Starting phenix.real_space_refine on Thu Mar 5 06:48:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lx3_23565/03_2026/7lx3_23565.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lx3_23565/03_2026/7lx3_23565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lx3_23565/03_2026/7lx3_23565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lx3_23565/03_2026/7lx3_23565.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lx3_23565/03_2026/7lx3_23565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lx3_23565/03_2026/7lx3_23565.map" } resolution = 3.45 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= 0.004 sd= 0.144 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 111 5.16 5 C 12645 2.51 5 N 3279 2.21 5 O 4161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20196 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4232 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 24, 'TRANS': 509} Chain breaks: 7 Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "H" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "B" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4232 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 24, 'TRANS': 509} Chain breaks: 7 Chain: "M" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "N" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "C" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4232 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 24, 'TRANS': 509} Chain breaks: 7 Chain: "O" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "P" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: "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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" 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 Chain: "B" 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 Chain: "C" 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: 5.26, per 1000 atoms: 0.26 Number of scatterers: 20196 At special positions: 0 Unit cell: (144.2, 153.47, 152.44, 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 111 16.00 O 4161 8.00 N 3279 7.00 C 12645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.14 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.10 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.15 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.09 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.02 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.18 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.05 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.15 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.09 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.18 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.05 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " 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 T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " " MAN W 4 " - " MAN W 5 " " MAN h 4 " - " MAN h 5 " " MAN h 5 " - " MAN h 6 " " MAN k 4 " - " MAN k 5 " " MAN v 4 " - " MAN v 5 " " MAN v 5 " - " MAN v 6 " " MAN y 4 " - " MAN y 5 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 8 " " BMA W 3 " - " MAN W 4 " " BMA c 3 " - " MAN c 4 " " MAN c 4 " - " MAN c 5 " " BMA h 3 " - " MAN h 4 " " MAN h 7 " - " MAN h 8 " " BMA k 3 " - " MAN k 4 " " BMA q 3 " - " MAN q 4 " " MAN q 4 " - " MAN q 5 " " BMA v 3 " - " MAN v 4 " " MAN v 7 " - " MAN v 8 " " BMA y 3 " - " MAN y 4 " ALPHA1-6 " BMA J 3 " - " MAN J 6 " " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 9 " " BMA W 3 " - " MAN W 6 " " BMA c 3 " - " MAN c 6 " " BMA h 3 " - " MAN h 7 " " MAN h 7 " - " MAN h 9 " " BMA k 3 " - " MAN k 6 " " BMA q 3 " - " MAN q 6 " " BMA v 3 " - " MAN v 7 " " MAN v 7 " - " MAN v 9 " " BMA y 3 " - " MAN y 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " NAG-ASN " NAG A 701 " - " ASN A 160 " " NAG A 702 " - " ASN A 190 " " NAG A 703 " - " ASN A 289 " " NAG A 704 " - " ASN A 339 " " NAG A 705 " - " ASN A 611 " " NAG B 701 " - " ASN B 160 " " NAG B 702 " - " ASN B 190 " " NAG B 703 " - " ASN B 289 " " NAG B 704 " - " ASN B 339 " " NAG B 705 " - " ASN B 611 " " NAG C 701 " - " ASN C 160 " " NAG C 702 " - " ASN C 190 " " NAG C 703 " - " ASN C 289 " " NAG C 704 " - " ASN C 339 " " NAG C 705 " - " ASN C 611 " " NAG D 1 " - " ASN A 88 " " NAG E 1 " - " ASN A 130 " " NAG F 1 " - " ASN A 197 " " NAG G 1 " - " ASN A 276 " " NAG I 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 262 " " NAG K 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 392 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 295 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 234 " " NAG V 1 " - " ASN A 241 " " NAG W 1 " - " ASN A 138 " " NAG X 1 " - " ASN B 88 " " NAG Y 1 " - " ASN B 130 " " NAG Z 1 " - " ASN B 197 " " NAG a 1 " - " ASN B 276 " " NAG b 1 " - " ASN B 301 " " NAG c 1 " - " ASN B 262 " " NAG d 1 " - " ASN B 386 " " NAG e 1 " - " ASN B 392 " " NAG f 1 " - " ASN B 448 " " NAG g 1 " - " ASN B 295 " " NAG h 1 " - " ASN B 332 " " NAG i 1 " - " ASN B 234 " " NAG j 1 " - " ASN B 241 " " NAG k 1 " - " ASN B 138 " " NAG l 1 " - " ASN C 88 " " NAG m 1 " - " ASN C 130 " " NAG n 1 " - " ASN C 197 " " NAG o 1 " - " ASN C 276 " " NAG p 1 " - " ASN C 301 " " NAG q 1 " - " ASN C 262 " " NAG r 1 " - " ASN C 386 " " NAG s 1 " - " ASN C 392 " " NAG t 1 " - " ASN C 448 " " NAG u 1 " - " ASN C 295 " " NAG v 1 " - " ASN C 332 " " NAG w 1 " - " ASN C 234 " " NAG x 1 " - " ASN C 241 " " NAG y 1 " - " ASN C 138 " Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 976.5 milliseconds 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4314 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 45 sheets defined 20.8% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.292A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.993A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.803A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 528 removed outlier: 4.305A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 546 removed outlier: 3.806A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 597 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 650 removed outlier: 4.259A pdb=" N SER A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100D through 100H Processing helix chain 'B' and resid 98 through 116 removed outlier: 4.288A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.997A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.807A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.453A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.783A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 597 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 650 removed outlier: 4.199A pdb=" N SER B 644 " --> pdb=" O ASP B 640 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 100D through 