Starting phenix.real_space_refine on Sun Aug 24 15:56:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dto_27706/08_2025/8dto_27706.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dto_27706/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dto_27706/08_2025/8dto_27706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dto_27706/08_2025/8dto_27706.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dto_27706/08_2025/8dto_27706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dto_27706/08_2025/8dto_27706.map" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.55, per 1000 atoms: 0.17 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: 1.65 Conformation dependent library (CDL) restraints added in 599.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.63 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: 3.29 Time building geometry restraints manager: 2.08 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 703) selection = (chain 'I' and resid 33 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: 2.170 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.280 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.280 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG J 585 TYR 0.017 0.002 TYR K 27 PHE 0.018 0.002 PHE A 376 TRP 0.030 0.002 TRP A 112 HIS 0.007 0.002 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00666 (21340) covalent geometry : angle 0.94098 (29025) SS BOND : bond 0.00409 ( 39) SS BOND : angle 1.19274 ( 78) hydrogen bonds : bond 0.08052 ( 668) hydrogen bonds : angle 6.02119 ( 1851) 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) 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_NAG-ASN : bond 0.00570 ( 50) link_NAG-ASN : angle 2.63075 ( 150) *********************** 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 : 0.624 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: 0.0968 time to fit residues: 13.7287 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 : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 0.0970 overall best weight: 1.7782 ------------------------------------------------------------------------------- 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 424 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.056300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.041209 restraints weight = 101240.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.042006 restraints weight = 71091.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.042239 restraints weight = 54024.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.042737 restraints weight = 52310.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.042752 restraints weight = 47380.135| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21524 Z= 0.136 Angle : 0.639 9.782 29538 Z= 0.294 Chirality : 0.046 0.258 3690 Planarity : 0.004 0.039 3492 Dihedral : 15.567 85.866 5597 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.24 % Allowed : 5.19 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.17), residues: 2415 helix: 0.91 (0.28), residues: 375 sheet: -0.50 (0.19), residues: 729 loop : -1.11 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 585 TYR 0.012 0.001 TYR H 51 PHE 0.010 0.001 PHE I 383 TRP 0.016 0.001 TRP A 112 HIS 0.006 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00304 (21340) covalent geometry : angle 0.59391 (29025) SS BOND : bond 0.00171 ( 39) SS BOND : angle 0.65140 ( 78) hydrogen bonds : bond 0.03526 ( 668) hydrogen bonds : angle 5.07948 ( 1851) link_ALPHA1-2 : bond 0.00392 ( 6) link_ALPHA1-2 : angle 2.11506 ( 18) link_ALPHA1-3 : bond 0.01015 ( 9) link_ALPHA1-3 : angle 2.13323 ( 27) link_ALPHA1-6 : bond 0.00555 ( 12) link_ALPHA1-6 : angle 1.87559 ( 36) link_BETA1-4 : bond 0.00507 ( 68) link_BETA1-4 : angle 2.12209 ( 204) link_NAG-ASN : bond 0.00272 ( 50) link_NAG-ASN : angle 1.92909 ( 150) *********************** 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: 5 poor density : 67 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: E 95 MET cc_start: 0.8753 (ptm) cc_final: 0.8483 (ptm) REVERT: I 433 MET cc_start: 0.8750 (ttm) cc_final: 0.8456 (ttm) REVERT: K 70 MET cc_start: 0.7928 (mmm) cc_final: 0.6369 (mmt) REVERT: K 76 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8580 (tt) outliers start: 5 outliers final: 3 residues processed: 69 average time/residue: 0.1097 time to fit residues: 13.1313 Evaluate side-chains 69 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 20 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 chunk 226 optimal weight: 9.9990 chunk 185 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 653 GLN D 16 GLN I 105 HIS I 229 ASN J 540 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.054734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.039024 restraints weight = 104940.