Starting phenix.real_space_refine on Wed Jun 18 10:29:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dto_27706/06_2025/8dto_27706.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dto_27706/06_2025/8dto_27706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dto_27706/06_2025/8dto_27706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dto_27706/06_2025/8dto_27706.map" model { file = "/net/cci-nas-00/data/ceres_data/8dto_27706/06_2025/8dto_27706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dto_27706/06_2025/8dto_27706.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.146 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 132 5.16 5 C 12990 2.51 5 N 3366 2.21 5 O 4435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20923 Number of models: 1 Model: "" Number of chains: 54 Chain: "E" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3604 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 23, 'TRANS': 437} Chain: "F" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "G" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 999 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "H" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 771 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "A" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3604 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 23, 'TRANS': 437} Chain: "B" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 999 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "D" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 771 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "I" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3604 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 23, 'TRANS': 437} Chain: "J" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "K" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 999 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "L" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 771 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" 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: "O" 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: "P" 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "T" 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: "U" 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: "V" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" 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: "X" 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" 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: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 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: "i" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" 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: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" 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: "m" 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: "n" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "o" 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: "p" 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: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 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: "w" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "x" 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: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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 Time building chain proxies: 13.61, per 1000 atoms: 0.65 Number of scatterers: 20923 At special positions: 0 Unit cell: (163.08, 157.68, 137.16, 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 132 16.00 O 4435 8.00 N 3366 7.00 C 12990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 444 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 417 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 432 " 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=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 444 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 155 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 432 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 444 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 417 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 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 ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN f 4 " - " MAN f 5 " " MAN f 5 " - " MAN f 6 " " MAN t 4 " - " MAN t 5 " " MAN t 5 " - " MAN t 6 " ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA b 3 " - " MAN b 4 " " BMA f 3 " - " MAN f 4 " " BMA h 3 " - " MAN h 4 " " BMA p 3 " - " MAN p 4 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " ALPHA1-6 " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 5 " " BMA S 3 " - " MAN S 7 " " BMA U 3 " - " MAN U 5 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 5 " " BMA f 3 " - " MAN f 7 " " BMA h 3 " - " MAN h 5 " " BMA n 3 " - " MAN n 4 " " BMA p 3 " - " MAN p 5 " " BMA t 3 " - " MAN t 7 " " BMA v 3 " - " MAN v 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " NAG V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " NAG i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " NAG w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A 701 " - " ASN A 355 " " NAG A 702 " - " ASN A 234 " " NAG A 703 " - " ASN A 396 " " NAG E 701 " - " ASN E 355 " " NAG E 702 " - " ASN E 234 " " NAG E 703 " - " ASN E 339 " " NAG E 704 " - " ASN E 396 " " NAG I 701 " - " ASN I 355 " " NAG I 702 " - " ASN I 234 " " NAG I 703 " - " ASN I 276 " " NAG I 704 " - " ASN I 339 " " NAG I 705 " - " ASN I 396 " " NAG M 1 " - " ASN E 441 " " NAG N 1 " - " ASN E 301 " " NAG O 1 " - " ASN E 154 " " NAG P 1 " - " ASN E 197 " " NAG Q 1 " - " ASN E 392 " " NAG R 1 " - " ASN E 241 " " NAG S 1 " - " ASN E 332 " " NAG T 1 " - " ASN E 158 " " NAG V 1 " - " ASN E 447 " " NAG W 1 " - " ASN E 276 " " NAG X 