100H Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.295A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.008A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.828A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 528 removed outlier: 4.444A pdb=" N GLY C 527 " --> pdb=" O GLY C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 546 removed outlier: 3.801A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C 544 " --> pdb=" O GLN C 540 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 597 Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 650 removed outlier: 4.255A pdb=" N SER C 644 " --> pdb=" O ASP C 640 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 52 through 56 removed outlier: 4.103A pdb=" N GLY P 55 " --> pdb=" O HIS P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 100D through 100H Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.672A pdb=" N VAL A 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.909A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 132 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.659A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.621A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.007A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.931A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.749A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 315 through 323 removed outlier: 6.572A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 393 through 395 Processing sheet with id=AB2, first strand: chain 'L' and resid 8 through 13 removed outlier: 6.400A pdb=" N THR L 8 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE L 105 " --> pdb=" O THR L 8 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL L 11 " --> pdb=" O ILE L 105 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.821A pdb=" N TYR H 33 " --> pdb=" O THR H 95 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB7, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.307A pdb=" N VAL B 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL B 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR B 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N TYR B 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N CYS B 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.047A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AC3, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AC4, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.665A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.617A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY B 451 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N GLU B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 11.888A pdb=" N LEU B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 11.998A pdb=" N LEU B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 10.935A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 315 through 323 removed outlier: 6.568A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE B 322 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASN B 301 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLU B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER B 334 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 393 through 395 Processing sheet with id=AC8, first strand: chain 'M' and resid 8 through 13 removed outlier: 6.399A pdb=" N THR M 8 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE M 105 " --> pdb=" O THR M 8 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL M 11 " --> pdb=" O ILE M 105 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLU M 100 " --> pdb=" O CYS M 88 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N CYS M 88 " --> pdb=" O GLU M 100 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP M 35 " --> pdb=" O ILE M 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 19 through 23 Processing sheet with id=AD1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.820A pdb=" N TYR N 33 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AD4, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.641A pdb=" N VAL C 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.047A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AD9, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AE1, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.687A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.611A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.917A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 12.060A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.796A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 315 through 323 removed outlier: 6.572A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 393 through 395 Processing sheet with id=AE5, first strand: chain 'O' and resid 8 through 13 removed outlier: 6.388A pdb=" N THR O 8 " --> pdb=" O THR O 103 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE O 105 " --> pdb=" O THR O 8 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL O 11 " --> pdb=" O ILE O 105 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP O 35 " --> pdb=" O ILE O 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 19 through 23 Processing sheet with id=AE7, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'P' and resid 11 through 12 removed outlier: 3.782A pdb=" N TYR P 33 " --> pdb=" O THR P 95 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY P 49 " --> pdb=" O TRP P 36 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 11 through 12 732 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 5563 1.33 - 1.48: 6744 1.48 - 1.63: 8159 1.63 - 1.78: 58 1.78 - 1.93: 83 Bond restraints: 20607 Sorted by residual: bond pdb=" CB CYS C 247 " pdb=" SG CYS C 247 " ideal model delta sigma weight residual 1.808 1.587 0.221 3.30e-02 9.18e+02 4.49e+01 bond pdb=" CB CYS B 247 " pdb=" SG CYS B 247 " ideal model delta sigma weight residual 1.808 1.588 0.220 3.30e-02 9.18e+02 4.45e+01 bond pdb=" CB HIS L 89 " pdb=" CG HIS L 89 " ideal model delta sigma weight residual 1.497 1.411 0.086 1.40e-02 5.10e+03 3.75e+01 bond pdb=" NE1 TRP C 427 " pdb=" CE2 TRP C 427 " ideal model delta sigma weight residual 1.370 1.305 0.065 1.10e-02 8.26e+03 3.49e+01 bond pdb=" CB CYS M 88 " pdb=" SG CYS M 88 " ideal model delta sigma weight residual 1.808 1.614 0.194 3.30e-02 9.18e+02 3.44e+01 ... (remaining 20602 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 23443 2.28 - 4.57: 3949 4.57 - 6.85: 532 6.85 - 9.14: 71 9.14 - 11.42: 16 Bond angle restraints: 28011 Sorted by residual: angle pdb=" C VAL A 75 " pdb=" N PRO A 76 " pdb=" CA PRO A 76 " ideal model delta sigma weight residual 120.03 128.16 -8.13 9.90e-01 1.02e+00 6.74e+01 angle pdb=" C VAL C 75 " pdb=" N PRO C 76 " pdb=" CA PRO C 76 " ideal model delta sigma weight residual 120.03 128.04 -8.01 9.90e-01 1.02e+00 6.55e+01 angle pdb=" C VAL B 75 " pdb=" N PRO B 76 " pdb=" CA PRO B 76 " ideal model delta sigma weight residual 120.03 128.00 -7.97 9.90e-01 1.02e+00 6.49e+01 angle pdb=" C ALA C 219 " pdb=" N PRO C 220 " pdb=" CA PRO C 220 " ideal model delta sigma weight residual 120.52 127.81 -7.29 9.90e-01 1.02e+00 5.42e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.87 127.52 -7.65 1.04e+00 9.25e-01 5.41e+01 ... (remaining 28006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.19: 13633 22.19 - 44.37: 320 44.37 - 66.56: 109 66.56 - 88.74: 48 88.74 - 110.93: 38 Dihedral angle restraints: 14148 sinusoidal: 7464 harmonic: 6684 Sorted by residual: dihedral pdb=" CB CYS C 218 " pdb=" SG CYS C 218 " pdb=" SG CYS C 247 " pdb=" CB CYS C 247 " ideal model delta sinusoidal sigma weight residual 93.00 43.89 49.11 1 1.00e+01 1.00e-02 3.32e+01 dihedral pdb=" CB CYS B 218 " pdb=" SG CYS B 218 " pdb=" SG CYS B 247 " pdb=" CB CYS B 247 " ideal model delta sinusoidal sigma weight residual 93.00 43.92 49.08 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -132.14 46.14 1 1.00e+01 1.00e-02 2.95e+01 ... (remaining 14145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2524 0.108 - 0.217: 900 0.217 - 0.325: 133 0.325 - 0.433: 20 0.433 - 0.542: 2 Chirality restraints: 3579 Sorted by residual: chirality pdb=" C1 BMA v 3 " pdb=" O4 NAG v 2 " pdb=" C2 BMA v 3 " pdb=" O5 BMA v 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.96e+01 chirality pdb=" C1 BMA y 3 " pdb=" O4 NAG y 2 " pdb=" C2 BMA y 3 " pdb=" O5 BMA y 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.00e+01 ... (remaining 3576 not shown) Planarity restraints: 3393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 190 " 0.111 2.00e-02 2.50e+03 1.13e-01 1.61e+02 pdb=" CG ASN C 190 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN C 190 " -0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN C 190 " -0.175 2.00e-02 2.50e+03 pdb=" C1 NAG C 702 " 0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 190 " -0.107 2.00e-02 2.50e+03 1.09e-01 1.47e+02 pdb=" CG ASN A 190 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 190 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN A 190 " 0.167 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 190 " 0.106 2.00e-02 2.50e+03 1.08e-01 1.47e+02 pdb=" CG ASN B 190 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN B 190 " -0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN B 190 " -0.167 2.00e-02 2.50e+03 pdb=" C1 NAG B 702 " 0.130 2.00e-02 2.50e+03 ... (remaining 3390 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3190 2.74 - 3.28: 17887 3.28 - 3.82: 33184 3.82 - 4.36: 39825 4.36 - 4.90: 65381 Nonbonded interactions: 159467 Sorted by model distance: nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.198 3.040 nonbonded pdb=" O4 NAG C 704 " pdb=" O6 NAG C 704 " model vdw 2.248 3.040 nonbonded pdb=" O4 MAN T 9 " pdb=" O6 MAN T 9 " model vdw 2.265 3.040 nonbonded pdb=" O4 MAN h 9 " pdb=" O6 MAN h 9 " model vdw 2.269 3.040 nonbonded pdb=" O4 MAN v 9 " pdb=" O6 MAN v 9 " model vdw 2.299 3.040 ... (remaining 159462 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'w' selection = chain 'x' } ncs_group { reference = chain 'H' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'J' selection = chain 'W' selection = chain 'c' selection = chain 'k' selection = chain 'q' selection = chain 'y' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'T' selection = chain 'h' selection = chain 'v' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.740 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.100 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:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 : 0.021 0.221 20790 Z= 1.137 Angle : 1.777 11.918 28521 Z= 1.107 Chirality : 0.106 0.542 3579 Planarity : 0.009 0.047 3336 Dihedral : 12.953 110.925 9717 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.10 % Allowed : 0.34 % Favored : 99.56 % Cbeta Deviations : 0.28 % 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 are not related in a simple way. whole: 1.02 (0.17), residues: 2262 helix: -0.38 (0.25), residues: 354 sheet: 1.02 (0.19), residues: 684 loop : 1.01 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 31 TYR 0.050 0.007 TYR N 100O PHE 0.039 0.007 PHE L 67C TRP 0.039 0.009 TRP B 96 HIS 0.006 0.002 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.02074 (20607) covalent geometry : angle 1.73957 (28011) SS BOND : bond 0.04964 ( 39) SS BOND : angle 4.30291 ( 78) hydrogen bonds : bond 0.15800 ( 717) hydrogen bonds : angle 7.66935 ( 1866) link_ALPHA1-2 : bond 0.05633 ( 9) link_ALPHA1-2 : angle 2.83963 ( 27) link_ALPHA1-3 : bond 0.05726 ( 15) link_ALPHA1-3 : angle 2.77040 ( 45) link_ALPHA1-6 : bond 0.05708 ( 12) link_ALPHA1-6 : angle 2.74677 ( 36) link_BETA1-4 : bond 0.05424 ( 51) link_BETA1-4 : angle 3.77597 ( 153) link_NAG-ASN : bond 0.07843 ( 57) link_NAG-ASN : angle 2.19655 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 391 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 HIS cc_start: 0.6698 (t70) cc_final: 0.6400 (t-90) REVERT: H 91 TYR cc_start: 0.7703 (m-80) cc_final: 0.7449 (m-80) REVERT: B 180 ASP cc_start: 0.6989 (m-30) cc_final: 0.6787 (m-30) REVERT: M 49 TYR cc_start: 0.8053 (p90) cc_final: 0.7739 (p90) REVERT: M 104 LEU cc_start: 0.7808 (tp) cc_final: 0.7415 (tp) REVERT: N 24 VAL cc_start: 0.7996 (t) cc_final: 0.7698 (t) REVERT: N 91 TYR cc_start: 0.7558 (m-80) cc_final: 0.6873 (m-80) REVERT: N 92 CYS cc_start: 0.6264 (t) cc_final: 0.6014 (t) REVERT: C 180 ASP cc_start: 0.6995 (m-30) cc_final: 0.6787 (m-30) REVERT: O 37 GLN cc_start: 0.7963 (tt0) cc_final: 0.7717 (tt0) REVERT: O 49 TYR cc_start: 0.8086 (p90) cc_final: 0.7665 (p90) REVERT: O 52 ASN cc_start: 0.8730 (t0) cc_final: 0.8465 (t0) REVERT: O 78 VAL cc_start: 0.8416 (t) cc_final: 0.8176 (p) REVERT: O 79 GLU cc_start: 0.8091 (pt0) cc_final: 0.7827 (pm20) REVERT: P 91 TYR cc_start: 0.7735 (m-80) cc_final: 0.7470 (m-80) outliers start: 2 outliers final: 2 residues processed: 393 average time/residue: 0.1777 time to fit residues: 100.5940 Evaluate side-chains 194 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 192 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain C residue 138 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 543 ASN B 105 HIS B 543 ASN N 32 ASN C 105 HIS C 478 ASN P 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.109434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.078701 restraints weight = 40931.343| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.60 r_work: 0.2963 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20790 Z= 0.174 Angle : 0.739 9.411 28521 Z= 0.364 Chirality : 0.048 0.238 3579 Planarity : 0.005 0.059 3336 Dihedral : 10.731 86.374 5416 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.06 % Favored : 98.85 % Rotamer: Outliers : 2.29 % Allowed : 6.24 % Favored : 91.47 % 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 are not related in a simple way. whole: 0.93 (0.17), residues: 2262 helix: 0.82 (0.26), residues: 363 sheet: 0.77 (0.18), residues: 690 loop : 0.62 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 61 TYR 0.024 0.002 TYR H 33 PHE 0.019 0.002 PHE A 383 TRP 0.026 0.002 TRP P 36 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00394 (20607) covalent geometry : angle 0.68877 (28011) SS BOND : bond 0.00449 ( 39) SS BOND : angle 1.90496 ( 78) hydrogen bonds : bond 0.04806 ( 717) hydrogen bonds : angle 6.11702 ( 1866) link_ALPHA1-2 : bond 0.00495 ( 9) link_ALPHA1-2 : angle 1.75285 ( 27) link_ALPHA1-3 : bond 0.01011 ( 15) link_ALPHA1-3 : angle 1.64340 ( 45) link_ALPHA1-6 : bond 0.00725 ( 12) link_ALPHA1-6 : angle 1.62009 ( 36) link_BETA1-4 : bond 0.00773 ( 51) link_BETA1-4 : angle 2.63729 ( 153) link_NAG-ASN : bond 0.00304 ( 57) link_NAG-ASN : angle 1.93087 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 257 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLN cc_start: 0.7310 (mm-40) cc_final: 0.6202 (mt0) REVERT: L 25 GLU cc_start: 0.7890 (tt0) cc_final: 0.7448 (tt0) REVERT: L 79 GLU cc_start: 0.7521 (pm20) cc_final: 0.7234 (pm20) REVERT: L 87 TYR cc_start: 0.8350 (m-80) cc_final: 0.8015 (m-80) REVERT: L 95 ARG cc_start: 0.7991 (mtt-85) cc_final: 0.7733 (mtt-85) REVERT: H 5 GLN cc_start: 0.8645 (tm-30) cc_final: 0.7853 (mp10) REVERT: H 6 GLU cc_start: 0.6316 (mp0) cc_final: 0.4554 (mp0) REVERT: H 64 LYS cc_start: 0.7008 (ttpp) cc_final: 0.6798 (ttpp) REVERT: H 100 ASP cc_start: 0.8380 (t0) cc_final: 0.8140 (t0) REVERT: H 103 LYS cc_start: 0.7341 (mmmt) cc_final: 0.7057 (mmmt) REVERT: B 54 CYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6939 (p) REVERT: B 82 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7345 (pm20) REVERT: B 180 ASP cc_start: 0.8193 (m-30) cc_final: 0.7972 (m-30) REVERT: M 17 GLN cc_start: 0.7343 (mm-40) cc_final: 0.6149 (mt0) REVERT: M 49 TYR cc_start: 0.8167 (p90) cc_final: 0.7560 (p90) REVERT: N 5 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8773 (tm-30) REVERT: N 13 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8529 (ttpt) REVERT: N 81 ARG cc_start: 0.8389 (ttp80) cc_final: 0.7618 (ttm-80) REVERT: C 54 CYS cc_start: 0.6946 (OUTLIER) cc_final: 0.6443 (p) REVERT: C 69 TRP cc_start: 0.8203 (m-90) cc_final: 0.7060 (m-90) REVERT: C 82 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: C 180 ASP cc_start: 0.8332 (m-30) cc_final: 0.8097 (m-30) REVERT: O 17 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6252 (mt0) REVERT: O 36 TYR cc_start: 0.8622 (m-80) cc_final: 0.8197 (m-80) REVERT: O 49 TYR cc_start: 0.7891 (p90) cc_final: 0.7072 (p90) REVERT: O 87 TYR cc_start: 0.8264 (m-80) cc_final: 0.7941 (m-80) REVERT: P 5 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8614 (tm-30) REVERT: P 41 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8674 (mm) REVERT: P 81 ARG cc_start: 0.8166 (ttp80) cc_final: 0.7921 (ttp80) REVERT: P 91 TYR cc_start: 0.8137 (m-80) cc_final: 0.7730 (m-80) outliers start: 47 outliers final: 23 residues processed: 292 average time/residue: 0.1614 time to fit residues: 69.7553 Evaluate side-chains 236 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 18 LEU Chi-restraints excluded: chain P residue 41 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 211 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 206 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.108507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.078632 restraints weight = 40851.718| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.37 r_work: 0.2940 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 20790 Z= 0.196 Angle : 0.691 8.692 28521 Z= 0.336 Chirality : 0.047 0.241 3579 Planarity : 0.004 0.044 3336 Dihedral : 9.763 86.712 5412 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.78 % Allowed : 7.70 % Favored : 89.52 % 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 are not related in a simple way. whole: 0.66 (0.17), residues: 2262 helix: 1.13 (0.27), residues: 366 sheet: 0.61 (0.19), residues: 678 loop : 0.24 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 476 TYR 0.025 0.002 TYR N 33 PHE 0.019 0.002 PHE H 100K TRP 0.034 0.002 TRP H 36 HIS 0.007 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00466 (20607) covalent geometry : angle 0.64802 (28011) SS BOND : bond 0.00572 ( 39) SS BOND : angle 1.94995 ( 78) hydrogen bonds : bond 0.04183 ( 717) hydrogen bonds : angle 5.68947 ( 1866) link_ALPHA1-2 : bond 0.00492 ( 9) link_ALPHA1-2 : angle 1.79464 ( 27) link_ALPHA1-3 : bond 0.00796 ( 15) link_ALPHA1-3 : angle 1.67352 ( 45) link_ALPHA1-6 : bond 0.00621 ( 12) link_ALPHA1-6 : angle 1.74277 ( 36) link_BETA1-4 : bond 0.00644 ( 51) link_BETA1-4 : angle 2.32847 ( 153) link_NAG-ASN : bond 0.00268 ( 57) link_NAG-ASN : angle 1.56235 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 230 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLN cc_start: 0.7765 (mm-40) cc_final: 0.6638 (mt0) REVERT: L 26 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8445 (pm20) REVERT: H 5 GLN cc_start: 0.8596 (tm-30) cc_final: 0.7888 (mp10) REVERT: H 31 ASP cc_start: 0.8879 (t0) cc_final: 0.8527 (t0) REVERT: H 81 ARG cc_start: 0.8431 (ttp80) cc_final: 0.7929 (ttm-80) REVERT: B 135 ASN cc_start: 0.7420 (m-40) cc_final: 0.7215 (m-40) REVERT: B 180 ASP cc_start: 0.7635 (m-30) cc_final: 0.7434 (m-30) REVERT: M 49 TYR cc_start: 0.8276 (p90) cc_final: 0.7662 (p90) REVERT: N 81 ARG cc_start: 0.8283 (ttp80) cc_final: 0.7922 (ttp-110) REVERT: C 82 GLN cc_start: 0.7980 (pt0) cc_final: 0.7673 (pm20) REVERT: C 95 MET cc_start: 0.9263 (ptm) cc_final: 0.8759 (ttp) REVERT: O 36 TYR cc_start: 0.8471 (m-80) cc_final: 0.8153 (m-80) REVERT: O 49 TYR cc_start: 0.8063 (p90) cc_final: 0.7527 (p90) REVERT: O 87 TYR cc_start: 0.8691 (m-80) cc_final: 0.8482 (m-80) REVERT: P 41 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8765 (mm) REVERT: P 56 ASP cc_start: 0.5521 (t0) cc_final: 0.5137 (t70) REVERT: P 91 TYR cc_start: 0.8051 (m-80) cc_final: 0.7541 (m-80) outliers start: 57 outliers final: 28 residues processed: 271 average time/residue: 0.1672 time to fit residues: 67.4672 Evaluate side-chains 228 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 18 LEU Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 89 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 153 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 223 optimal weight: 40.0000 chunk 182 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 200 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.108115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.078462 restraints weight = 40807.256| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.34 r_work: 0.2934 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20790 