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.040427 restraints weight = 73676.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.040454 restraints weight = 55464.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.040561 restraints weight = 56382.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.040619 restraints weight = 51896.310| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 21524 Z= 0.341 Angle : 0.807 8.231 29538 Z= 0.383 Chirality : 0.051 0.267 3690 Planarity : 0.005 0.047 3492 Dihedral : 13.156 80.090 5597 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.71 % Allowed : 10.37 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.17), residues: 2415 helix: 0.73 (0.29), residues: 375 sheet: -0.44 (0.19), residues: 705 loop : -1.36 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 579 TYR 0.021 0.002 TYR E 223 PHE 0.021 0.002 PHE A 376 TRP 0.020 0.002 TRP I 69 HIS 0.015 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00798 (21340) covalent geometry : angle 0.76519 (29025) SS BOND : bond 0.00364 ( 39) SS BOND : angle 1.22531 ( 78) hydrogen bonds : bond 0.04736 ( 668) hydrogen bonds : angle 5.56332 ( 1851) link_ALPHA1-2 : bond 0.00499 ( 6) link_ALPHA1-2 : angle 2.17725 ( 18) link_ALPHA1-3 : bond 0.00614 ( 9) link_ALPHA1-3 : angle 1.93724 ( 27) link_ALPHA1-6 : bond 0.00549 ( 12) link_ALPHA1-6 : angle 1.84450 ( 36) link_BETA1-4 : bond 0.00578 ( 68) link_BETA1-4 : angle 2.15266 ( 204) link_NAG-ASN : bond 0.00532 ( 50) link_NAG-ASN : angle 2.44011 ( 150) *********************** 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 80 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: G 70 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8397 (mtt) REVERT: C 70 MET cc_start: 0.8825 (mtt) cc_final: 0.8164 (mtt) REVERT: K 70 MET cc_start: 0.8446 (mmm) cc_final: 0.6632 (mmt) outliers start: 15 outliers final: 5 residues processed: 77 average time/residue: 0.1022 time to fit residues: 13.6468 Evaluate side-chains 70 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain A residue 433 MET 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 223 optimal weight: 4.9990 chunk 230 optimal weight: 30.0000 chunk 213 optimal weight: 8.9990 chunk 220 optimal weight: 8.9990 chunk 136 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 chunk 120 optimal weight: 0.9990 chunk 187 optimal weight: 0.0030 chunk 204 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN D 16 GLN I 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.056158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.040792 restraints weight = 103513.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.041721 restraints weight = 73781.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.041923 restraints weight = 56818.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.042069 restraints weight = 55665.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.042150 restraints weight = 51268.314| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21524 Z= 0.104 Angle : 0.588 7.419 29538 Z= 0.275 Chirality : 0.045 0.274 3690 Planarity : 0.003 0.036 3492 Dihedral : 10.907 69.457 5597 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.57 % Allowed : 11.55 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.17), residues: 2415 helix: 1.46 (0.29), residues: 372 sheet: -0.44 (0.19), residues: 735 loop : -1.05 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 585 TYR 0.013 0.001 TYR D 51 PHE 0.008 0.001 PHE I 383 TRP 0.018 0.001 TRP A 112 HIS 0.003 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00219 (21340) covalent geometry : angle 0.54990 (29025) SS BOND : bond 0.00197 ( 39) SS BOND : angle 0.50887 ( 78) hydrogen bonds : bond 0.03414 ( 668) hydrogen bonds : angle 4.97217 ( 1851) link_ALPHA1-2 : bond 0.00311 ( 6) link_ALPHA1-2 : angle 1.97662 ( 18) link_ALPHA1-3 : bond 0.01000 ( 9) link_ALPHA1-3 : angle 1.68864 ( 27) link_ALPHA1-6 : bond 0.00898 ( 12) link_ALPHA1-6 : angle 1.83472 ( 36) link_BETA1-4 : bond 0.00464 ( 68) link_BETA1-4 : angle 1.78408 ( 204) link_NAG-ASN : bond 0.00309 ( 50) link_NAG-ASN : angle 1.83833 ( 150) *********************** 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 81 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8669 (tt) REVERT: G 70 MET cc_start: 0.8500 (mtt) cc_final: 0.7945 (mtt) REVERT: C 70 MET cc_start: 0.8844 (mtt) cc_final: 0.8158 (mtt) REVERT: I 259 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9052 (mp) REVERT: K 70 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.6539 (mmt) outliers start: 12 outliers final: 4 residues processed: 78 average time/residue: 0.1032 time to fit residues: 14.1182 Evaluate side-chains 73 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 114 GLN Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE 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 96 optimal weight: 0.3980 chunk 230 optimal weight: 30.0000 chunk 209 optimal weight: 0.8980 chunk 126 optimal weight: 0.0570 chunk 95 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 170 optimal weight: 8.9990 chunk 185 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 overall best weight: 1.