1 " - " ASN E 386 " " NAG Y 1 " - " ASN E 362 " " NAG Z 1 " - " ASN A 441 " " NAG a 1 " - " ASN A 301 " " NAG b 1 " - " ASN A 154 " " NAG c 1 " - " ASN A 197 " " NAG d 1 " - " ASN A 392 " " NAG e 1 " - " ASN A 241 " " NAG f 1 " - " ASN A 332 " " NAG g 1 " - " ASN A 158 " " NAG h 1 " - " ASN A 262 " " NAG i 1 " - " ASN A 447 " " NAG j 1 " - " ASN A 386 " " NAG k 1 " - " ASN A 362 " " NAG l 1 " - " ASN A 276 " " NAG m 1 " - " ASN A 339 " " NAG n 1 " - " ASN I 441 " " NAG o 1 " - " ASN I 301 " " NAG p 1 " - " ASN I 154 " " NAG q 1 " - " ASN I 197 " " NAG r 1 " - " ASN I 392 " " NAG s 1 " - " ASN I 241 " " NAG t 1 " - " ASN I 332 " " NAG u 1 " - " ASN I 158 " " NAG v 1 " - " ASN I 262 " " NAG w 1 " - " ASN I 447 " " NAG x 1 " - " ASN I 386 " " NAG y 1 " - " ASN I 362 " Time building additional restraints: 7.42 Conformation dependent library (CDL) restraints added in 2.8 seconds 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4518 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 45 sheets defined 17.5% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.554A pdb=" N CYS E 74 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 351 removed outlier: 4.035A pdb=" N LYS E 351 " --> pdb=" O ILE E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 429 Processing helix chain 'E' and resid 474 through 480 removed outlier: 4.064A pdb=" N TRP E 478 " --> pdb=" O MET E 474 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER E 480 " --> pdb=" O ASP E 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.666A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.626A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 663 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.932A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 85 removed outlier: 3.872A pdb=" N ALA H 85 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 335 through 351 removed outlier: 4.023A pdb=" N LYS A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.726A pdb=" N GLY A 428 " --> pdb=" O MET A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.941A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 534 Processing helix chain 'B' and resid 570 through 597 removed outlier: 3.684A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.635A pdb=" N ASN B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.733A pdb=" N SER B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.854A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.848A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 74 removed outlier: 3.609A pdb=" N CYS I 74 " --> pdb=" O THR I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 117 Processing helix chain 'I' and resid 335 through 351 removed outlier: 4.108A pdb=" N LYS I 351 " --> pdb=" O ILE I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 425 through 429 Processing helix chain 'I' and resid 475 through 480 removed outlier: 3.681A pdb=" N SER I 480 " --> pdb=" O ASP I 476 " (cutoff:3.500A) Processing helix chain 'J' and resid 537 through 543 removed outlier: 3.969A pdb=" N ALA J 541 " --> pdb=" O LEU J 537 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 570 through 596 removed outlier: 3.656A pdb=" N VAL J 583 " --> pdb=" O ARG J 579 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP J 589 " --> pdb=" O ARG J 585 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 625 Processing helix chain 'J' and resid 627 through 636 removed outlier: 3.982A pdb=" N SER J 636 " --> pdb=" O ASP J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 663 removed outlier: 3.611A pdb=" N ILE J 642 " --> pdb=" O TYR J 638 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.912A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.862A pdb=" N ALA L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 36 through 40 Processing sheet with id=AA2, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'E' and resid 75 through 76 removed outlier: 7.337A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'E' and resid 167 through 175 Processing sheet with id=AA6, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.984A pdb=" N THR E 202 " --> pdb=" O TYR E 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.597A pdb=" N LEU E 260 " --> pdb=" O THR E 449 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N THR E 443 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.446A pdb=" N ILE E 294 " --> pdb=" O THR E 443 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N ARG E 445 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.827A pdb=" N VAL E 292 " --> pdb=" O ARG E 445 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N ASN E 447 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.863A pdb=" N THR E 290 " --> pdb=" O ASN E 447 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR E 449 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER E 334 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS E 420 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE E 382 " --> pdb=" O LYS E 420 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS E 378 " --> pdb=" O GLU E 381 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.818A pdb=" N THR E 449 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.863A pdb=" N THR E 290 " --> pdb=" O ASN E 447 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N ASN E 447 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.827A pdb=" N VAL E 292 " --> pdb=" O ARG E 445 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N ARG E 445 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.446A pdb=" N ILE E 294 " --> pdb=" O THR E 443 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N THR E 443 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR E 466 " --> pdb=" O ASP E 456 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR E 357 " --> pdb=" O GLU E 465 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N