Starting phenix.real_space_refine on Thu Mar 5 06:51:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lx2_23564/03_2026/7lx2_23564.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lx2_23564/03_2026/7lx2_23564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lx2_23564/03_2026/7lx2_23564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lx2_23564/03_2026/7lx2_23564.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lx2_23564/03_2026/7lx2_23564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lx2_23564/03_2026/7lx2_23564.map" } resolution = 3.12 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= 0.002 sd= 0.146 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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 63 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: 4.74, per 1000 atoms: 0.23 Number of scatterers: 20196 At special positions: 0 Unit cell: (152.874, 144.666, 150.822, 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=2.27 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=2.08 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.23 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 605 " distance=2.07 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.08 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=2.27 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.11 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.08 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.04 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 605 " distance=2.07 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.07 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=2.27 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.08 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 605 " distance=2.07 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 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: 2.33 Conformation dependent library (CDL) restraints added in 846.7 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: 54 helices and 48 sheets defined 20.5% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 99 through 116 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: 4.015A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.962A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 528 removed outlier: 4.267A 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 542 removed outlier: 4.279A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (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 removed outlier: 3.654A pdb=" N LYS A 633 " --> pdb=" O MET A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 651 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100D through 100H Processing helix chain 'B' and resid 99 through 116 Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 335 through 348 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.957A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.924A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.273A 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 542 removed outlier: 4.280A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (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 removed outlier: 3.816A pdb=" N LYS B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 651 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 61 through 64 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 100D through 100H Processing helix chain 'C' and resid 99 through 117 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: 3.959A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.935A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 528 removed outlier: 4.283A 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 542 removed outlier: 4.283A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 597 removed outlier: 3.724A pdb=" N TYR C 586 " --> pdb=" O ALA C 582 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.652A pdb=" N LYS C 633 " --> pdb=" O MET C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 651 Processing helix chain 'O' and resid 79 through 83 Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 61 through 64 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: 4.874A 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: 4.053A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.760A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) 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: 6.640A 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: 6.687A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.811A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.907A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.905A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.156A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 