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 187 ASN 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 = 0.3452 r_free = 0.3452 target = 0.055804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.040707 restraints weight = 102300.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.041443 restraints weight = 70750.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.041605 restraints weight = 54829.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.041787 restraints weight = 53387.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.041821 restraints weight = 50064.555| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21524 Z= 0.140 Angle : 0.587 7.087 29538 Z= 0.275 Chirality : 0.045 0.244 3690 Planarity : 0.003 0.035 3492 Dihedral : 10.046 67.115 5597 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.04 % Allowed : 12.21 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.17), residues: 2415 helix: 1.60 (0.29), residues: 375 sheet: -0.36 (0.19), residues: 708 loop : -0.98 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 585 TYR 0.013 0.001 TYR H 51 PHE 0.008 0.001 PHE E 317 TRP 0.014 0.001 TRP A 112 HIS 0.006 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00320 (21340) covalent geometry : angle 0.55181 (29025) SS BOND : bond 0.00223 ( 39) SS BOND : angle 0.65450 ( 78) hydrogen bonds : bond 0.03415 ( 668) hydrogen bonds : angle 4.91611 ( 1851) link_ALPHA1-2 : bond 0.00308 ( 6) link_ALPHA1-2 : angle 1.96810 ( 18) link_ALPHA1-3 : bond 0.00874 ( 9) link_ALPHA1-3 : angle 1.72008 ( 27) link_ALPHA1-6 : bond 0.00899 ( 12) link_ALPHA1-6 : angle 1.70273 ( 36) link_BETA1-4 : bond 0.00471 ( 68) link_BETA1-4 : angle 1.66838 ( 204) link_NAG-ASN : bond 0.00286 ( 50) link_NAG-ASN : angle 1.79031 ( 150) *********************** 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 89 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8753 (tt) REVERT: E 152 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8648 (mtm) REVERT: A 125 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8710 (tt) REVERT: C 70 MET cc_start: 0.8800 (mtt) cc_final: 0.8139 (mtt) REVERT: I 259 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9062 (mp) REVERT: J 530 MET cc_start: 0.7385 (mtt) cc_final: 0.7125 (mtt) REVERT: K 70 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7333 (mmm) outliers start: 22 outliers final: 6 residues processed: 83 average time/residue: 0.0994 time to fit residues: 14.6407 Evaluate side-chains 76 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 114 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain B residue 641 ILE 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 52 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 231 optimal weight: 30.0000 chunk 157 optimal weight: 30.0000 chunk 65 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 193 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 258 GLN A 105 HIS B 650 GLN B 653 GLN I 187 ASN L 16 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.055296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.040205 restraints weight = 104502.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.040582 restraints weight = 78140.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.040726 restraints weight = 62707.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.040940 restraints weight = 60789.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.040980 restraints weight = 57987.162| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 21524 Z= 0.273 Angle : 0.697 7.002 29538 Z= 0.330 Chirality : 0.048 0.247 3690 Planarity : 0.004 0.036 3492 Dihedral : 10.148 68.899 5597 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.37 % Allowed : 13.11 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.17), residues: 2415 helix: 1.31 (0.29), residues: 375 sheet: -0.44 (0.20), residues: 708 loop : -1.15 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 585 TYR 0.015 0.002 TYR E 223 PHE 0.013 0.002 PHE I 53 TRP 0.014 0.002 TRP I 69 HIS 0.009 0.002 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00641 (21340) covalent geometry : angle 0.66268 (29025) SS BOND : bond 0.00307 ( 39) SS BOND : angle 0.95494 ( 78) hydrogen bonds : bond 0.04177 ( 668) hydrogen bonds : angle 5.26685 ( 1851) link_ALPHA1-2 : bond 0.00429 ( 6) link_ALPHA1-2 : angle 2.09824 ( 18) link_ALPHA1-3 : bond 0.00664 ( 9) link_ALPHA1-3 : angle 1.85665 ( 27) link_ALPHA1-6 : bond 0.00785 ( 12) link_ALPHA1-6 : angle 1.58683 ( 