Z= 0.174 Angle : 0.648 8.387 28521 Z= 0.313 Chirality : 0.046 0.199 3579 Planarity : 0.004 0.045 3336 Dihedral : 9.044 85.573 5412 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.92 % Allowed : 7.80 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.17), residues: 2262 helix: 1.59 (0.28), residues: 348 sheet: 0.52 (0.19), residues: 690 loop : 0.13 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 476 TYR 0.020 0.001 TYR N 33 PHE 0.016 0.002 PHE H 100K TRP 0.042 0.002 TRP N 36 HIS 0.011 0.001 HIS P 97 Details of bonding type rmsd covalent geometry : bond 0.00409 (20607) covalent geometry : angle 0.60583 (28011) SS BOND : bond 0.00456 ( 39) SS BOND : angle 1.55906 ( 78) hydrogen bonds : bond 0.03814 ( 717) hydrogen bonds : angle 5.53633 ( 1866) link_ALPHA1-2 : bond 0.00444 ( 9) link_ALPHA1-2 : angle 1.82651 ( 27) link_ALPHA1-3 : bond 0.00766 ( 15) link_ALPHA1-3 : angle 1.86059 ( 45) link_ALPHA1-6 : bond 0.00746 ( 12) link_ALPHA1-6 : angle 1.72031 ( 36) link_BETA1-4 : bond 0.00682 ( 51) link_BETA1-4 : angle 2.30580 ( 153) link_NAG-ASN : bond 0.00210 ( 57) link_NAG-ASN : angle 1.40223 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 213 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 17 GLN cc_start: 0.7966 (mm-40) cc_final: 0.6925 (pt0) REVERT: L 26 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8431 (pm20) REVERT: L 95 ARG cc_start: 0.8110 (mtt-85) cc_final: 0.7862 (mmt90) REVERT: H 5 GLN cc_start: 0.8611 (tm-30) cc_final: 0.7735 (mp10) REVERT: H 6 GLU cc_start: 0.6299 (mp0) cc_final: 0.6027 (mp0) REVERT: H 81 ARG cc_start: 0.8364 (ttp80) cc_final: 0.7924 (ttp-110) REVERT: M 13 VAL cc_start: 0.8813 (m) cc_final: 0.8557 (t) REVERT: M 17 GLN cc_start: 0.7749 (mm-40) cc_final: 0.6712 (mt0) REVERT: M 49 TYR cc_start: 0.8287 (p90) cc_final: 0.7736 (p90) REVERT: M 54 ARG cc_start: 0.8348 (ptp-170) cc_final: 0.8133 (ptp90) REVERT: N 6 GLU cc_start: 0.7070 (mp0) cc_final: 0.6108 (mp0) REVERT: N 81 ARG cc_start: 0.8333 (ttp80) cc_final: 0.8006 (ttp-110) REVERT: C 82 GLN cc_start: 0.8012 (pt0) cc_final: 0.7743 (pm20) REVERT: C 95 MET cc_start: 0.9331 (ptm) cc_final: 0.8865 (ttp) REVERT: C 626 MET cc_start: 0.7874 (mtp) cc_final: 0.7661 (ttm) REVERT: O 17 GLN cc_start: 0.7578 (mp10) cc_final: 0.6510 (mt0) REVERT: O 36 TYR cc_start: 0.8457 (m-80) cc_final: 0.8132 (m-80) REVERT: O 49 TYR cc_start: 0.8051 (p90) cc_final: 0.7524 (p90) REVERT: P 41 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8760 (mm) REVERT: P 56 ASP cc_start: 0.5498 (t0) cc_final: 0.5099 (t70) REVERT: P 81 ARG cc_start: 0.8245 (ttp80) cc_final: 0.7664 (ttm-80) REVERT: P 91 TYR cc_start: 0.7960 (m-80) cc_final: 0.7544 (m-80) outliers start: 60 outliers final: 37 residues processed: 252 average time/residue: 0.1640 time to fit residues: 61.5048 Evaluate side-chains 225 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 18 LEU Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 89 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 136 optimal weight: 0.0870 chunk 217 optimal weight: 40.0000 chunk 130 optimal weight: 30.0000 chunk 19 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN N 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.106715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.076214 restraints weight = 41324.559| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.92 r_work: 0.2905 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20790 Z= 0.145 Angle : 0.619 8.101 28521 Z= 0.298 Chirality : 0.045 0.186 3579 Planarity : 0.004 0.039 3336 Dihedral : 8.558 83.860 5412 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.88 % Allowed : 8.24 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 2262 helix: 1.76 (0.29), residues: 348 sheet: 0.51 (0.19), residues: 690 loop : 0.09 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 476 TYR 0.017 0.001 TYR H 33 PHE 0.016 0.002 PHE M 9 TRP 0.028 0.001 TRP H 36 HIS 0.012 0.001 HIS P 97 Details of bonding type rmsd covalent geometry : bond 0.00342 (20607) covalent geometry : angle 0.57729 (28011) SS BOND : bond 0.00425 ( 39) SS BOND : angle 1.65454 ( 78) hydrogen bonds : bond 0.03510 ( 717) hydrogen bonds : angle 5.36069 ( 1866) link_ALPHA1-2 : bond 0.00483 ( 9) link_ALPHA1-2 : angle 1.84208 ( 27) link_ALPHA1-3 : bond 0.00816 ( 15) link_ALPHA1-3 : angle 1.87117 ( 45) link_ALPHA1-6 : bond 0.00627 ( 12) link_ALPHA1-6 : angle 1.69726 ( 36) link_BETA1-4 : bond 0.00643 ( 51) link_BETA1-4 : angle 2.22788 ( 153) link_NAG-ASN : bond 0.00168 ( 57) link_NAG-ASN : angle 1.27626 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 213 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 THR cc_start: 0.9073 (m) cc_final: 0.8779 (t) REVERT: L 17 GLN cc_start: 0.8071 (mm-40) cc_final: 0.6971 (pt0) REVERT: L 26 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8737 (mp0) REVERT: L 95 ARG cc_start: 0.7998 (mtt-85) cc_final: 0.7715 (mmt90) REVERT: H 5 GLN cc_start: 0.8814 (tm-30) cc_final: 0.7730 (mp10) REVERT: H 6 GLU cc_start: 0.5939 (mp0) cc_final: 0.5535 (mp0) REVERT: H 81 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8061 (mtm110) REVERT: B 202 THR cc_start: 0.9130 (m) cc_final: 0.8853 (t) REVERT: B 475 MET cc_start: 0.8774 (mmm) cc_final: 0.8217 (mmp) REVERT: M 17 GLN cc_start: 0.7896 (mm-40) cc_final: 0.6697 (mt0) REVERT: M 25 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7498 (tm-30) REVERT: M 49 TYR cc_start: 0.8141 (p90) cc_final: 0.7560 (p90) REVERT: N 3 HIS cc_start: 0.7615 (t-90) cc_final: 0.7382 (t70) REVERT: N 5 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8009 (mp10) REVERT: N 6 GLU cc_start: 0.6282 (mp0) cc_final: 0.5812 (mp0) REVERT: N 81 ARG cc_start: 0.8413 (ttp80) cc_final: 0.8081 (ttp-110) REVERT: C 82 GLN cc_start: 0.8278 (pt0) cc_final: 0.7625 (pm20) REVERT: C 95 MET cc_start: 0.9336 (ptm) cc_final: 0.9118 (ttp) REVERT: C 626 MET cc_start: 0.8008 (mtp) cc_final: 0.7476 (ttm) REVERT: O 17 GLN cc_start: 0.8168 (mp10) cc_final: 0.7185 (pt0) REVERT: O 49 TYR cc_start: 0.7821 (p90) cc_final: 0.7394 (p90) REVERT: P 5 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8003 (mp10) REVERT: P 6 GLU cc_start: 0.7065 (mp0) cc_final: 0.6385 (mp0) REVERT: P 41 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8683 (mm) REVERT: P 81 ARG cc_start: 0.8398 (ttp80) cc_final: 0.7834 (ttm-80) REVERT: P 91 TYR cc_start: 0.8253 (m-80) cc_final: 0.7609 (m-80) outliers start: 59 outliers final: 33 residues processed: 250 average time/residue: 0.1673 time to fit residues: 61.9132 Evaluate side-chains 223 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 18 LEU Chi-restraints excluded: chain P residue 41 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 12 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 217 optimal weight: 40.0000 chunk 156 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 