274 removed outlier: 11.156A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.905A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.907A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.811A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE A 359 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.602A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 8 through 13 removed outlier: 6.761A pdb=" N THR L 8 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE L 105 " --> pdb=" O THR L 8 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL L 11 " --> pdb=" O ILE L 105 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N CYS L 88 " --> pdb=" O GLY L 99 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY L 101 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR L 86 " --> pdb=" O GLY L 101 " (cutoff:3.500A) removed outlier: 6.590A 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 Processing sheet with id=AB6, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.892A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR H 33 " --> pdb=" O THR H 95 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.892A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR H 33 " --> pdb=" O THR H 95 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 494 through 499 removed outlier: 4.872A pdb=" N VAL B 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.883A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.830A pdb=" N VAL B 75 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AC4, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AC5, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.645A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 259 through 261 removed outlier: 6.709A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLY B 451 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 10.287A pdb=" N GLU B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 11.831A pdb=" N LEU B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 11.931A pdb=" N LEU B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 10.918A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.173A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N GLU B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER B 334 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 271 through 274 removed outlier: 11.173A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.918A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.931A pdb=" N LEU B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 11.831A pdb=" N LEU B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 10.287A pdb=" N GLU B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLY B 451 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE B 359 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 304 through 312 removed outlier: 6.582A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 8 through 13 removed outlier: 6.730A pdb=" N THR M 8 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE M 105 " --> pdb=" O THR M 8 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL M 11 " --> pdb=" O ILE M 105 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLU M 100 " --> pdb=" O CYS M 88 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N CYS M 88 " --> pdb=" O GLU M 100 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP M 35 " --> pdb=" O ILE M 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 19 through 23 Processing sheet with id=AD2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AD4, first strand: chain 'N' and resid 58 through 59 removed outlier: 6.919A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR N 33 " --> pdb=" O THR N 95 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 58 through 59 removed outlier: 6.919A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR N 33 " --> pdb=" O THR N 95 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.870A pdb=" N VAL C 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.859A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.774A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AE1, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AE2, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AE3, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.648A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.706A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.920A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 10.908A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 271 through 274 removed outlier: 11.171A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.908A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.920A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE C 359 