36) link_BETA1-4 : bond 0.00503 ( 68) link_BETA1-4 : angle 1.76697 ( 204) link_NAG-ASN : bond 0.00425 ( 50) link_NAG-ASN : angle 2.08038 ( 150) *********************** 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 90 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.8863 (tt) REVERT: G 70 MET cc_start: 0.8738 (mtt) cc_final: 0.7727 (mtt) REVERT: A 125 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8772 (tt) REVERT: C 70 MET cc_start: 0.8896 (mtt) cc_final: 0.8199 (mtt) REVERT: I 259 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9126 (mp) REVERT: K 70 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.6808 (mmm) outliers start: 29 outliers final: 13 residues processed: 83 average time/residue: 0.0915 time to fit residues: 13.6272 Evaluate side-chains 79 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 495 VAL Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain A residue 44 VAL 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 641 ILE Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 259 LEU 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 24 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 chunk 236 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 189 optimal weight: 0.7980 chunk 205 optimal weight: 0.0470 chunk 8 optimal weight: 4.9990 overall best weight: 1.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 187 ASN B 653 GLN I 66 HIS I 187 ASN I 374 HIS L 16 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.055715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.040889 restraints weight = 103953.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.041256 restraints weight = 75940.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.041460 restraints weight = 60323.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.041615 restraints weight = 57199.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.041697 restraints weight = 54077.320| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21524 Z= 0.134 Angle : 0.584 7.842 29538 Z= 0.275 Chirality : 0.044 0.263 3690 Planarity : 0.003 0.038 3492 Dihedral : 9.468 64.628 5597 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.13 % Allowed : 13.81 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.17), residues: 2415 helix: 1.62 (0.29), residues: 375 sheet: -0.38 (0.19), residues: 708 loop : -0.99 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 585 TYR 0.014 0.001 TYR H 51 PHE 0.008 0.001 PHE E 317 TRP 0.018 0.001 TRP A 112 HIS 0.007 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00305 (21340) covalent geometry : angle 0.55222 (29025) SS BOND : bond 0.00230 ( 39) SS BOND : angle 0.62384 ( 78) hydrogen bonds : bond 0.03433 ( 668) hydrogen bonds : angle 4.93596 ( 1851) link_ALPHA1-2 : bond 0.00305 ( 6) link_ALPHA1-2 : angle 1.93636 ( 18) link_ALPHA1-3 : bond 0.00902 ( 9) link_ALPHA1-3 : angle 1.56505 ( 27) link_ALPHA1-6 : bond 0.00933 ( 12) link_ALPHA1-6 : angle 1.47911 ( 36) link_BETA1-4 : bond 0.00463 ( 68) link_BETA1-4 : angle 1.58445 ( 204) link_NAG-ASN : bond 0.00267 ( 50) link_NAG-ASN : angle 1.77386 ( 150) *********************** 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 89 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8769 (tt) REVERT: G 70 MET cc_start: 0.8735 (mtt) cc_final: 0.7739 (mtt) REVERT: C 70 MET cc_start: 0.8869 (mtt) cc_final: 0.8237 (mtt) REVERT: I 44 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8209 (t) REVERT: I 259 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9095 (mp) REVERT: K 70 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.6939 (mmm) outliers start: 24 outliers final: 15 residues processed: 84 average time/residue: 0.0998 time to fit residues: 14.6454 Evaluate side-chains 83 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 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 114 GLN 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 185 THR Chi-restraints excluded: chain I residue 203 GLN 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 42 optimal weight: 0.9980 chunk 223 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 220 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.055981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.040578 restraints weight = 102636.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.041627 restraints weight = 71160.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.041840 restraints weight = 53937.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.041960 restraints weight = 54521.