PHE E 467 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS E 360 " --> pdb=" O PHE E 467 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY E 393 " --> pdb=" O TYR E 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 305 through 308 Processing sheet with id=AB1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.784A pdb=" N GLU G 10 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TYR G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.784A pdb=" N GLU G 10 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR G 116 " --> pdb=" O THR G 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 9 through 12 Processing sheet with id=AB5, first strand: chain 'H' and resid 9 through 12 Processing sheet with id=AB6, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AB7, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AB8, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.553A pdb=" N LEU A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 75 through 76 removed outlier: 7.497A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.596A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 167 through 175 Processing sheet with id=AC3, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.816A pdb=" N THR A 202 " --> pdb=" O TYR A 434 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.041A pdb=" N GLY A 450 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.041A pdb=" N GLY A 450 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 393 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 374 through 375 removed outlier: 4.623A pdb=" N PHE A 382 " --> pdb=" O LYS A 420 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 420 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 301 through 302 removed outlier: 4.057A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 305 through 308 Processing sheet with id=AC9, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AD1, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.779A pdb=" N LYS C 12 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AD3, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.775A pdb=" N THR D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AD5, first strand: chain 'I' and resid 36 through 40 Processing sheet with id=AD6, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AD7, first strand: chain 'I' and resid 75 through 76 removed outlier: 7.427A pdb=" N CYS I 54 " --> pdb=" O VAL I 75 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 91 through 93 Processing sheet with id=AD9, first strand: chain 'I' and resid 167 through 175 Processing sheet with id=AE1, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.954A pdb=" N THR I 202 " --> pdb=" O TYR I 434 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 259 through 261 removed outlier: 4.006A pdb=" N GLY I 450 " --> pdb=" O LEU I 260 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N THR I 443 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.395A pdb=" N ILE I 294 " --> pdb=" O THR I 443 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N ARG I 445 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 10.990A pdb=" N VAL I 292 " --> pdb=" O ARG I 445 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N ASN I 447 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N THR I 290 " --> pdb=" O ASN I 447 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR I 449 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLU I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER I 334 " --> pdb=" O GLU I 293 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 271 through 273 removed outlier: 6.811A pdb=" N THR I 449 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N THR I 290 " --> pdb=" O ASN I 447 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N ASN I 447 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.990A pdb=" N VAL I 292 " --> pdb=" O ARG I 445 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N ARG I 445 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.395A pdb=" N ILE I 294 " --> pdb=" O THR I 443 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N THR I 443 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY I 393 " --> pdb=" O TYR I 361 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 305 through 309 removed outlier: 3.759A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.693A pdb=" N LYS K 12 " --> pdb=" O THR K 124 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TYR K 33 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TRP K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AE8, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AE9, first strand: chain 'L' and resid 18 through 23 698 hydrogen bonds defined for protein. 1851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.89 Time building geometry restraints manager: 8.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6356 1.34 - 1.46: 5312 1.46 - 1.58: 9495 1.58 - 1.70: 0 1.70 - 1.82: 177 Bond restraints: 21340 Sorted by residual: bond pdb=" C LYS A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.331 1.367 -0.036 7.90e-03 1.60e+04 2.04e+01 bond pdb=" C1 MAN S 4 " pdb=" O5 MAN S 4 " ideal model delta sigma weight residual 1.399 1.443 -0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" C1 NAG w 3 " pdb=" O5 NAG w 3 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.77e+00 bond pdb=" C1 NAG I 703 " pdb=" O5 NAG I 703 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" C1 NAG i 3 " pdb=" O5 NAG i 3 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.71e+00 ... (remaining 21335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 28259 2.64 - 5.27: 656 5.27 - 7.91: 95 7.91 - 10.54: 13 10.54 - 13.18: 2 Bond angle restraints: 29025 Sorted by residual: angle pdb=" C THR I 257 " pdb=" N GLN I 258 " pdb=" CA GLN I 258 " ideal model delta sigma weight