ILE Chi-restraints excluded: chain J residue 365 SER Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 66 ARG Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 163 THR Chi-restraints excluded: chain Q residue 165 ILE Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 267 GLU Chi-restraints excluded: chain Q residue 322 GLU Chi-restraints excluded: chain Q residue 365 SER Chi-restraints excluded: chain Q residue 414 ILE Chi-restraints excluded: chain Q residue 505 VAL Chi-restraints excluded: chain R residue 536 THR Chi-restraints excluded: chain R residue 595 ILE Chi-restraints excluded: chain R residue 660 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 228 optimal weight: 7.9990 chunk 287 optimal weight: 0.4980 chunk 226 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 171 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 chunk 141 optimal weight: 5.9990 chunk 159 optimal weight: 0.0570 chunk 61 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 overall best weight: 0.4900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 89 GLN J 234 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN Q 190 ASN R 651 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.218478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.163874 restraints weight = 28642.909| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.09 r_work: 0.3564 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27090 Z= 0.115 Angle : 0.558 11.698 37062 Z= 0.268 Chirality : 0.044 0.233 4431 Planarity : 0.004 0.048 4476 Dihedral : 7.147 57.904 6144 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.64 % Allowed : 15.05 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.10 % Twisted Proline : 0.69 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.15), residues: 3069 helix: 1.68 (0.24), residues: 438 sheet: 1.14 (0.15), residues: 1044 loop : 0.89 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 633 TYR 0.020 0.001 TYR D 36 PHE 0.020 0.001 PHE O 29 TRP 0.024 0.001 TRP Q 479 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00267 (26901) covalent geometry : angle 0.52042 (36549) SS BOND : bond 0.00278 ( 54) SS BOND : angle 1.21736 ( 108) hydrogen bonds : bond 0.03871 ( 669) hydrogen bonds : angle 4.68900 ( 1683) link_ALPHA1-3 : bond 0.01061 ( 9) link_ALPHA1-3 : angle 2.28170 ( 27) link_ALPHA1-6 : bond 0.00690 ( 12) link_ALPHA1-6 : angle 1.66129 ( 36) link_BETA1-4 : bond 0.00416 ( 51) link_BETA1-4 : angle 1.65357 ( 153) link_NAG-ASN : bond 0.00498 ( 63) link_NAG-ASN : angle 2.07226 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 330 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6846 (ptt90) REVERT: A 205 CYS cc_start: 0.6737 (OUTLIER) cc_final: 0.6364 (m) REVERT: A 264 SER cc_start: 0.8893 (p) cc_final: 0.8343 (m) REVERT: B 652 GLN cc_start: 0.7419 (mt0) cc_final: 0.7052 (tp-100) REVERT: B 654 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7138 (mt-10) REVERT: C 44 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.6434 (mtp85) REVERT: C 84 VAL cc_start: 0.8049 (m) cc_final: 0.7829 (t) REVERT: D 42 GLN cc_start: 0.8213 (mt0) cc_final: 0.7984 (mt0) REVERT: D 100 GLN cc_start: 0.7349 (mm-40) cc_final: 0.5837 (tp-100) REVERT: E 32 CYS cc_start: 0.6907 (m) cc_final: 0.6583 (m) REVERT: E 92 CYS cc_start: 0.7086 (m) cc_final: 0.6847 (m) REVERT: F 48 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7393 (mp) REVERT: F 71 TYR cc_start: 0.5336 (t80) cc_final: 0.4885 (t80) REVERT: G 69 MET cc_start: 0.1351 (mtt) cc_final: 0.0539 (ptp) REVERT: J 102 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7366 (mm-30) REVERT: J 173 TYR cc_start: 0.7177 (m-80) cc_final: 0.6711 (p90) REVERT: J 264 SER cc_start: 0.8626 (p) cc_final: 0.8025 (m) REVERT: J 271 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8329 (tp) REVERT: J 319 THR cc_start: 0.7724 (t) cc_final: 0.7439 (t) REVERT: K 577 GLN cc_start: 0.6273 (mm-40) cc_final: 0.5904 (mt0) REVERT: K 588 ARG cc_start: 0.7058 (mtt180) cc_final: 0.6629 (mmm160) REVERT: K 621 LYS cc_start: 0.5561 (mmpt) cc_final: 0.5239 (mtmt) REVERT: K 632 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7713 (mm-30) REVERT: K 652 GLN cc_start: 0.7379 (mt0) cc_final: 0.6969 (tp-100) REVERT: M 23 ARG cc_start: 0.7493 (ttm110) cc_final: 0.7074 (tpt170) REVERT: M 73 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8327 (t) REVERT: O 69 MET cc_start: 0.3027 (mtt) cc_final: 0.1604 (ptt) REVERT: Q 102 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7614 (mm-30) REVERT: Q 205 CYS cc_start: 0.6435 (OUTLIER) cc_final: 0.6011 (m) REVERT: R 518 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.6354 (mmt) REVERT: R 595 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.8053 (mm) REVERT: R 661 LEU cc_start: 0.7482 (tp) cc_final: 0.7114 (tp) outliers start: 72 outliers final: 34 residues processed: 369 average time/residue: 0.6440 time to fit residues: 273.1638 Evaluate side-chains 364 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 319 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 267 GLU Chi-restraints excluded: chain J residue 271 ILE Chi-restraints excluded: chain K residue 640 SER Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain Q residue 66 ARG Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 163 THR Chi-restraints excluded: chain Q residue 165 ILE Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 414 ILE Chi-restraints excluded: chain Q residue 505 VAL Chi-restraints excluded: chain R residue 518 MET Chi-restraints excluded: chain R residue 595 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 291 optimal weight: 3.9990 chunk 224 optimal weight: 0.4980 chunk 203 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 58 optimal weight: 0.1980 chunk 174 optimal weight: 0.9980 chunk 268 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 89 GLN J 234 ASN J 308 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN N 89 GLN P 6 GLN Q 190 ASN R 651 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.217837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.177613 restraints weight = 28829.593| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 3.36 r_work: 0.3490 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27090 Z= 0.132 Angle : 0.572 14.212 37062 Z= 0.274 Chirality : 0.044 0.227 4431 Planarity : 0.004 0.051 4476 Dihedral : 6.897 54.238 6144 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.20 % Allowed : 15.68 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.10 % Twisted Proline : 0.69 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.15), residues: 3069 helix: 1.66 (0.24), residues: 438 sheet: 1.23 (0.15), residues: 1014 loop : 0.80 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 252 TYR 0.013 0.001 TYR J 191 PHE 0.014 0.001 PHE H 72H TRP 0.021 0.001 TRP Q 479 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00314 (26901) covalent geometry : angle 0.53457 (36549) SS BOND : bond 0.00324 ( 54) SS BOND : angle 1.25813 ( 108) hydrogen bonds : bond 0.03941 ( 669) hydrogen bonds : angle 4.68763 ( 1683) link_ALPHA1-3 : bond 0.00974 ( 9) link_ALPHA1-3 : angle 2.27602 ( 27) link_ALPHA1-6 : bond 0.00709 ( 12) link_ALPHA1-6 : angle 1.64271 ( 36) link_BETA1-4 : bond 0.00392 ( 51) link_BETA1-4 : angle 1.65839 ( 153) link_NAG-ASN : bond 0.00498 ( 63) link_NAG-ASN : angle 2.10506 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 322 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6920 (ptt90) REVERT: A 205 CYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6820 (m) REVERT: A 264 SER cc_start: 0.8935 (p) cc_final: 0.8396 (m) REVERT: A 504 ARG cc_start: 0.7791 (mpt90) cc_final: 0.7582 (mpt90) REVERT: B 633 ARG cc_start: 0.6679 (mtm-85) cc_final: 0.6435 (mtm-85) REVERT: B 652 GLN cc_start: 0.7620 (mt0) cc_final: 0.7329 (tp-100) REVERT: B 654 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7262 (mt-10) REVERT: C 44 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.6550 (mtp85) REVERT: C 84 VAL cc_start: 0.8132 (m) cc_final: 0.7892 (t) REVERT: D 42 GLN cc_start: 0.8223 (mt0) cc_final: 0.7988 (mt0) REVERT: D 100 GLN cc_start: 0.7559 (mm-40) cc_final: 0.5970 (tp-100) REVERT: E 32 CYS cc_start: 0.7368 (m) cc_final: 0.7066 (m) REVERT: E 92 CYS cc_start: 0.7503 (m) cc_final: 0.7278 (m) REVERT: F 20 ILE cc_start: 0.7402 (mm) cc_final: 0.6804 (mt) REVERT: F 48 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7501 (mp) REVERT: G 69 MET cc_start: 0.1477 (mtt) cc_final: 0.0782 (ptp) REVERT: J 102 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7744 (mm-30) REVERT: J 173 TYR cc_start: 0.7384 (m-80) cc_final: 0.6956 (p90) REVERT: J 264 SER cc_start: 0.8698 (p) cc_final: 0.8049 (m) REVERT: J 271 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8381 (tp) REVERT: J 319 THR cc_start: 0.7951 (t) cc_final: 0.7675 (t) REVERT: K 577 GLN cc_start: 0.6568 (mm-40) cc_final: 0.6203 (mt0) REVERT: K 588 ARG cc_start: 0.7370 (mtt180) cc_final: 0.6949 (mmm160) REVERT: K 632 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7777 (mm-30) REVERT: K 652 GLN cc_start: 0.7566 (mt0) cc_final: 0.7242 (tp-100) REVERT: M 23 ARG cc_start: 0.7667 (ttm110) cc_final: 0.7292 (tpt170) REVERT: M 73 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8439 (t) REVERT: M 105 ARG cc_start: 0.7270 (ptt180) cc_final: 0.6859 (tpp-160) REVERT: O 69 MET cc_start: 0.2687 (mtt) cc_final: 0.1470 (ptt) REVERT: Q 102 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7918 (mm-30) REVERT: Q 205 CYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6385 (m) REVERT: R 518 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.6595 (mmt) REVERT: R 652 GLN cc_start: 0.7696 (mt0) cc_final: 0.7101 (tp40) REVERT: R 661 LEU cc_start: 0.7402 (tp) cc_final: 0.7104 (tp) outliers start: 60 outliers final: 38 residues processed: 352 average time/residue: 0.6374 time to fit residues: 257.6263 Evaluate side-chains 359 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 311 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 267 GLU Chi-restraints excluded: chain J residue 271 ILE Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain K residue 640 SER Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 66 ARG Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 117 LYS Chi-restraints excluded: chain Q residue 163 THR Chi-restraints excluded: chain Q residue 165 ILE Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 365 SER Chi-restraints excluded: chain Q residue 414 ILE Chi-restraints excluded: chain Q residue 505 VAL Chi-restraints excluded: chain R residue 518 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 222 optimal weight: 0.0970 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 220 optimal weight: 0.5980 chunk 165 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN J 234 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN R 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.217255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.171210 restraints weight = 28507.430| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 4.55 r_work: 0.3533 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 27090 Z= 0.144 Angle : 0.581 13.511 37062 Z= 0.278 Chirality : 0.045 0.225 4431 Planarity : 0.004 0.056 4476 Dihedral : 6.783 53.449 6144 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.17 % Allowed : 15.49 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.10 % Twisted Proline : 0.69 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.15), residues: 3069 helix: 1.60 (0.24), residues: 438 sheet: 1.21 (0.16), residues: 1014 loop : 0.77 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 252 TYR 0.018 0.001 TYR F 71 PHE 0.013 0.002 PHE H 72H TRP 0.026 0.001 TRP Q 479 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00344 (26901) covalent geometry : angle 0.54244 (36549) SS BOND : bond 0.00317 ( 54) SS BOND : angle 1.26854 ( 108) hydrogen bonds : bond 0.03990 ( 669) hydrogen bonds : angle 4.68953 ( 1683) link_ALPHA1-3 : bond 0.01033 ( 9) link_ALPHA1-3 : angle 2.32328 ( 27) link_ALPHA1-6 : bond 0.00718 ( 12) link_ALPHA1-6 : angle 1.61171 ( 36) link_BETA1-4 : bond 0.00403 ( 51) link_BETA1-4 : angle 1.65514 ( 153) link_NAG-ASN : bond 0.00549 ( 63) link_NAG-ASN : angle 2.18928 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 316 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.6869 (ptt90) REVERT: A 205 CYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6695 (m) REVERT: A 264 SER cc_start: 0.8996 (p) cc_final: 0.8409 (m) REVERT: B 633 ARG cc_start: 0.6676 (mtm-85) cc_final: 0.6303 (mtt90) REVERT: B 652 GLN cc_start: 0.7528 (mt0) cc_final: 0.7196 (tp-100) REVERT: B 654 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7184 (mt-10) REVERT: C 44 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.6542 (mtp85) REVERT: C 84 VAL cc_start: 0.8092 (m) cc_final: 0.7882 (t) REVERT: D 42 GLN cc_start: 0.8147 (mt0) cc_final: 0.7927 (mt0) REVERT: D 100 GLN cc_start: 0.7490 (mm-40) cc_final: 0.5968 (tp-100) REVERT: E 32 CYS cc_start: 0.7133 (m) cc_final: 0.6806 (m) REVERT: E 43 LYS cc_start: 0.8345 (mttm) cc_final: 