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.041990 restraints weight = 50433.446| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 : 0.003 0.024 21524 Z= 0.115 Angle : 0.568 7.757 29538 Z= 0.266 Chirality : 0.044 0.246 3690 Planarity : 0.003 0.037 3492 Dihedral : 9.159 61.859 5597 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.08 % Allowed : 14.00 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.18), residues: 2415 helix: 1.74 (0.29), residues: 375 sheet: -0.31 (0.19), residues: 708 loop : -0.88 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 585 TYR 0.014 0.001 TYR H 51 PHE 0.014 0.001 PHE I 383 TRP 0.015 0.001 TRP A 112 HIS 0.015 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00255 (21340) covalent geometry : angle 0.53688 (29025) SS BOND : bond 0.00218 ( 39) SS BOND : angle 0.57325 ( 78) hydrogen bonds : bond 0.03290 ( 668) hydrogen bonds : angle 4.81531 ( 1851) link_ALPHA1-2 : bond 0.00289 ( 6) link_ALPHA1-2 : angle 1.94772 ( 18) link_ALPHA1-3 : bond 0.00901 ( 9) link_ALPHA1-3 : angle 1.55548 ( 27) link_ALPHA1-6 : bond 0.00981 ( 12) link_ALPHA1-6 : angle 1.42862 ( 36) link_BETA1-4 : bond 0.00472 ( 68) link_BETA1-4 : angle 1.54537 ( 204) link_NAG-ASN : bond 0.00261 ( 50) link_NAG-ASN : angle 1.69033 ( 150) *********************** 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 87 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8719 (tt) REVERT: G 70 MET cc_start: 0.8679 (mtt) cc_final: 0.7710 (mtt) REVERT: C 70 MET cc_start: 0.8807 (mtt) cc_final: 0.8179 (mtt) REVERT: I 44 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8178 (t) REVERT: I 259 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9076 (mp) REVERT: K 70 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.6893 (mmm) outliers start: 23 outliers final: 16 residues processed: 83 average time/residue: 0.0969 time to fit residues: 14.1563 Evaluate side-chains 83 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 E residue 495 VAL Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 148 THR 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 185 THR Chi-restraints excluded: chain I residue 203 GLN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 208 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 182 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 237 optimal weight: 30.0000 chunk 111 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 201 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.055963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.041171 restraints weight = 103532.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.041462 restraints weight = 74186.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.041671 restraints weight = 60361.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.041823 restraints weight = 57164.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.041902 restraints weight = 54050.617| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21524 Z= 0.131 Angle : 0.573 7.565 29538 Z= 0.268 Chirality : 0.044 0.237 3690 Planarity : 0.003 0.037 3492 Dihedral : 9.010 60.441 5597 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.13 % Allowed : 14.14 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.18), residues: 2415 helix: 1.81 (0.29), residues: 375 sheet: -0.28 (0.19), residues: 708 loop : -0.85 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 585 TYR 0.013 0.001 TYR H 51 PHE 0.012 0.001 PHE I 383 TRP 0.014 0.001 TRP A 112 HIS 0.008 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00297 (21340) covalent geometry : angle 0.54335 (29025) SS BOND : bond 0.00221 ( 39) SS BOND : angle 0.60112 ( 78) hydrogen bonds : bond 0.03290 ( 668) hydrogen bonds : angle 4.78664 ( 1851) link_ALPHA1-2 : bond 0.00293 ( 6) link_ALPHA1-2 : angle 1.94928 ( 18) link_ALPHA1-3 : bond 0.00868 ( 9) link_ALPHA1-3 : angle 1.56552 ( 27) link_ALPHA1-6 : bond 0.00965 ( 12) link_ALPHA1-6 : angle 1.40338 ( 36) link_BETA1-4 : bond 0.00464 ( 68) link_BETA1-4 : angle 1.53796 ( 204) link_NAG-ASN : bond 0.00263 ( 50) link_NAG-ASN : angle 1.67459 ( 150) *********************** 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 89 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8697 (tt) REVERT: G 70 MET cc_start: 0.8709 (mtt) cc_final: 0.7749 (mtt) REVERT: C 70 MET cc_start: 0.8859 (mtt) cc_final: 0.8255 (mtt) REVERT: I 44 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8188 (t) REVERT: I 259 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9141 (mt) REVERT: K 70 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7014 (mmm) outliers start: 24 outliers final: 17 residues processed: 85 average time/residue: 0.0956 time to fit residues: 14.6101 Evaluate side-chains 84 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 E residue 495 VAL Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 148 THR 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 641 ILE Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 203 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 161 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 184 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 chunk 3 optimal weight: 0.0870 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 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 = 0.3446 r_free = 0.3446 target = 0.055523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.040330 restraints weight = 104774.