residual 121.54 129.93 -8.39 1.91e+00 2.74e-01 1.93e+01 angle pdb=" C ASN I 276 " pdb=" N LEU I 277 " pdb=" CA LEU I 277 " ideal model delta sigma weight residual 121.54 129.34 -7.80 1.91e+00 2.74e-01 1.67e+01 angle pdb=" N SER A 388 " pdb=" CA SER A 388 " pdb=" C SER A 388 " ideal model delta sigma weight residual 114.04 109.27 4.77 1.24e+00 6.50e-01 1.48e+01 angle pdb=" CA LEU I 259 " pdb=" CB LEU I 259 " pdb=" CG LEU I 259 " ideal model delta sigma weight residual 116.30 129.48 -13.18 3.50e+00 8.16e-02 1.42e+01 angle pdb=" CB MET I 474 " pdb=" CG MET I 474 " pdb=" SD MET I 474 " ideal model delta sigma weight residual 112.70 123.80 -11.10 3.00e+00 1.11e-01 1.37e+01 ... (remaining 29020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.39: 13264 22.39 - 44.79: 902 44.79 - 67.18: 172 67.18 - 89.58: 173 89.58 - 111.97: 104 Dihedral angle restraints: 14615 sinusoidal: 7562 harmonic: 7053 Sorted by residual: dihedral pdb=" CB CYS I 126 " pdb=" SG CYS I 126 " pdb=" SG CYS I 196 " pdb=" CB CYS I 196 " ideal model delta sinusoidal sigma weight residual 93.00 152.84 -59.84 1 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 151.29 -58.29 1 1.00e+01 1.00e-02 4.55e+01 dihedral pdb=" CB CYS I 378 " pdb=" SG CYS I 378 " pdb=" SG CYS I 444 " pdb=" CB CYS I 444 " ideal model delta sinusoidal sigma weight residual -86.00 -36.15 -49.85 1 1.00e+01 1.00e-02 3.41e+01 ... (remaining 14612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3016 0.075 - 0.149: 581 0.149 - 0.224: 58 0.224 - 0.299: 30 0.299 - 0.374: 5 Chirality restraints: 3690 Sorted by residual: chirality pdb=" C1 NAG I 704 " pdb=" ND2 ASN I 339 " pdb=" C2 NAG I 704 " pdb=" O5 NAG I 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" C1 NAG m 1 " pdb=" ND2 ASN A 339 " pdb=" C2 NAG m 1 " pdb=" O5 NAG m 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 3687 not shown) Planarity restraints: 3542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 42 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO E 43 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 176 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO E 177 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 177 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 177 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 45 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO L 46 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO L 46 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 46 " -0.025 5.00e-02 4.00e+02 ... (remaining 3539 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3919 2.77 - 3.30: 18111 3.30 - 3.84: 34342 3.84 - 4.37: 38167 4.37 - 4.90: 67764 Nonbonded interactions: 162303 Sorted by model distance: nonbonded pdb=" O MET I 369 " pdb=" OG1 THR I 373 " model vdw 2.241 3.040 nonbonded pdb=" O MET A 369 " pdb=" OG1 THR A 373 " model vdw 2.245 3.040 nonbonded pdb=" O VAL E 36 " pdb=" OG1 THR F 606 " model vdw 2.248 3.040 nonbonded pdb=" O VAL I 36 " pdb=" OG1 THR J 606 " model vdw 2.253 3.040 nonbonded pdb=" O MET E 369 " pdb=" OG1 THR E 373 " model vdw 2.258 3.040 ... (remaining 162298 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 33 through 504 or resid 701 through 703)) selection = (chain 'I' and (resid 33 through 504 or resid 701 through 703)) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Z' selection = chain 'n' } ncs_group { reference = (chain 'N' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'l' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'o' and resid 1 through 2) selection = (chain 'u' and resid 1 through 2) selection = (chain 'w' and resid 1 through 2) selection = (chain 'x' and resid 1 through 2) } ncs_group { reference = chain 'O' selection = chain 'U' selection = chain 'b' selection = chain 'h' selection = chain 'p' selection = chain 'v' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'Y' selection = chain 'd' selection = chain 'e' selection = chain 'k' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 'y' } ncs_group { reference = chain 'S' selection = chain 'f' selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.940 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 54.350 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 0.007 0.053 21524 Z= 0.313 Angle : 0.981 13.178 29538 Z= 0.445 Chirality : 0.063 0.374 3690 Planarity : 0.005 0.050 3492 Dihedral : 19.844 111.972 9980 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.16), residues: 2415 helix: -0.46 (0.24), residues: 375 sheet: -0.41 (0.20), residues: 678 loop : -1.38 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 112 HIS 0.007 0.002 HIS I 374 PHE 0.018 0.002 PHE A 376 TYR 0.017 0.002 TYR K 27 ARG 0.002 0.000 ARG J 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00570 ( 50) link_NAG-ASN : angle 2.63075 ( 150) link_ALPHA1-6 : bond 0.00460 ( 12) link_ALPHA1-6 : angle 1.53750 ( 36) link_BETA1-4 : bond 0.00733 ( 68) link_BETA1-4 : angle 2.47543 ( 204) link_ALPHA1-2 : bond 0.00442 ( 6) link_ALPHA1-2 : angle 2.63971 ( 18) link_ALPHA1-3 : bond 0.00304 ( 9) link_ALPHA1-3 : angle 1.82640 ( 27) hydrogen bonds : bond 0.08052 ( 668) hydrogen bonds : angle 6.02119 ( 1851) SS BOND : bond 0.00409 ( 39) SS BOND : angle 1.19274 ( 78) covalent geometry : bond 0.00666 (21340) covalent geometry : angle 0.94098 (29025) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.413 Fit side-chains revert: symmetry clash REVERT: E 95 MET cc_start: 0.8846 (ptm) cc_final: 0.8566 (ptp) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2955 time to fit residues: 41.6807 Evaluate side-chains 66 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 0.1980 chunk 188 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 217 optimal weight: 6.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 HIS E 262 ASN A 258 GLN I 229 ASN I 424 ASN J 540 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.055337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.039885 restraints weight = 102027.