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.611A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 8 through 13 removed outlier: 6.740A pdb=" N THR O 8 " --> pdb=" O THR O 103 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE O 105 " --> pdb=" O THR O 8 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL O 11 " --> pdb=" O ILE O 105 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP O 35 " --> pdb=" O ILE O 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 19 through 23 Processing sheet with id=AE9, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'P' and resid 11 through 12 Processing sheet with id=AF2, first strand: chain 'P' and resid 58 through 59 removed outlier: 6.891A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR P 50 " --> pdb=" O TRP P 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP P 34 " --> pdb=" O TYR P 50 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR P 33 " --> pdb=" O THR P 95 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 58 through 59 removed outlier: 6.891A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR P 50 " --> pdb=" O TRP P 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP P 34 " --> pdb=" O TYR P 50 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR P 33 " --> pdb=" O THR P 95 " (cutoff:3.500A) 767 hydrogen bonds defined for protein. 1941 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: 3.78 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.34: 6252 1.34 - 1.50: 7021 1.50 - 1.65: 7193 1.65 - 1.81: 128 1.81 - 1.96: 13 Bond restraints: 20607 Sorted by residual: bond pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " ideal model delta sigma weight residual 1.808 1.582 0.226 3.30e-02 9.18e+02 4.71e+01 bond pdb=" NE1 TRP B 427 " pdb=" CE2 TRP B 427 " ideal model delta sigma weight residual 1.370 1.307 0.063 1.10e-02 8.26e+03 3.31e+01 bond pdb=" NE1 TRP A 427 " pdb=" CE2 TRP A 427 " ideal model delta sigma weight residual 1.370 1.307 0.063 1.10e-02 8.26e+03 3.24e+01 bond pdb=" CB CYS M 88 " pdb=" SG CYS M 88 " ideal model delta sigma weight residual 1.808 1.621 0.187 3.30e-02 9.18e+02 3.20e+01 bond pdb=" NE1 TRP C 427 " pdb=" CE2 TRP C 427 " ideal model delta sigma weight residual 1.370 1.308 0.062 1.10e-02 8.26e+03 3.14e+01 ... (remaining 20602 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 24100 2.44 - 4.87: 3472 4.87 - 7.31: 398 7.31 - 9.74: 34 9.74 - 12.18: 7 Bond angle restraints: 28011 Sorted by residual: angle pdb=" C ILE M 58 " pdb=" N PRO M 59 " pdb=" CA PRO M 59 " ideal model delta sigma weight residual 119.78 127.50 -7.72 1.03e+00 9.43e-01 5.62e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.87 127.65 -7.78 1.04e+00 9.25e-01 5.60e+01 angle pdb=" C ALA A 219 " pdb=" N PRO A 220 " pdb=" CA PRO A 220 " ideal model delta sigma weight residual 120.52 127.93 -7.41 9.90e-01 1.02e+00 5.59e+01 angle pdb=" C ALA B 219 " pdb=" N PRO B 220 " pdb=" CA PRO B 220 " ideal model delta sigma weight residual 120.31 127.63 -7.32 9.80e-01 1.04e+00 5.58e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.87 127.58 -7.71 1.04e+00 9.25e-01 5.50e+01 ... (remaining 28006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.33: 13615 22.33 - 44.66: 332 44.66 - 66.98: 111 66.98 - 89.31: 54 89.31 - 111.64: 36 Dihedral angle restraints: 14148 sinusoidal: 7464 harmonic: 6684 Sorted by residual: dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 24.08 68.92 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CB CYS B 54 " pdb=" SG CYS B 54 " pdb=" SG CYS B 74 " pdb=" CB CYS B 74 " ideal model delta sinusoidal sigma weight residual 93.00 24.58 68.42 1 1.00e+01 1.00e-02 6.07e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 25.20 67.80 1 1.00e+01 1.00e-02 5.97e+01 ... (remaining 14145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2608 0.115 - 0.231: 868 0.231 - 0.346: 95 0.346 - 0.462: 7 0.462 - 0.577: 1 Chirality restraints: 3579 Sorted by residual: 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 -2.59 0.19 2.00e-02 2.50e+03 9.17e+01 chirality pdb=" C1 BMA h 3 " pdb=" O4 NAG h 2 " pdb=" C2 BMA h 3 " pdb=" O5 BMA h 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.12e+01 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 -2.59 0.19 2.00e-02 2.50e+03 9.10e+01 ... (remaining 3576 not shown) Planarity restraints: 3393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 190 " 0.112 2.00e-02 2.50e+03 1.15e-01 1.64e+02 pdb=" CG ASN C 190 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN C 190 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN C 190 " -0.178 2.00e-02 2.50e+03 pdb=" C1 NAG C 702 " 0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 190 " 0.112 2.00e-02 2.50e+03 1.15e-01 1.64e+02 pdb=" CG ASN A 190 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 190 