0.8062 (mtpt) REVERT: E 92 CYS cc_start: 0.7209 (m) cc_final: 0.6955 (m) REVERT: F 20 ILE cc_start: 0.7333 (mm) cc_final: 0.6734 (mt) REVERT: F 48 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7480 (mp) REVERT: G 69 MET cc_start: 0.1369 (mtt) cc_final: 0.0712 (ptp) REVERT: J 102 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7543 (mm-30) REVERT: J 173 TYR cc_start: 0.7305 (m-80) cc_final: 0.6883 (p90) REVERT: J 264 SER cc_start: 0.8663 (p) cc_final: 0.8021 (m) REVERT: J 271 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8370 (tp) REVERT: J 319 THR cc_start: 0.7876 (t) cc_final: 0.7603 (t) REVERT: K 577 GLN cc_start: 0.6444 (mm-40) cc_final: 0.6134 (mt0) REVERT: K 588 ARG cc_start: 0.7214 (mtt180) cc_final: 0.6808 (mmm160) REVERT: K 621 LYS cc_start: 0.5746 (mmpt) cc_final: 0.5456 (mtmt) REVERT: K 632 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7641 (mm-30) REVERT: K 634 GLU cc_start: 0.7549 (tt0) cc_final: 0.7274 (mt-10) REVERT: K 652 GLN cc_start: 0.7495 (mt0) cc_final: 0.7168 (tp-100) REVERT: M 23 ARG cc_start: 0.7562 (ttm110) cc_final: 0.7195 (tpt170) REVERT: M 73 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8449 (t) REVERT: M 105 ARG cc_start: 0.7213 (ptt180) cc_final: 0.6852 (tpp-160) REVERT: O 69 MET cc_start: 0.2740 (mtt) cc_final: 0.1590 (ptt) REVERT: Q 102 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7788 (mm-30) REVERT: Q 205 CYS cc_start: 0.6611 (OUTLIER) cc_final: 0.6145 (m) REVERT: Q 264 SER cc_start: 0.8733 (p) cc_final: 0.8052 (m) REVERT: R 518 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6630 (mmt) outliers start: 59 outliers final: 35 residues processed: 347 average time/residue: 0.6649 time to fit residues: 265.0136 Evaluate side-chains 353 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 308 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 267 GLU Chi-restraints excluded: chain J residue 271 ILE Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain K residue 640 SER Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 66 ARG Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 117 LYS Chi-restraints excluded: chain Q residue 163 THR Chi-restraints excluded: chain Q residue 165 ILE Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 365 SER Chi-restraints excluded: chain Q residue 414 ILE Chi-restraints excluded: chain Q residue 505 VAL Chi-restraints excluded: chain R residue 518 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 1 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 231 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 253 optimal weight: 0.6980 chunk 188 optimal weight: 0.0370 chunk 224 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 overall best weight: 0.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN J 234 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN R 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.217835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.171740 restraints weight = 28393.119| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 4.95 r_work: 0.3539 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 27090 Z= 0.129 Angle : 0.563 13.120 37062 Z= 0.271 Chirality : 0.044 0.227 4431 Planarity : 0.004 0.052 4476 Dihedral : 6.526 52.922 6144 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.80 % Allowed : 16.04 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.10 % Twisted Proline : 0.69 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.15), residues: 3069 helix: 1.62 (0.25), residues: 441 sheet: 1.12 (0.15), residues: 1038 loop : 0.75 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 252 TYR 0.017 0.001 TYR F 71 PHE 0.012 0.001 PHE A 176 TRP 0.026 0.001 TRP Q 479 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00307 (26901) covalent geometry : angle 0.52721 (36549) SS BOND : bond 0.00299 ( 54) SS BOND : angle 1.18295 ( 108) hydrogen bonds : bond 0.03812 ( 669) hydrogen bonds : angle 4.62727 ( 1683) link_ALPHA1-3 : bond 0.00989 ( 9) link_ALPHA1-3 : angle 2.19602 ( 27) link_ALPHA1-6 : bond 0.00725 ( 12) link_ALPHA1-6 : angle 1.60392 ( 36) link_BETA1-4 : bond 0.00401 ( 51) link_BETA1-4 : angle 1.61556 ( 153) link_NAG-ASN : bond 0.00507 ( 63) link_NAG-ASN : angle 2.08720 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8517.04 seconds wall clock time: 145 minutes 58.64 seconds (8758.64 seconds total)