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.041024 restraints weight = 68186.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.041140 restraints weight = 51057.567| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 21524 Z= 0.232 Angle : 0.705 8.443 29538 Z= 0.331 Chirality : 0.047 0.273 3690 Planarity : 0.004 0.047 3492 Dihedral : 16.123 89.302 5597 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.28 % Allowed : 6.13 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.17), residues: 2415 helix: 0.67 (0.28), residues: 375 sheet: -0.40 (0.19), residues: 711 loop : -1.28 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 112 HIS 0.008 0.002 HIS I 374 PHE 0.017 0.002 PHE A 376 TYR 0.021 0.002 TYR I 483 ARG 0.004 0.001 ARG J 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 50) link_NAG-ASN : angle 2.18876 ( 150) link_ALPHA1-6 : bond 0.00356 ( 12) link_ALPHA1-6 : angle 1.89310 ( 36) link_BETA1-4 : bond 0.00528 ( 68) link_BETA1-4 : angle 2.14191 ( 204) link_ALPHA1-2 : bond 0.00550 ( 6) link_ALPHA1-2 : angle 2.12177 ( 18) link_ALPHA1-3 : bond 0.00715 ( 9) link_ALPHA1-3 : angle 2.06605 ( 27) hydrogen bonds : bond 0.04046 ( 668) hydrogen bonds : angle 5.34273 ( 1851) SS BOND : bond 0.00241 ( 39) SS BOND : angle 0.88795 ( 78) covalent geometry : bond 0.00540 (21340) covalent geometry : angle 0.66026 (29025) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 2.156 Fit side-chains revert: symmetry clash REVERT: E 95 MET cc_start: 0.8811 (ptm) cc_final: 0.8537 (ptm) REVERT: C 70 MET cc_start: 0.8678 (mtt) cc_final: 0.8391 (mtt) REVERT: I 433 MET cc_start: 0.8881 (ttm) cc_final: 0.8615 (ttm) REVERT: K 76 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8760 (tt) outliers start: 6 outliers final: 3 residues processed: 69 average time/residue: 0.2790 time to fit residues: 34.0066 Evaluate side-chains 68 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain K residue 76 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 192 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 228 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 658 GLN A 421 GLN B 650 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.055160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.039529 restraints weight = 104109.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.040571 restraints weight = 72941.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.040708 restraints weight = 57033.070| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 21524 Z= 0.265 Angle : 0.724 7.224 29538 Z= 0.342 Chirality : 0.049 0.271 3690 Planarity : 0.004 0.040 3492 Dihedral : 12.509 76.882 5597 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.71 % Allowed : 10.33 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.17), residues: 2415 helix: 0.86 (0.29), residues: 375 sheet: -0.43 (0.19), residues: 711 loop : -1.28 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 112 HIS 0.010 0.002 HIS A 374 PHE 0.025 0.002 PHE A 376 TYR 0.016 0.002 TYR H 51 ARG 0.003 0.000 ARG J 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 50) link_NAG-ASN : angle 2.26636 ( 150) link_ALPHA1-6 : bond 0.00658 ( 12) link_ALPHA1-6 : angle 1.86000 ( 36) link_BETA1-4 : bond 0.00562 ( 68) link_BETA1-4 : angle 2.02479 ( 204) link_ALPHA1-2 : bond 0.00377 ( 6) link_ALPHA1-2 : angle 2.07455 ( 18) link_ALPHA1-3 : bond 0.00791 ( 9) link_ALPHA1-3 : angle 1.83425 ( 27) hydrogen bonds : bond 0.04272 ( 668) hydrogen bonds : angle 5.38630 ( 1851) SS BOND : bond 0.00302 ( 39) SS BOND : angle 1.04438 ( 78) covalent geometry : bond 0.00618 (21340) covalent geometry : angle 0.68230 (29025) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 2.531 Fit side-chains revert: symmetry clash REVERT: F 530 MET cc_start: 0.8153 (mtt) cc_final: 0.7731 (mtt) REVERT: G 70 MET cc_start: 0.8651 (mtt) cc_final: 0.7824 (mtt) REVERT: C 70 MET cc_start: 0.8853 (mtt) cc_final: 0.7932 (mtt) REVERT: K 70 MET cc_start: 0.8453 (mmm) cc_final: 0.6684 (mmt) outliers start: 15 outliers final: 7 residues processed: 76 average time/residue: 0.3125 time to fit residues: 41.4370 Evaluate side-chains 69 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 374 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 54 optimal weight: 9.9990 chunk 152 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 195 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 134 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.055693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.040608 restraints weight = 104070.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.041189 restraints weight = 76296.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.041386 restraints weight = 59593.803| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21524 Z= 0.146 Angle : 0.605 7.115 29538 Z= 0.283 Chirality : 0.045 0.270 3690 Planarity : 0.003 0.037 3492 Dihedral : 10.790 69.745 5597 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.85 % Allowed : 12.02 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.17), residues: 2415 helix: 1.32 (0.29), residues: 375 sheet: -0.46 (0.19), residues: 708 loop : -1.12 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 112 HIS 0.004 0.001 HIS I 374 PHE 0.009 0.001 PHE I 383 TYR 0.015 0.001 TYR H 51 ARG 0.003 0.000 ARG F 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 50) link_NAG-ASN : angle 1.91385 ( 150) link_ALPHA1-6 : bond 0.00841 ( 12) link_ALPHA1-6 : angle 1.84447 ( 36) link_BETA1-4 : bond 0.00452 ( 68) link_BETA1-4 : angle 1.77114 ( 204) link_ALPHA1-2 : bond 0.00310 ( 6) link_ALPHA1-2 : angle 1.99814 ( 18) link_ALPHA1-3 : bond 0.00883 ( 9) link_ALPHA1-3 : angle 1.77911 ( 27) hydrogen bonds : bond 0.03591 ( 668) hydrogen bonds : angle 5.06215 ( 1851) SS BOND : bond 0.00210 ( 39) SS BOND : angle 0.61382 ( 