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 190 " -0.178 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " 0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 190 " -0.109 2.00e-02 2.50e+03 1.12e-01 1.57e+02 pdb=" CG ASN B 190 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN B 190 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN B 190 " 0.174 2.00e-02 2.50e+03 pdb=" C1 NAG B 702 " -0.134 2.00e-02 2.50e+03 ... (remaining 3390 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3444 2.75 - 3.29: 17515 3.29 - 3.82: 32894 3.82 - 4.36: 39748 4.36 - 4.90: 65714 Nonbonded interactions: 159315 Sorted by model distance: nonbonded pdb=" OG1 THR B 37 " pdb=" OG1 THR B 499 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.212 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.212 3.040 nonbonded pdb=" O4 MAN T 5 " pdb=" O6 MAN T 5 " model vdw 2.260 3.040 nonbonded pdb=" O4 NAG b 2 " pdb=" O6 NAG b 2 " model vdw 2.267 3.040 ... (remaining 159310 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.690 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.022 0.240 20790 Z= 1.115 Angle : 1.754 12.178 28521 Z= 1.094 Chirality : 0.104 0.577 3579 Planarity : 0.009 0.047 3336 Dihedral : 13.137 111.640 9717 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.15 % Allowed : 0.73 % Favored : 99.12 % Cbeta Deviations : 0.14 % 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: 0.73 (0.17), residues: 2262 helix: -1.22 (0.24), residues: 393 sheet: 1.00 (0.18), residues: 675 loop : 0.99 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 66 TYR 0.053 0.007 TYR H 100O PHE 0.043 0.007 PHE B 353 TRP 0.044 0.009 TRP A 96 HIS 0.007 0.002 HIS H 52 Details of bonding type rmsd covalent geometry : bond 0.02062 (20607) covalent geometry : angle 1.71874 (28011) SS BOND : bond 0.07876 ( 39) SS BOND : angle 3.96237 ( 78) hydrogen bonds : bond 0.15876 ( 707) hydrogen bonds : angle 7.67387 ( 1941) link_ALPHA1-2 : bond 0.06013 ( 9) link_ALPHA1-2 : angle 2.83075 ( 27) link_ALPHA1-3 : bond 0.05997 ( 15) link_ALPHA1-3 : angle 2.75687 ( 45) link_ALPHA1-6 : bond 0.05672 ( 12) link_ALPHA1-6 : angle 3.14139 ( 36) link_BETA1-4 : bond 0.05711 ( 51) link_BETA1-4 : angle 3.65963 ( 153) link_NAG-ASN : bond 0.07870 ( 57) link_NAG-ASN : angle 2.16311 ( 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 412 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 409 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 68 VAL cc_start: 0.9181 (p) cc_final: 0.8954 (p) REVERT: B 173 TYR cc_start: 0.8034 (m-80) cc_final: 0.7809 (m-80) REVERT: N 100 LYS cc_start: 0.8460 (mttt) cc_final: 0.8218 (mmtt) outliers start: 3 outliers final: 3 residues processed: 412 average time/residue: 0.1651 time to fit residues: 100.9355 Evaluate side-chains 197 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASN 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: 10.0000 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 229 ASN L 52 ASN B 105 HIS B 625 ASN M 52 ASN C 105 HIS C 114 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.148986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106945 restraints weight = 26993.399| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.19 r_work: 0.3233 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20790 Z= 0.203 Angle : 0.754 10.234 28521 Z= 0.369 Chirality : 0.050 0.271 3579 Planarity : 0.004 0.031 3336 Dihedral : 10.699 84.498 5418 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.06 % Favored : 98.81 % Rotamer: Outliers : 1.85 % Allowed : 5.21 % Favored : 92.93 % 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: 0.61 (0.16), residues: 2262 helix: 0.24 (0.26), residues: 384 sheet: 0.74 (0.19), residues: 663 loop : 0.41 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 350 TYR 0.016 0.002 TYR H 100M PHE 0.016 0.002 PHE B 382 TRP 0.017 0.002 TRP A 479 HIS 0.007 0.001 HIS P 3 Details of bonding type rmsd covalent geometry : bond 0.00480 (20607) covalent geometry : angle 0.70610 (28011) SS BOND : bond 0.00486 ( 39) SS BOND : angle 1.79781 ( 78) hydrogen bonds : bond 0.04881 ( 707) hydrogen bonds : angle 5.94584 ( 1941) link_ALPHA1-2 : bond 0.00556 ( 9) link_ALPHA1-2 : angle 1.72019 ( 27) link_ALPHA1-3 : bond 0.01019 ( 15) link_ALPHA1-3 : angle 1.58171 ( 45) link_ALPHA1-6 : bond 0.00730 ( 12) link_ALPHA1-6 : angle 1.50891 ( 36) link_BETA1-4 : bond 0.00664 ( 51) link_BETA1-4 : angle 2.49762 ( 153) link_NAG-ASN : bond 0.00322 ( 57) link_NAG-ASN : angle 2.09172 ( 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 278 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 240 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8070 (tpp) cc_final: 0.7431 (mmt) REVERT: A 648 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7494 (mp0) REVERT: B 173 TYR cc_start: 