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.040833 restraints weight = 78548.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.041020 restraints weight = 62603.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.041607 restraints weight = 60738.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.041551 restraints weight = 56450.203| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1785 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 : 0.667 7.476 29538 Z= 0.316 Chirality : 0.046 0.245 3690 Planarity : 0.004 0.037 3492 Dihedral : 9.295 63.055 5597 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.99 % Allowed : 14.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.18), residues: 2415 helix: 1.49 (0.29), residues: 375 sheet: -0.38 (0.19), residues: 714 loop : -0.99 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 585 TYR 0.014 0.002 TYR H 51 PHE 0.014 0.002 PHE I 383 TRP 0.013 0.002 TRP E 96 HIS 0.020 0.002 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00585 (21340) covalent geometry : angle 0.63606 (29025) SS BOND : bond 0.00315 ( 39) SS BOND : angle 0.90500 ( 78) hydrogen bonds : bond 0.03947 ( 668) hydrogen bonds : angle 5.07045 ( 1851) link_ALPHA1-2 : bond 0.00344 ( 6) link_ALPHA1-2 : angle 2.05674 ( 18) link_ALPHA1-3 : bond 0.00693 ( 9) link_ALPHA1-3 : angle 1.74071 ( 27) link_ALPHA1-6 : bond 0.00866 ( 12) link_ALPHA1-6 : angle 1.37553 ( 36) link_BETA1-4 : bond 0.00495 ( 68) link_BETA1-4 : angle 1.65138 ( 204) link_NAG-ASN : bond 0.00393 ( 50) link_NAG-ASN : angle 1.89291 ( 150) ********************** 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 83 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8803 (tt) REVERT: G 70 MET cc_start: 0.8772 (mtt) cc_final: 0.7847 (mtt) REVERT: C 70 MET cc_start: 0.8881 (mtt) cc_final: 0.8237 (mtt) REVERT: I 259 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9110 (mp) REVERT: I 433 MET cc_start: 0.8726 (ttm) cc_final: 0.8476 (ttm) REVERT: J 530 MET cc_start: 0.7492 (mtt) cc_final: 0.7271 (mtt) REVERT: K 70 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7285 (mmm) outliers start: 21 outliers final: 17 residues processed: 80 average time/residue: 0.1057 time to fit residues: 14.7746 Evaluate side-chains 82 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 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 114 GLN 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 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 180 VAL Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 487 VAL Chi-restraints excluded: chain K residue 70 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 162 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 94 optimal weight: 0.3980 chunk 82 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.055408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.040322 restraints weight = 103681.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.041001 restraints weight = 72958.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.041066 restraints weight = 57830.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.041231 restraints weight = 56460.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.041299 restraints weight = 53808.868| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21524 Z= 0.169 Angle : 0.609 7.271 29538 Z= 0.287 Chirality : 0.045 0.249 3690 Planarity : 0.003 0.037 3492 Dihedral : 9.074 61.248 5597 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.04 % Allowed : 14.71 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.18), residues: 2415 helix: 1.57 (0.29), residues: 378 sheet: -0.39 (0.19), residues: 720 loop : -0.93 (0.18), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 585 TYR 0.013 0.001 TYR L 51 PHE 0.009 0.001 PHE I 383 TRP 0.015 0.001 TRP A 112 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00389 (21340) covalent geometry : angle 0.57839 (29025) SS BOND : bond 0.00258 ( 39) SS BOND : angle 0.71168 ( 78) hydrogen bonds : bond 0.03622 ( 668) hydrogen bonds : angle 4.95412 ( 1851) link_ALPHA1-2 : bond 0.00309 ( 6) link_ALPHA1-2 : angle 2.00566 ( 18) link_ALPHA1-3 : bond 0.00818 ( 9) link_ALPHA1-3 : angle 1.56315 ( 27) link_ALPHA1-6 : bond 0.00914 ( 12) link_ALPHA1-6 : angle 1.38642 ( 36) link_BETA1-4 : bond 0.00465 ( 68) link_BETA1-4 : angle 1.58566 ( 204) link_NAG-ASN : bond 0.00300 ( 50) link_NAG-ASN : angle 1.79317 ( 150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2289.34 seconds wall clock time: 40 minutes 56.47 seconds (2456.47 seconds total)