78) covalent geometry : bond 0.00330 (21340) covalent geometry : angle 0.56645 (29025) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 2.347 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8743 (tt) REVERT: F 530 MET cc_start: 0.8107 (mtt) cc_final: 0.7793 (mtt) REVERT: G 70 MET cc_start: 0.8636 (mtt) cc_final: 0.8059 (mtt) REVERT: C 70 MET cc_start: 0.8920 (mtt) cc_final: 0.8032 (mtt) REVERT: I 259 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9094 (mp) REVERT: K 70 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.7324 (mmm) outliers start: 18 outliers final: 5 residues processed: 80 average time/residue: 0.2805 time to fit residues: 39.7585 Evaluate side-chains 72 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain K residue 70 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 98 optimal weight: 6.9990 chunk 199 optimal weight: 0.0170 chunk 133 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 138 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 258 GLN A 421 GLN I 187 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.055800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.040467 restraints weight = 103374.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.041529 restraints weight = 71563.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.041683 restraints weight = 54979.083| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21524 Z= 0.132 Angle : 0.580 7.156 29538 Z= 0.272 Chirality : 0.044 0.244 3690 Planarity : 0.003 0.035 3492 Dihedral : 9.773 65.507 5597 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.27 % Allowed : 12.97 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.17), residues: 2415 helix: 1.64 (0.29), residues: 375 sheet: -0.37 (0.19), residues: 708 loop : -1.01 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 112 HIS 0.005 0.001 HIS A 374 PHE 0.009 0.001 PHE G 64 TYR 0.014 0.001 TYR H 51 ARG 0.003 0.000 ARG F 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 50) link_NAG-ASN : angle 1.75649 ( 150) link_ALPHA1-6 : bond 0.00974 ( 12) link_ALPHA1-6 : angle 1.59106 ( 36) link_BETA1-4 : bond 0.00471 ( 68) link_BETA1-4 : angle 1.60486 ( 204) link_ALPHA1-2 : bond 0.00291 ( 6) link_ALPHA1-2 : angle 1.93989 ( 18) link_ALPHA1-3 : bond 0.00921 ( 9) link_ALPHA1-3 : angle 1.62669 ( 27) hydrogen bonds : bond 0.03352 ( 668) hydrogen bonds : angle 4.90872 ( 1851) SS BOND : bond 0.00289 ( 39) SS BOND : angle 0.63557 ( 78) covalent geometry : bond 0.00299 (21340) covalent geometry : angle 0.54658 (29025) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 2.172 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8757 (tt) REVERT: F 530 MET cc_start: 0.8234 (mtt) cc_final: 0.7925 (mtt) REVERT: G 70 MET cc_start: 0.8365 (mtt) cc_final: 0.8135 (mtt) REVERT: A 125 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8701 (tt) REVERT: C 70 MET cc_start: 0.8827 (mtt) cc_final: 0.7964 (mtt) REVERT: I 44 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8224 (t) REVERT: I 259 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9070 (mp) REVERT: K 70 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7317 (mmm) outliers start: 27 outliers final: 11 residues processed: 87 average time/residue: 0.2717 time to fit residues: 41.2634 Evaluate side-chains 78 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain K residue 70 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 67 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.055275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.039765 restraints weight = 104382.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.040377 restraints weight = 78435.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.040594 restraints weight = 61416.113| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 21524 Z= 0.250 Angle : 0.668 7.051 29538 Z= 0.316 Chirality : 0.047 0.242 3690 Planarity : 0.004 0.037 3492 Dihedral : 9.895 67.214 5597 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.56 % Allowed : 13.48 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.17), residues: 2415 helix: 1.42 (0.29), residues: 375 sheet: -0.44 (0.19), residues: 714 loop : -1.09 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 112 HIS 0.008 0.001 HIS A 374 PHE 0.012 0.002 PHE I 53 TYR 0.015 0.001 TYR H 51 ARG 0.003 0.000 ARG J 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 50) link_NAG-ASN : angle 1.98270 ( 150) link_ALPHA1-6 : bond 0.00825 ( 12) link_ALPHA1-6 : angle 1.52666 ( 36) link_BETA1-4 : bond 0.00489 ( 68) link_BETA1-4 : angle 1.70517 ( 204) link_ALPHA1-2 : bond 0.00364 ( 6) link_ALPHA1-2 : angle 2.04477 ( 18) link_ALPHA1-3 : bond 0.00696 ( 9) link_ALPHA1-3 : angle 1.81775 ( 27) hydrogen bonds : bond 0.03981 ( 668) hydrogen bonds : angle 5.16762 ( 1851) SS BOND : bond 0.00318 ( 39) SS BOND : angle 0.92197 ( 78) covalent geometry : bond 0.00588 (21340) covalent geometry : angle 0.63463 (29025) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 63 time to evaluate : 2.119 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8854 (tt) REVERT: G 70 MET cc_start: 0.8731 (mtt) cc_final: 0.7780 (mtt) REVERT: A 125 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8745 (tt) REVERT: C 70 MET cc_start: 0.8926 (mtt) cc_final: 0.8058 (mtt) REVERT: I 44 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8305 (t) REVERT: I 259 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9139 (mp) REVERT: K 70 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.6883 (mmm) outliers start: 33 outliers final: 21 residues processed: 91 average time/residue: 0.2590 time to fit residues: 41.5675 Evaluate side-chains 89 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 374 HIS Chi-restraints excluded: chain I residue 487 VAL Chi-restraints excluded: chain K residue 70 MET Chi-restraints excluded: chain K residue 89 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 112 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 127 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 222 optimal weight: 0.0970 chunk 56 optimal weight: 5.9990 chunk 199 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 66 HIS I 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.056231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.041330 restraints weight = 102659.