0.8408 (m-80) cc_final: 0.8166 (m-80) REVERT: B 246 GLN cc_start: 0.8574 (mt0) cc_final: 0.8088 (tp40) REVERT: B 296 CYS cc_start: 0.7445 (m) cc_final: 0.7217 (m) REVERT: N 100 LYS cc_start: 0.8490 (mttt) cc_final: 0.8001 (mmtt) REVERT: N 100 MET cc_start: 0.8357 (mpp) cc_final: 0.7455 (mpp) REVERT: C 246 GLN cc_start: 0.8564 (mt0) cc_final: 0.8029 (tp-100) REVERT: C 475 MET cc_start: 0.8123 (mmt) cc_final: 0.7750 (mmt) REVERT: P 100 LYS cc_start: 0.8489 (mttp) cc_final: 0.8248 (mmtm) outliers start: 38 outliers final: 15 residues processed: 272 average time/residue: 0.1513 time to fit residues: 62.4929 Evaluate side-chains 194 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 109 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 211 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 362 ASN L 52 ASN N 3 HIS C 94 ASN C 362 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.140118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.100983 restraints weight = 26320.473| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.16 r_work: 0.3103 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20790 Z= 0.166 Angle : 0.649 9.328 28521 Z= 0.316 Chirality : 0.047 0.225 3579 Planarity : 0.004 0.041 3336 Dihedral : 9.625 79.717 5412 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.14 % Allowed : 7.75 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.42 (0.17), residues: 2262 helix: 0.80 (0.27), residues: 384 sheet: 0.45 (0.18), residues: 693 loop : 0.12 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 31 TYR 0.012 0.001 TYR N 100O PHE 0.014 0.002 PHE A 53 TRP 0.016 0.001 TRP C 479 HIS 0.008 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00390 (20607) covalent geometry : angle 0.60947 (28011) SS BOND : bond 0.00652 ( 39) SS BOND : angle 1.84380 ( 78) hydrogen bonds : bond 0.03939 ( 707) hydrogen bonds : angle 5.43542 ( 1941) link_ALPHA1-2 : bond 0.00593 ( 9) link_ALPHA1-2 : angle 1.68910 ( 27) link_ALPHA1-3 : bond 0.00893 ( 15) link_ALPHA1-3 : angle 1.46618 ( 45) link_ALPHA1-6 : bond 0.00718 ( 12) link_ALPHA1-6 : angle 1.58075 ( 36) link_BETA1-4 : bond 0.00687 ( 51) link_BETA1-4 : angle 2.10266 ( 153) link_NAG-ASN : bond 0.00238 ( 57) link_NAG-ASN : angle 1.50971 ( 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 232 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7574 (tpp) cc_final: 0.6600 (mmm) REVERT: H 28 LEU cc_start: 0.7522 (mt) cc_final: 0.7228 (tp) REVERT: H 100 LYS cc_start: 0.8049 (mttm) cc_final: 0.7831 (mmtt) REVERT: B 110 SER cc_start: 0.8020 (m) cc_final: 0.7740 (t) REVERT: B 173 TYR cc_start: 0.8439 (m-80) cc_final: 0.8173 (m-80) REVERT: B 246 GLN cc_start: 0.8381 (mt0) cc_final: 0.7733 (tp-100) REVERT: N 100 LYS cc_start: 0.8187 (mttt) cc_final: 0.7625 (mmmt) REVERT: N 100 MET cc_start: 0.7960 (mpp) cc_final: 0.7168 (mpp) REVERT: C 95 MET cc_start: 0.8944 (ptm) cc_final: 0.8686 (ptm) REVERT: C 246 GLN cc_start: 0.8535 (mt0) cc_final: 0.7925 (tp-100) REVERT: C 475 MET cc_start: 0.7725 (mmt) cc_final: 0.7404 (mmt) REVERT: C 581 LEU cc_start: 0.8252 (mt) cc_final: 0.7910 (mt) REVERT: P 100 LYS cc_start: 0.8016 (mttp) cc_final: 0.7533 (mmtt) outliers start: 44 outliers final: 23 residues processed: 220 average time/residue: 0.1515 time to fit residues: 51.2370 Evaluate side-chains 193 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 41 LEU Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 153 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 223 optimal weight: 30.0000 chunk 182 optimal weight: 6.9990 chunk 204 optimal weight: 4.9990 chunk 208 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.146937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105016 restraints weight = 27316.721| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.20 r_work: 0.3204 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20790 Z= 0.167 Angle : 0.631 8.475 28521 Z= 0.304 Chirality : 0.046 0.217 3579 Planarity : 0.004 0.040 3336 Dihedral : 9.117 80.459 5412 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.85 % Allowed : 8.58 % Favored : 89.57 % 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: 0.31 (0.17), residues: 2262 helix: 0.94 (0.28), residues: 384 sheet: 0.34 (0.18), residues: 699 loop : -0.01 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 31 TYR 0.012 0.001 TYR N 100O PHE 0.014 0.002 PHE B 53 TRP 0.012 0.001 TRP C 112 HIS 0.009 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00403 (20607) covalent geometry : angle 0.59029 (28011) SS BOND : bond 0.00376 ( 39) SS BOND : angle 1.72338 ( 78) hydrogen bonds : bond 0.03634 ( 707) hydrogen bonds : angle 5.24255 ( 1941) link_ALPHA1-2 : bond 0.00527 ( 9) link_ALPHA1-2 : angle 1.70797 ( 27) link_ALPHA1-3 : bond 0.00822 ( 15) link_ALPHA1-3 : angle 1.66460 ( 45) link_ALPHA1-6 : bond 0.00647 ( 12) link_ALPHA1-6 : angle 1.55092 ( 36) link_BETA1-4 : bond 0.00587 ( 51) link_BETA1-4 : angle 2.11042 ( 153) link_NAG-ASN : bond 0.00237 ( 57) link_NAG-ASN : angle 1.53574 ( 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 222 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7847 (tpp) cc_final: 0.7044 (mmm) REVERT: A 620 ASP cc_start: 0.8375 (t0) cc_final: 0.7818 (t0) REVERT: H 28 LEU cc_start: 0.7670 (mt) cc_final: 0.7384 (tp) REVERT: H 80 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7653 (tp) REVERT: B 110 SER cc_start: 0.8657 (m) cc_final: 0.8374 (t) REVERT: B 173 TYR cc_start: 0.8483 (m-80) cc_final: 0.8229 (m-80) REVERT: B 246 GLN cc_start: 0.8561 (mt0) cc_final: 0.8067 (tp-100) REVERT: N 100 LYS cc_start: 0.8510 (mttt) cc_final: 0.7952 (mmmt) REVERT: C 246 GLN cc_start: 0.8522 (mt0) cc_final: 0.8066 (tp-100) REVERT: C 475 MET cc_start: 0.7909 (mmt) cc_final: 0.7606 (mmt) REVERT: C 581 LEU cc_start: 0.8671 (mt) cc_final: 0.8346 (mt) REVERT: P 100 LYS cc_start: 0.8498 (mttp) cc_final: 0.8069 (mmtt) outliers start: 38 outliers final: 20 residues processed: 212 average time/residue: 0.1436 time to fit residues: 46.6928 Evaluate side-chains 192 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 136 optimal weight: 10.0000 chunk 217 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 173 optimal weight: 0.2980 chunk 122 optimal weight: 2.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.146414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.104554 restraints weight = 27176.347| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.19 r_work: 0.3199 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20790 Z= 0.162 Angle : 0.614 8.382 28521 Z= 0.294 Chirality : 0.046 0.218 3579 Planarity : 0.004 0.039 3336 Dihedral : 8.819 79.414 5412 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.34 % Allowed : 8.19 % Favored : 89.47 % 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: 0.32 (0.17), residues: 2262 helix: 1.03 (0.28), residues: 384 sheet: 0.37 (0.18), residues: 699 loop : -0.07 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 31 TYR 0.012 0.001 TYR P 100M PHE 0.013 0.002 PHE B 53 TRP 0.011 0.001 TRP B 112 HIS 0.008 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00390 (20607) covalent geometry : angle 0.57114 (28011) SS BOND : bond 0.00425 ( 39) SS BOND : angle 1.94928 ( 78) hydrogen bonds : bond 0.03508 ( 707) hydrogen bonds : angle 5.18162 ( 1941) link_ALPHA1-2 : bond 0.00536 ( 9) link_ALPHA1-2 : angle 1.68435 ( 27) link_ALPHA1-3 : bond 0.00814 ( 15) link_ALPHA1-3 : angle 1.64379 ( 45) link_ALPHA1-6 : bond 0.00688 ( 12) link_ALPHA1-6 : angle 1.52700 ( 36) link_BETA1-4 : bond 0.00612 ( 51) link_BETA1-4 : angle 2.08945 ( 153) link_NAG-ASN : bond 0.00220 ( 57) link_NAG-ASN : angle 1.47051 ( 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 215 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7859 (tpp) cc_final: 0.7375 (mmp) REVERT: A 620 ASP cc_start: 0.8384 (t0) cc_final: 0.7822 (t0) REVERT: H 28 LEU cc_start: 0.7652 (mt) cc_final: 0.7378 (tp) REVERT: B 51 THR cc_start: 0.9388 (m) cc_final: 0.9163 (p) REVERT: B 110 SER cc_start: 0.8661 (m) cc_final: 0.8373 (t) REVERT: B 173 TYR cc_start: 0.8498 (m-80) cc_final: 0.8289 (m-80) REVERT: B 246 GLN cc_start: 0.8592 (mt0) cc_final: 0.8050 (tp-100) REVERT: B 620 ASP cc_start: 0.8472 (t0) cc_final: 0.7893 (t0) REVERT: N 100 LYS cc_start: 0.8510 (mttt) cc_final: 0.7945 (mmmt) REVERT: C 246 GLN cc_start: 0.8658 (mt0) cc_final: 0.8102 (tp-100) REVERT: C 475 MET cc_start: 0.7884 (mmt) cc_final: 0.7587 (mmt) REVERT: C 581 LEU cc_start: 0.8671 (mt) cc_final: 0.8342 (mt) REVERT: P 100 LYS cc_start: 0.8498 (mttp) cc_final: 0.8058 (mmtt) outliers start: 48 outliers final: 32 residues processed: 205 average time/residue: 0.1421 time to fit residues: 45.0903 Evaluate side-chains 199 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 12 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 217 optimal weight: 20.0000 chunk 156 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 chunk 163 optimal weight: 0.0040 chunk 199 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.149566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.108024 restraints weight = 26877.607| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.18 r_work: 0.3203 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 20790 Z= 0.099 Angle : 0.557 7.852 28521 Z= 0.267 Chirality : 0.044 0.222 3579 Planarity : 0.003 0.032 3336 Dihedral : 8.185 75.252 5412 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.80 % Allowed : 8.58 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.17), residues: 2262 helix: 1.40 (0.28), residues: 384 sheet: 0.49 (0.18), residues: 723 loop : 0.01 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 