chunk 199 optimal weight: 8.9990 chunk 204 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 97 optimal weight: 0.4980 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.106777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.077085 restraints weight = 40303.001| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.46 r_work: 0.2924 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20790 Z= 0.127 Angle : 0.608 7.949 28521 Z= 0.292 Chirality : 0.045 0.177 3579 Planarity : 0.004 0.043 3336 Dihedral : 8.291 82.242 5412 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.44 % Allowed : 9.31 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.18), residues: 2262 helix: 1.88 (0.29), residues: 348 sheet: 0.60 (0.20), residues: 678 loop : 0.01 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 95 TYR 0.016 0.001 TYR P 33 PHE 0.012 0.001 PHE N 100K TRP 0.050 0.002 TRP N 36 HIS 0.012 0.001 HIS N 97 Details of bonding type rmsd covalent geometry : bond 0.00289 (20607) covalent geometry : angle 0.56923 (28011) SS BOND : bond 0.00415 ( 39) SS BOND : angle 1.47154 ( 78) hydrogen bonds : bond 0.03307 ( 717) hydrogen bonds : angle 5.20173 ( 1866) link_ALPHA1-2 : bond 0.00499 ( 9) link_ALPHA1-2 : angle 1.85200 ( 27) link_ALPHA1-3 : bond 0.00841 ( 15) link_ALPHA1-3 : angle 1.78821 ( 45) link_ALPHA1-6 : bond 0.00690 ( 12) link_ALPHA1-6 : angle 1.65900 ( 36) link_BETA1-4 : bond 0.00623 ( 51) link_BETA1-4 : angle 2.17943 ( 153) link_NAG-ASN : bond 0.00154 ( 57) link_NAG-ASN : angle 1.21545 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 204 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6806 (p) REVERT: A 202 THR cc_start: 0.9093 (m) cc_final: 0.8807 (t) REVERT: A 626 MET cc_start: 0.7971 (mtp) cc_final: 0.7429 (ttm) REVERT: L 17 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7046 (pt0) REVERT: L 26 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8710 (mp0) REVERT: L 83 GLU cc_start: 0.7503 (tp30) cc_final: 0.7206 (tp30) REVERT: L 95 ARG cc_start: 0.7991 (mtt-85) cc_final: 0.7697 (mmt90) REVERT: H 5 GLN cc_start: 0.8841 (tm-30) cc_final: 0.7882 (mp10) REVERT: H 6 GLU cc_start: 0.5963 (mp0) cc_final: 0.5737 (mp0) REVERT: H 81 ARG cc_start: 0.8447 (ttp80) cc_final: 0.8108 (mtm110) REVERT: B 202 THR cc_start: 0.9100 (m) cc_final: 0.8823 (t) REVERT: B 475 MET cc_start: 0.8654 (mmm) cc_final: 0.8223 (mmt) REVERT: B 626 MET cc_start: 0.8001 (mtp) cc_final: 0.7768 (ttm) REVERT: M 17 GLN cc_start: 0.8315 (mm-40) cc_final: 0.7158 (pt0) REVERT: N 3 HIS cc_start: 0.7651 (t-90) cc_final: 0.7418 (t70) REVERT: N 5 GLN cc_start: 0.8920 (tm-30) cc_final: 0.7784 (mp10) REVERT: N 81 ARG cc_start: 0.8389 (ttp80) cc_final: 0.8081 (ttp-110) REVERT: C 82 GLN cc_start: 0.8307 (pt0) cc_final: 0.7665 (pm20) REVERT: C 95 MET cc_start: 0.9350 (ptm) cc_final: 0.9095 (ttp) REVERT: C 202 THR cc_start: 0.9037 (m) cc_final: 0.8726 (t) REVERT: C 626 MET cc_start: 0.7879 (mtp) cc_final: 0.7278 (ttm) REVERT: O 17 GLN cc_start: 0.8158 (mp10) cc_final: 0.7291 (pt0) REVERT: O 49 TYR cc_start: 0.7830 (p90) cc_final: 0.7424 (p90) REVERT: O 60 ASP cc_start: 0.8372 (m-30) cc_final: 0.8138 (t0) REVERT: O 83 GLU cc_start: 0.7693 (tp30) cc_final: 0.7256 (tp30) REVERT: P 5 GLN cc_start: 0.8713 (tm-30) cc_final: 0.7773 (mp10) REVERT: P 6 GLU cc_start: 0.6855 (mp0) cc_final: 0.6546 (mp0) REVERT: P 41 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8711 (mm) REVERT: P 46 GLU cc_start: 0.8361 (tp30) cc_final: 0.8128 (tp30) REVERT: P 81 ARG cc_start: 0.8398 (ttp80) cc_final: 0.7929 (ttp-110) REVERT: P 91 TYR cc_start: 0.8089 (m-80) cc_final: 0.7592 (m-80) outliers start: 50 outliers final: 33 residues processed: 236 average time/residue: 0.1548 time to fit residues: 54.6739 Evaluate side-chains 228 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 41 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 76 optimal weight: 10.0000 chunk 131 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 180 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 213 optimal weight: 0.9990 chunk 121 optimal weight: 0.0270 chunk 101 optimal weight: 6.9990 chunk 204 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 109 GLN N 97 HIS O 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.108812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.078474 restraints weight = 40793.441| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.57 r_work: 0.2952 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20790 Z= 0.101 Angle : 0.580 9.125 28521 Z= 0.278 Chirality : 0.044 0.178 3579 Planarity : 0.004 0.039 3336 Dihedral : 7.897 78.843 5412 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.49 % Allowed : 9.36 % Favored : 88.16 % 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 are not related in a simple way. whole: 0.83 (0.18), residues: 2262 helix: 2.12 (0.29), residues: 348 sheet: 0.73 (0.20), residues: 666 loop : 0.07 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 95 TYR 0.019 0.001 TYR N 50 PHE 0.011 0.001 PHE B 383 TRP 0.047 0.001 TRP H 36 HIS 0.012 0.001 HIS N 97 Details of bonding type rmsd covalent geometry : bond 0.00218 (20607) covalent geometry : angle 0.54137 (28011) SS BOND : bond 0.00353 ( 39) SS BOND : angle 1.54815 ( 78) hydrogen bonds : bond 0.02976 ( 717) hydrogen bonds : angle 4.95125 ( 1866) link_ALPHA1-2 : bond 0.00561 ( 9) link_ALPHA1-2 : angle 1.81758 ( 27) link_ALPHA1-3 : bond 0.00919 ( 15) link_ALPHA1-3 : angle 1.65123 ( 45) link_ALPHA1-6 : bond 0.00702 ( 12) link_ALPHA1-6 : angle 1.59151 ( 36) link_BETA1-4 : bond 0.00681 ( 51) link_BETA1-4 : angle 2.12709 ( 153) link_NAG-ASN : bond 0.00172 ( 57) link_NAG-ASN : angle 1.08876 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 215 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6625 (p) REVERT: A 626 MET cc_start: 0.7934 (mtp) cc_final: 0.7442 (ttm) REVERT: L 17 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7139 (pt0) REVERT: L 83 GLU cc_start: 0.7495 (tp30) cc_final: 0.7187 (tp30) REVERT: H 5 GLN cc_start: 0.8837 (tm-30) cc_final: 0.7867 (mp10) REVERT: H 81 ARG cc_start: 0.8432 (ttp80) cc_final: 0.8145 (mtm110) REVERT: B 202 THR cc_start: 0.9010 (m) cc_final: 0.8809 (t) REVERT: B 434 MET cc_start: 0.8713 (ttp) cc_final: 0.8300 (ttt) REVERT: M 17 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7130 (pt0) REVERT: N 3 HIS cc_start: 0.7634 (t-90) cc_final: 0.7267 (t70) REVERT: N 5 GLN cc_start: 0.8733 (tm-30) cc_final: 0.7859 (mp10) REVERT: N 38 ARG cc_start: 0.7172 (ptm-80) cc_final: 0.6940 (ptm-80) REVERT: N 81 ARG cc_start: 0.8345 (ttp80) cc_final: 0.7988 (ttp-110) REVERT: C 82 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7660 (pm20) REVERT: C 95 MET cc_start: 0.9326 (ptm) cc_final: 0.9108 (ttp) REVERT: C 202 THR cc_start: 0.8981 (m) cc_final: 0.8699 (t) REVERT: C 626 MET cc_start: 0.7832 (mtp) cc_final: 