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.042025 restraints weight = 70562.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.042219 restraints weight = 54261.134| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 21524 Z= 0.096 Angle : 0.558 7.350 29538 Z= 0.264 Chirality : 0.043 0.251 3690 Planarity : 0.003 0.035 3492 Dihedral : 9.112 61.022 5597 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.99 % Allowed : 14.43 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.17), residues: 2415 helix: 1.81 (0.29), residues: 375 sheet: -0.32 (0.19), residues: 708 loop : -0.90 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 112 HIS 0.013 0.001 HIS I 374 PHE 0.008 0.001 PHE A 376 TYR 0.013 0.001 TYR L 51 ARG 0.003 0.000 ARG F 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 50) link_NAG-ASN : angle 1.62712 ( 150) link_ALPHA1-6 : bond 0.01049 ( 12) link_ALPHA1-6 : angle 1.46705 ( 36) link_BETA1-4 : bond 0.00460 ( 68) link_BETA1-4 : angle 1.53619 ( 204) link_ALPHA1-2 : bond 0.00305 ( 6) link_ALPHA1-2 : angle 1.90892 ( 18) link_ALPHA1-3 : bond 0.00993 ( 9) link_ALPHA1-3 : angle 1.47592 ( 27) hydrogen bonds : bond 0.03164 ( 668) hydrogen bonds : angle 4.78583 ( 1851) SS BOND : bond 0.00196 ( 39) SS BOND : angle 0.50666 ( 78) covalent geometry : bond 0.00201 (21340) covalent geometry : angle 0.52790 (29025) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 2.212 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8728 (tt) REVERT: G 70 MET cc_start: 0.8676 (mtt) cc_final: 0.7752 (mtt) REVERT: C 70 MET cc_start: 0.8871 (mtt) cc_final: 0.8043 (mtt) REVERT: I 44 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8202 (t) REVERT: I 259 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9027 (mp) REVERT: I 433 MET cc_start: 0.8782 (ttm) cc_final: 0.8577 (ttm) REVERT: K 70 MET cc_start: 0.8498 (mmm) cc_final: 0.6470 (mmt) outliers start: 21 outliers final: 12 residues processed: 81 average time/residue: 0.2613 time to fit residues: 38.2220 Evaluate side-chains 79 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 374 HIS Chi-restraints excluded: chain I residue 487 VAL Chi-restraints excluded: chain K residue 89 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 150 optimal weight: 30.0000 chunk 129 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 179 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.056091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.040669 restraints weight = 103210.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.041767 restraints weight = 71325.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.041760 restraints weight = 53490.841| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 21524 Z= 0.115 Angle : 0.557 7.302 29538 Z= 0.261 Chirality : 0.044 0.229 3690 Planarity : 0.003 0.034 3492 Dihedral : 8.890 59.299 5597 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.04 % Allowed : 14.52 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 2415 helix: 1.90 (0.29), residues: 375 sheet: -0.29 (0.19), residues: 714 loop : -0.76 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 112 HIS 0.004 0.001 HIS I 374 PHE 0.009 0.001 PHE E 317 TYR 0.012 0.001 TYR L 51 ARG 0.003 0.000 ARG J 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 50) link_NAG-ASN : angle 1.61552 ( 150) link_ALPHA1-6 : bond 0.00976 ( 12) link_ALPHA1-6 : angle 1.41368 ( 36) link_BETA1-4 : bond 0.00477 ( 68) link_BETA1-4 : angle 1.51670 ( 204) link_ALPHA1-2 : bond 0.00304 ( 6) link_ALPHA1-2 : angle 1.90684 ( 18) link_ALPHA1-3 : bond 0.00913 ( 9) link_ALPHA1-3 : angle 1.55654 ( 27) hydrogen bonds : bond 0.03159 ( 668) hydrogen bonds : angle 4.75247 ( 1851) SS BOND : bond 0.00209 ( 39) SS BOND : angle 0.54009 ( 78) covalent geometry : bond 0.00257 (21340) covalent geometry : angle 0.52738 (29025) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 2.219 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8720 (tt) REVERT: G 70 MET cc_start: 0.8626 (mtt) cc_final: 0.7702 (mtt) REVERT: C 70 MET cc_start: 0.8826 (mtt) cc_final: 0.8029 (mtt) REVERT: K 70 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.6792 (mmm) outliers start: 22 outliers final: 14 residues processed: 86 average time/residue: 0.2832 time to fit residues: 42.8478 Evaluate side-chains 79 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 374 HIS Chi-restraints excluded: chain I residue 487 VAL Chi-restraints excluded: chain K residue 70 MET Chi-restraints excluded: chain K residue 89 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 11 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 226 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN D 16 GLN I 374 HIS L 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.055281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.039975 restraints weight = 104556.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.040742 restraints weight = 75441.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.040780 restraints weight = 59582.077| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 21524 Z= 0.277 Angle : 0.698 12.148 29538 Z= 0.331 Chirality : 0.047 0.245 3690 Planarity : 0.004 0.036 3492 Dihedral : 9.371 63.271 5597 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.27 % Allowed : 14.62 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.17), residues: 2415 helix: 1.45 (0.29), residues: 378 sheet: -0.41 (0.19), residues: 714 loop : -1.04 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 96 HIS 0.016 0.002 HIS I 374 PHE 0.020 0.002 PHE I 376 TYR 0.015 0.002 TYR E 223 ARG 0.002 0.000 ARG E 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 50) link_NAG-ASN : angle 1.95454 ( 150) link_ALPHA1-6 : bond 0.00833 ( 12) link_ALPHA1-6 : angle 1.37793 ( 36) link_BETA1-4 : bond 0.00506 ( 68) link_BETA1-4 : angle 1.69522 ( 204) link_ALPHA1-2 : bond 0.00409 ( 6) link_ALPHA1-2 : angle 2.09779 ( 18) link_ALPHA1-3 : bond 0.00622 ( 9) link_ALPHA1-3 : angle 1.81295 ( 27) hydrogen bonds : bond 0.04137 ( 668) hydrogen bonds : angle 5.19667 ( 1851) SS BOND : bond 0.00347 ( 39) SS BOND : angle 0.98949 ( 78) covalent geometry : bond 0.00650 (21340) covalent geometry : angle 0.66732 (29025) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 2.230 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8870 (tt) REVERT: G 70 MET cc_start: 0.8749 (mtt) cc_final: 0.7799 (mtt) REVERT: C 70 MET cc_start: 0.8893 (mtt) cc_final: 0.8081 (mtt) REVERT: K 70 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.7234 (mmm) outliers start: 27 outliers final: 20 residues processed: 87 average time/residue: 0.2722 time to fit residues: 42.1736 Evaluate side-chains 85 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 374 HIS Chi-restraints excluded: chain I residue 487 VAL Chi-restraints excluded: chain I residue 495 VAL Chi-restraints excluded: chain K residue 70 MET Chi-restraints excluded: chain K residue 89 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 218 optimal weight: 3.9990 chunk 225 optimal weight: 9.9990 chunk 203 optimal weight: 0.0570 chunk 238 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 217 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 187 optimal weight: 0.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.055565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.040758 restraints weight = 104171.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.041054 restraints weight = 77855.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.041204 restraints weight = 61586.095| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21524 Z= 0.145 Angle : 0.601 11.546 29538 Z= 0.283 Chirality : 0.044 0.239 3690 Planarity : 0.003 0.038 3492 Dihedral : 9.019 60.247 5597 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.90 % Allowed : 15.18 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.17), residues: 2415 helix: 1.62 (0.29), residues: 378 sheet: -0.38 (0.19), residues: 720 loop : -0.94 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 112 HIS 0.005 0.001 HIS I 374 PHE 0.008 0.001 PHE E 317 TYR 0.014 0.001 TYR H 51 ARG 0.003 0.000 ARG J 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 50) link_NAG-ASN : angle 1.75194 ( 150) link_ALPHA1-6 : bond 0.00955 ( 12) link_ALPHA1-6 : angle 1.39947 ( 36) link_BETA1-4 : bond 0.00464 ( 68) link_BETA1-4 : angle 1.57598 ( 204) link_ALPHA1-2 : bond 0.00303 ( 6) link_ALPHA1-2 : angle 1.99696 ( 18) link_ALPHA1-3 : bond 0.00861 ( 9) link_ALPHA1-3 : angle 1.51770 ( 27) hydrogen bonds : bond 0.03559 ( 668) hydrogen bonds : angle 4.96596 ( 1851) SS BOND : bond 0.00240 ( 39) SS BOND : angle 0.66371 ( 78) covalent geometry : bond 0.00331 (21340) covalent geometry : angle 0.57148 (29025) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 2.284 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8785 (tt) REVERT: G 70 MET cc_start: 0.8703 (mtt) cc_final: 0.7765 (mtt) REVERT: C 70 MET cc_start: 0.8922 (mtt) cc_final: 0.8091 (mtt) REVERT: I 44 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8272 (t) REVERT: K 70 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7162 (mmm) outliers start: 19 outliers final: 16 residues processed: 79 average time/residue: 0.2605 time to fit residues: 37.2421 Evaluate side-chains 81 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 374 HIS Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 487 VAL Chi-restraints excluded: chain K residue 70 MET Chi-restraints excluded: chain K residue 89 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 125 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 231 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 174 optimal weight: 0.0050 chunk 21 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 226 optimal weight: 7.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.056184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.041374 restraints weight = 104335.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.041674 restraints weight = 74161.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.041877 restraints weight = 60210.561| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21524 Z= 0.103 Angle : 0.566 10.791 29538 Z= 0.266 Chirality : 0.043 0.229 3690 Planarity : 0.003 0.037 3492 Dihedral : 8.618 59.814 5597 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.80 % Allowed : 15.42 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 2415 helix: 1.90 (0.29), residues: 375 sheet: -0.24 (0.19), residues: 711 loop : -0.79 (0.18), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 112 HIS 0.004 0.001 HIS I 374 PHE 0.009 0.001 PHE E 317 TYR 0.013 0.001 TYR L 51 ARG 0.003 0.000 ARG J 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 50) link_NAG-ASN : angle 1.60478 ( 150) link_ALPHA1-6 : bond 0.01044 ( 12) link_ALPHA1-6 : angle 1.43615 ( 36) link_BETA1-4 : bond 0.00481 ( 68) link_BETA1-4 : angle 1.50669 ( 204) link_ALPHA1-2 : bond 0.00312 ( 6) link_ALPHA1-2 : angle 1.94016 ( 18) link_ALPHA1-3 : bond 0.00922 ( 9) link_ALPHA1-3 : angle 1.42203 ( 27) hydrogen bonds : bond 0.03186 ( 668) hydrogen bonds : angle 4.77858 ( 1851) SS BOND : bond 0.00208 ( 39) SS BOND : angle 0.54035 ( 78) covalent geometry : bond 0.00224 (21340) covalent geometry : angle 0.53764 (29025) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5477.50 seconds wall clock time: 97 minutes 4.67 seconds (5824.67 seconds total)