0.7398 (ttm) REVERT: O 17 GLN cc_start: 0.8205 (mp10) cc_final: 0.7490 (pt0) REVERT: O 49 TYR cc_start: 0.7721 (p90) cc_final: 0.7295 (p90) REVERT: O 83 GLU cc_start: 0.7729 (tp30) cc_final: 0.7343 (tp30) REVERT: P 5 GLN cc_start: 0.8741 (tm-30) cc_final: 0.7785 (mp10) REVERT: P 6 GLU cc_start: 0.6859 (mp0) cc_final: 0.6641 (mp0) REVERT: P 20 LEU cc_start: 0.8069 (mt) cc_final: 0.7388 (mt) REVERT: P 41 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8753 (mm) REVERT: P 81 ARG cc_start: 0.8435 (ttp80) cc_final: 0.7769 (ttm-80) REVERT: P 91 TYR cc_start: 0.8148 (m-80) cc_final: 0.7745 (m-80) outliers start: 51 outliers final: 28 residues processed: 249 average time/residue: 0.1629 time to fit residues: 61.0717 Evaluate side-chains 226 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 89 ILE Chi-restraints excluded: chain P residue 108 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 110 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 chunk 197 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 193 optimal weight: 0.9990 chunk 181 optimal weight: 0.6980 chunk 158 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN H 97 HIS N 97 HIS P 97 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.108146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.077380 restraints weight = 41044.938| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.63 r_work: 0.2931 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20790 Z= 0.121 Angle : 0.593 10.112 28521 Z= 0.285 Chirality : 0.044 0.165 3579 Planarity : 0.004 0.039 3336 Dihedral : 7.819 79.371 5412 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.10 % Allowed : 10.19 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.18), residues: 2262 helix: 2.15 (0.29), residues: 348 sheet: 0.73 (0.20), residues: 666 loop : 0.05 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 95 TYR 0.016 0.001 TYR N 50 PHE 0.013 0.001 PHE P 100K TRP 0.043 0.001 TRP N 36 HIS 0.013 0.001 HIS H 97 Details of bonding type rmsd covalent geometry : bond 0.00280 (20607) covalent geometry : angle 0.54864 (28011) SS BOND : bond 0.00417 ( 39) SS BOND : angle 2.19095 ( 78) hydrogen bonds : bond 0.03044 ( 717) hydrogen bonds : angle 4.92525 ( 1866) link_ALPHA1-2 : bond 0.00522 ( 9) link_ALPHA1-2 : angle 1.77425 ( 27) link_ALPHA1-3 : bond 0.00830 ( 15) link_ALPHA1-3 : angle 1.66580 ( 45) link_ALPHA1-6 : bond 0.00655 ( 12) link_ALPHA1-6 : angle 1.64856 ( 36) link_BETA1-4 : bond 0.00638 ( 51) link_BETA1-4 : angle 2.12663 ( 153) link_NAG-ASN : bond 0.00148 ( 57) link_NAG-ASN : angle 1.16456 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6740 (p) REVERT: A 626 MET cc_start: 0.8023 (mtp) cc_final: 0.7470 (ttm) REVERT: L 17 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7252 (pt0) REVERT: L 83 GLU cc_start: 0.7519 (tp30) cc_final: 0.7204 (tp30) REVERT: H 5 GLN cc_start: 0.8793 (tm-30) cc_final: 0.7713 (mp10) REVERT: H 46 GLU cc_start: 0.8389 (tt0) cc_final: 0.8112 (tp30) REVERT: H 81 ARG cc_start: 0.8402 (ttp80) cc_final: 0.8128 (mtm110) REVERT: B 434 MET cc_start: 0.8748 (ttp) cc_final: 0.8337 (ttt) REVERT: B 475 MET cc_start: 0.8420 (mmm) cc_final: 0.7998 (mmp) REVERT: M 17 GLN cc_start: 0.8457 (mm-40) cc_final: 0.7204 (pt0) REVERT: N 3 HIS cc_start: 0.7638 (t-90) cc_final: 0.7260 (t70) REVERT: N 5 GLN cc_start: 0.8805 (tm-30) cc_final: 0.7798 (mp10) REVERT: N 81 ARG cc_start: 0.8313 (ttp80) cc_final: 0.8018 (ttp-110) REVERT: C 82 GLN cc_start: 0.8348 (pt0) cc_final: 0.7694 (pm20) REVERT: C 95 MET cc_start: 0.9380 (ptm) cc_final: 0.9163 (ttp) REVERT: C 202 THR cc_start: 0.8880 (m) cc_final: 0.8600 (t) REVERT: C 626 MET cc_start: 0.8001 (mtp) cc_final: 0.7454 (ttm) REVERT: O 49 TYR cc_start: 0.7772 (p90) cc_final: 0.7335 (p90) REVERT: O 83 GLU cc_start: 0.7784 (tp30) cc_final: 0.7395 (tp30) REVERT: P 5 GLN cc_start: 0.8776 (tm-30) cc_final: 0.7773 (mp10) REVERT: P 20 LEU cc_start: 0.8039 (mt) cc_final: 0.7380 (mt) REVERT: P 41 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8757 (mm) REVERT: P 81 ARG cc_start: 0.8343 (ttp80) cc_final: 0.7715 (ttm-80) REVERT: P 91 TYR cc_start: 0.8148 (m-80) cc_final: 0.7715 (m-80) outliers start: 43 outliers final: 29 residues processed: 231 average time/residue: 0.1572 time to fit residues: 55.4954 Evaluate side-chains 219 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 105 ILE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 89 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 85 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 201 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 HIS N 97 HIS P 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.108823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.078221 restraints weight = 40904.367| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.94 r_work: 0.2935 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20790 Z= 0.110 Angle : 0.587 9.271 28521 Z= 0.282 Chirality : 0.044 0.170 3579 Planarity : 0.004 0.039 3336 Dihedral : 7.649 77.980 5412 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.05 % Allowed : 10.14 % Favored : 87.82 % 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 are not related in a simple way. whole: 0.91 (0.18), residues: 2262 helix: 2.26 (0.29), residues: 348 sheet: 0.82 (0.20), residues: 666 loop : 0.07 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 95 TYR 0.022 0.001 TYR N 91 PHE 0.012 0.001 PHE B 53 TRP 0.036 0.001 TRP N 36 HIS 0.013 0.001 HIS P 97 Details of bonding type rmsd covalent geometry : bond 0.00248 (20607) covalent geometry : angle 0.54610 (28011) SS BOND : bond 0.00343 ( 39) SS BOND : angle 1.96517 ( 78) hydrogen bonds : bond 0.02936 ( 717) hydrogen bonds : angle 4.85357 ( 1866) link_ALPHA1-2 : bond 0.00542 ( 9) link_ALPHA1-2 : angle 1.75370 ( 27) link_ALPHA1-3 : bond 0.00850 ( 15) link_ALPHA1-3 : angle 1.60073 ( 45) link_ALPHA1-6 : bond 0.00678 ( 12) link_ALPHA1-6 : angle 1.62590 ( 36) link_BETA1-4 : bond 0.00656 ( 51) link_BETA1-4 : angle 2.09803 ( 153) link_NAG-ASN : bond 0.00149 ( 57) link_NAG-ASN : angle 1.11766 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6615 (p) REVERT: A 103 GLN cc_start: 0.8660 (tp40) cc_final: 0.8182 (tt0) REVERT: A 626 MET cc_start: 0.8019 (mtp) cc_final: 0.7556 (ttm) REVERT: L 17 GLN cc_start: 0.8318 (mm-40) cc_final: 0.7356 (pt0) REVERT: L 83 GLU cc_start: 0.7590 (tp30) cc_final: 0.7261 (tp30) REVERT: H 5 GLN cc_start: 0.8770 (tm-30) cc_final: 0.7679 (mp10) REVERT: H 46 GLU cc_start: 0.8431 (tt0) cc_final: 0.8210 (tp30) REVERT: H 81 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8179 (mtm110) REVERT: B 66 ARG cc_start: 0.6996 (mtp85) cc_final: 0.6716 (mmt180) REVERT: B 434 MET cc_start: 0.8662 (ttp) cc_final: 0.8214 (ttt) REVERT: B 475 MET cc_start: 0.8420 (mmm) cc_final: 0.8159 (mmp) REVERT: M 17 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7206 (pt0) REVERT: N 3 HIS cc_start: 0.7552 (t-90) cc_final: 0.7144 (t70) REVERT: N 5 GLN cc_start: 0.8725 (tm-30) cc_final: 0.7699 (mp10) REVERT: N 81 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7949 (ttp-110) REVERT: C 82 GLN cc_start: 0.8341 (pt0) cc_final: 0.7670 (pm20) REVERT: C 95 MET cc_start: 0.9366 (ptm) cc_final: 0.9139 (ttp) REVERT: C 103 GLN cc_start: 0.8643 (tp40) cc_final: 0.8286 (tt0) REVERT: C 626 MET cc_start: 0.7988 (mtp) cc_final: 0.7500 (ttm) REVERT: O 83 GLU cc_start: 0.7840 (tp30) cc_final: 0.7475 (tp30) REVERT: P 5 GLN cc_start: 0.8731 (tm-30) cc_final: 0.7573 (mp10) REVERT: P 6 GLU cc_start: 0.7203 (mp0) cc_final: 0.6236 (mp0) REVERT: P 20 LEU cc_start: 0.8024 (mt) cc_final: 0.7420 (mt) REVERT: P 41 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8827 (mm) REVERT: P 81 ARG cc_start: 0.8358 (ttp80) cc_final: 0.7709 (ttm-80) REVERT: P 91 TYR cc_start: 0.8180 (m-80) cc_final: 0.7713 (m-80) outliers start: 42 outliers final: 31 residues processed: 225 average time/residue: 0.1554 time to fit residues: 53.3847 Evaluate side-chains 221 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 89 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 16 optimal weight: 0.0040 chunk 187 optimal weight: 1.9990 chunk 139 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 168 optimal weight: 3.9990 overall best weight: 3.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.104773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.075019 restraints weight = 40907.114| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.74 r_work: 0.2876 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20790 Z= 0.216 Angle : 0.675 9.440 28521 Z= 0.325 Chirality : 0.046 0.180 3579 Planarity : 0.004 0.051 3336 Dihedral : 8.035 84.016 5412 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.66 % Allowed : 10.53 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.18), residues: 2262 helix: 1.91 (0.28), residues: 348 sheet: 0.54 (0.19), residues: 696 loop : -0.02 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 95 TYR 0.016 0.002 TYR N 100M PHE 0.023 0.002 PHE P 100K TRP 0.044 0.002 TRP H 36 HIS 0.013 0.002 HIS P 97 Details of bonding type rmsd covalent geometry : bond 0.00515 (20607) covalent geometry : angle 0.63024 (28011) SS BOND : bond 0.00381 ( 39) SS BOND : angle 2.31503 ( 78) hydrogen bonds : bond 0.03609 ( 717) hydrogen bonds : angle 5.21771 ( 1866) link_ALPHA1-2 : bond 0.00415 ( 9) link_ALPHA1-2 : angle 1.77107 ( 27) link_ALPHA1-3 : bond 0.00624 ( 15) link_ALPHA1-3 : angle 1.83001 ( 45) link_ALPHA1-6 : bond 0.00471 ( 12) link_ALPHA1-6 : angle 1.79452 ( 36) link_BETA1-4 : bond 0.00559 ( 51) link_BETA1-4 : angle 2.21575 ( 153) link_NAG-ASN : bond 0.00294 ( 57) link_NAG-ASN : angle 1.41956 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7083 (mtp85) cc_final: 0.6720 (mmt180) REVERT: A 202 THR cc_start: 0.9122 (m) cc_final: 0.8830 (t) REVERT: A 352 HIS cc_start: 0.8451 (m90) cc_final: 0.8164 (m170) REVERT: L 25 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7771 (tm-30) REVERT: L 60 ASP cc_start: 0.8656 (m-30) cc_final: 0.8126 (t0) REVERT: L 83 GLU cc_start: 0.7536 (tp30) cc_final: 0.7239 (tp30) REVERT: H 5 GLN cc_start: 0.8742 (tm-30) cc_final: 0.7615 (mp10) REVERT: H 46 GLU cc_start: 0.8477 (tt0) cc_final: 0.8129 (tp30) REVERT: H 81 ARG cc_start: 0.8372 (ttp80) cc_final: 0.8058 (mtm110) REVERT: B 66 ARG cc_start: 0.7174 (mtp85) cc_final: 0.6856 (mmt180) REVERT: B 434 MET cc_start: 0.8848 (ttp) cc_final: 0.8407 (ttt) REVERT: B 475 MET cc_start: 0.8583 (mmm) cc_final: 0.8048 (mmp) REVERT: M 17 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8234 (mp10) REVERT: M 60 ASP cc_start: 0.8415 (m-30) cc_final: 0.8184 (t0) REVERT: M 105 ILE cc_start: 0.7560 (tp) cc_final: 0.7088 (pt) REVERT: N 3 HIS cc_start: 0.7639 (t-90) cc_final: 0.7217 (t70) REVERT: N 5 GLN cc_start: 0.8744 (tm-30) cc_final: 0.7724 (mp10) REVERT: N 28 LEU cc_start: 0.8289 (mp) cc_final: 0.8016 (tt) REVERT: N 81 ARG cc_start: 0.8243 (ttp80) cc_final: 0.8036 (mtm110) REVERT: C 66 ARG cc_start: 0.7141 (mtp85) cc_final: 0.6741 (mmt180) REVERT: C 82 GLN cc_start: 0.8340 (pt0) cc_final: 0.7692 (pm20) REVERT: C 95 MET cc_start: 0.9420 (ptm) cc_final: 0.9216 (ttp) REVERT: C 202 THR cc_start: 0.9012 (m) cc_final: 0.8734 (t) REVERT: O 17 GLN cc_start: 0.8339 (mp10) cc_final: 0.7482 (pt0) REVERT: O 83 GLU cc_start: 0.7805 (tp30) cc_final: 0.7381 (tp30) REVERT: P 5 GLN cc_start: 0.8766 (tm-30) cc_final: 0.7597 (mp10) REVERT: P 6 GLU cc_start: 0.7301 (mp0) cc_final: 0.6273 (mp0) REVERT: P 41 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8745 (mm) REVERT: P 81 ARG cc_start: 0.8266 (ttp80) cc_final: 0.7928 (mtm110) REVERT: P 91 TYR cc_start: 0.8207 (m-80) cc_final: 0.7686 (m-80) outliers start: 34 outliers final: 30 residues processed: 212 average time/residue: 0.1695 time to fit residues: 53.8017 Evaluate side-chains 211 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 89 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 44 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 156 optimal weight: 0.0270 chunk 57 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 225 optimal weight: 0.8980 overall best weight: 2.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.106592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.075756 restraints weight = 41136.779| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.62 r_work: 0.2901 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 20790 Z= 0.145 Angle : 0.628 10.536 28521 Z= 0.304 Chirality : 0.045 0.173 3579 Planarity : 0.004 0.055 3336 Dihedral : 7.853 81.389 5412 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.85 % Allowed : 10.58 % Favored : 87.57 % 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 are not related in a simple way. whole: 0.64 (0.18), residues: 2262 helix: 2.02 (0.28), residues: 348 sheet: 0.66 (0.20), residues: 666 loop : -0.11 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 95 TYR 0.023 0.002 TYR N 91 PHE 0.015 0.001 PHE H 100K TRP 0.043 0.001 TRP H 36 HIS 0.013 0.001 HIS P 97 Details of bonding type rmsd covalent geometry : bond 0.00342 (20607) covalent geometry : angle 0.58422 (28011) SS BOND : bond 0.00435 ( 39) SS BOND : angle 2.29902 ( 78) hydrogen bonds : bond 0.03254 ( 717) hydrogen bonds : angle 5.08807 ( 1866) link_ALPHA1-2 : bond 0.00474 ( 9) link_ALPHA1-2 : angle 1.77616 ( 27) link_ALPHA1-3 : bond 0.00733 ( 15) link_ALPHA1-3 : angle 1.67220 ( 45) link_ALPHA1-6 : bond 0.00591 ( 12) link_ALPHA1-6 : angle 1.69412 ( 36) link_BETA1-4 : bond 0.00600 ( 51) link_BETA1-4 : angle 2.12883 ( 153) link_NAG-ASN : bond 0.00170 ( 57) link_NAG-ASN : angle 1.27345 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4126.87 seconds wall clock time: 71 minutes 53.25 seconds (4313.25 seconds total)