95 TYR 0.011 0.001 TYR C 486 PHE 0.011 0.001 PHE C 383 TRP 0.012 0.001 TRP H 34 HIS 0.008 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00221 (20607) covalent geometry : angle 0.51666 (28011) SS BOND : bond 0.00374 ( 39) SS BOND : angle 1.67365 ( 78) hydrogen bonds : bond 0.02915 ( 707) hydrogen bonds : angle 4.90771 ( 1941) link_ALPHA1-2 : bond 0.00610 ( 9) link_ALPHA1-2 : angle 1.61003 ( 27) link_ALPHA1-3 : bond 0.00891 ( 15) link_ALPHA1-3 : angle 1.66648 ( 45) link_ALPHA1-6 : bond 0.00790 ( 12) link_ALPHA1-6 : angle 1.52172 ( 36) link_BETA1-4 : bond 0.00643 ( 51) link_BETA1-4 : angle 1.97746 ( 153) link_NAG-ASN : bond 0.00177 ( 57) link_NAG-ASN : angle 1.25399 ( 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 212 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7737 (tpp) cc_final: 0.7217 (mmt) REVERT: A 620 ASP cc_start: 0.8309 (t0) cc_final: 0.7710 (t0) REVERT: H 80 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7757 (tp) REVERT: B 95 MET cc_start: 0.9103 (ptm) cc_final: 0.8809 (ptm) REVERT: B 173 TYR cc_start: 0.8489 (m-80) cc_final: 0.8245 (m-80) REVERT: B 246 GLN cc_start: 0.8525 (mt0) cc_final: 0.8169 (tp-100) REVERT: B 620 ASP cc_start: 0.8358 (t0) cc_final: 0.7833 (t0) REVERT: M 36 TYR cc_start: 0.8446 (m-80) cc_final: 0.8151 (m-80) REVERT: N 99 ARG cc_start: 0.8200 (ttp-110) cc_final: 0.7769 (ttp80) REVERT: N 100 LYS cc_start: 0.8513 (mttt) cc_final: 0.7990 (mmmt) REVERT: C 109 ILE cc_start: 0.8411 (mm) cc_final: 0.7966 (mt) REVERT: C 246 GLN cc_start: 0.8589 (mt0) cc_final: 0.8092 (tp-100) REVERT: C 475 MET cc_start: 0.7710 (mmt) cc_final: 0.7419 (mmt) REVERT: C 581 LEU cc_start: 0.8622 (mt) cc_final: 0.8349 (mt) REVERT: P 100 LYS cc_start: 0.8541 (mttp) cc_final: 0.8095 (mmtt) outliers start: 37 outliers final: 27 residues processed: 208 average time/residue: 0.1394 time to fit residues: 44.8750 Evaluate side-chains 191 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 76 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 180 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 213 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 52 ASN C 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.146227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.104610 restraints weight = 27621.586| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.09 r_work: 0.3242 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 20790 Z= 0.287 Angle : 0.718 8.358 28521 Z= 0.344 Chirality : 0.049 0.244 3579 Planarity : 0.005 0.047 3336 Dihedral : 8.839 83.875 5412 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.29 % Allowed : 8.48 % Favored : 89.23 % 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: 0.15 (0.17), residues: 2262 helix: 0.91 (0.28), residues: 387 sheet: 0.28 (0.18), residues: 705 loop : -0.20 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 30 TYR 0.024 0.002 TYR P 100M PHE 0.021 0.003 PHE O 98 TRP 0.012 0.002 TRP H 101 HIS 0.009 0.002 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00703 (20607) covalent geometry : angle 0.67507 (28011) SS BOND : bond 0.00486 ( 39) SS BOND : angle 1.91459 ( 78) hydrogen bonds : bond 0.04233 ( 707) hydrogen bonds : angle 5.40653 ( 1941) link_ALPHA1-2 : bond 0.00410 ( 9) link_ALPHA1-2 : angle 1.81466 ( 27) link_ALPHA1-3 : bond 0.00665 ( 15) link_ALPHA1-3 : angle 1.60357 ( 45) link_ALPHA1-6 : bond 0.00516 ( 12) link_ALPHA1-6 : angle 1.54870 ( 36) link_BETA1-4 : bond 0.00590 ( 51) link_BETA1-4 : angle 2.28780 ( 153) link_NAG-ASN : bond 0.00403 ( 57) link_NAG-ASN : angle 1.78724 ( 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 212 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7992 (tpp) cc_final: 0.7362 (mmm) REVERT: A 620 ASP cc_start: 0.8253 (t0) cc_final: 0.7789 (t0) REVERT: L 95 ASN cc_start: 0.7860 (m-40) cc_final: 0.7599 (t0) REVERT: H 28 LEU cc_start: 0.8262 (tp) cc_final: 0.8035 (tp) REVERT: H 80 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7787 (tp) REVERT: B 246 GLN cc_start: 0.8587 (mt0) cc_final: 0.8235 (tp-100) REVERT: B 585 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7878 (mtp180) REVERT: B 648 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: N 99 ARG cc_start: 0.8154 (ttp-110) cc_final: 0.7811 (ttp80) REVERT: N 100 LYS cc_start: 0.8581 (mttt) cc_final: 0.8057 (mmmt) REVERT: C 246 GLN cc_start: 0.8657 (mt0) cc_final: 0.8231 (tp-100) REVERT: C 475 MET cc_start: 0.8003 (mmt) cc_final: 0.7648 (mmt) REVERT: O 31 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.7491 (mtp180) REVERT: P 100 LYS cc_start: 0.8565 (mttp) cc_final: 0.8266 (mmtt) outliers start: 47 outliers final: 35 residues processed: 203 average time/residue: 0.1463 time to fit residues: 45.3908 Evaluate side-chains 201 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain P residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 110 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 217 optimal weight: 20.0000 chunk 197 optimal weight: 0.0570 chunk 27 optimal weight: 0.8980 chunk 193 optimal weight: 0.9990 chunk 181 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.147707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.106041 restraints weight = 27086.455| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.19 r_work: 0.3171 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 20790 Z= 0.106 Angle : 0.584 9.757 28521 Z= 0.281 Chirality : 0.044 0.190 3579 Planarity : 0.003 0.035 3336 Dihedral : 8.135 76.290 5412 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.00 % Allowed : 9.26 % Favored : 88.74 % 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: 0.34 (0.17), residues: 2262 helix: 1.31 (0.28), residues: 384 sheet: 0.42 (0.19), residues: 708 loop : -0.18 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 95 TYR 0.013 0.001 TYR N 33 PHE 0.013 0.001 PHE B 53 TRP 0.017 0.001 TRP B 631 HIS 0.008 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00239 (20607) covalent geometry : angle 0.54393 (28011) SS BOND : bond 0.00507 ( 39) SS BOND : angle 1.71597 ( 78) hydrogen bonds : bond 0.03105 ( 707) hydrogen bonds : angle 5.04035 ( 1941) link_ALPHA1-2 : bond 0.00607 ( 9) link_ALPHA1-2 : angle 1.66931 ( 27) link_ALPHA1-3 : bond 0.00811 ( 15) link_ALPHA1-3 : angle 1.67060 ( 45) link_ALPHA1-6 : bond 0.00743 ( 12) link_ALPHA1-6 : angle 1.41952 ( 36) link_BETA1-4 : bond 0.00628 ( 51) link_BETA1-4 : angle 2.01419 ( 153) link_NAG-ASN : bond 0.00168 ( 57) link_NAG-ASN : angle 1.36955 ( 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 205 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7789 (tpp) cc_final: 0.7183 (mmt) REVERT: A 620 ASP cc_start: 0.8329 (t0) cc_final: 0.7698 (t0) REVERT: L 95 ASN cc_start: 0.7631 (m-40) cc_final: 0.7272 (t0) REVERT: H 28 LEU cc_start: 0.7885 (tp) cc_final: 0.7637 (tp) REVERT: H 80 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7615 (tp) REVERT: B 46 LYS cc_start: 0.8421 (ptmm) cc_final: 0.8031 (pttp) REVERT: B 246 GLN cc_start: 0.8563 (mt0) cc_final: 0.8061 (tp-100) REVERT: B 475 MET cc_start: 0.7661 (mmt) cc_final: 0.7353 (mmt) REVERT: M 36 TYR cc_start: 0.8246 (m-80) cc_final: 0.8008 (m-80) REVERT: N 99 ARG cc_start: 0.8234 (ttp-110) cc_final: 0.7819 (ttp80) REVERT: N 100 LYS cc_start: 0.8494 (mttt) cc_final: 0.7998 (mmmt) REVERT: C 246 GLN cc_start: 0.8626 (mt0) cc_final: 0.8113 (tp-100) REVERT: C 475 MET cc_start: 0.7719 (mmt) cc_final: 0.7364 (mmt) REVERT: C 581 LEU cc_start: 0.8604 (mt) cc_final: 0.8335 (mt) REVERT: O 31 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.7699 (mtp180) REVERT: P 100 LYS cc_start: 0.8462 (mttp) cc_final: 0.8008 (mmtt) outliers start: 41 outliers final: 28 residues processed: 200 average time/residue: 0.1574 time to fit residues: 47.7970 Evaluate side-chains 188 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 92 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 85 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 208 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.147009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.105380 restraints weight = 27024.317| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.17 r_work: 0.3170 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20790 Z= 0.131 Angle : 0.579 7.742 28521 Z= 0.278 Chirality : 0.044 0.179 3579 Planarity : 0.003 0.035 3336 Dihedral : 7.914 77.105 5412 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.75 % Allowed : 9.50 % Favored : 88.74 % 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: 0.39 (0.17), residues: 2262 helix: 1.35 (0.28), residues: 387 sheet: 0.45 (0.19), residues: 708 loop : -0.15 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 95 TYR 0.011 0.001 TYR N 33 PHE 0.012 0.001 PHE C 383 TRP 0.015 0.001 TRP B 631 HIS 0.008 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00313 (20607) covalent geometry : angle 0.53829 (28011) SS BOND : bond 0.00386 ( 39) SS BOND : angle 1.68614 ( 78) hydrogen bonds : bond 0.03131 ( 707) hydrogen bonds : angle 4.98648 ( 1941) link_ALPHA1-2 : bond 0.00559 ( 9) link_ALPHA1-2 : angle 1.62345 ( 27) link_ALPHA1-3 : bond 0.00762 ( 15) link_ALPHA1-3 : angle 1.58384 ( 45) link_ALPHA1-6 : bond 0.00713 ( 12) link_ALPHA1-6 : angle 1.43452 ( 36) link_BETA1-4 : bond 0.00623 ( 51) link_BETA1-4 : angle 2.05062 ( 153) link_NAG-ASN : bond 0.00180 ( 57) link_NAG-ASN : angle 1.39159 ( 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 200 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9372 (m) cc_final: 0.9163 (p) REVERT: A 475 MET cc_start: 0.7737 (tpp) cc_final: 0.7111 (mmt) REVERT: A 620 ASP cc_start: 0.8358 (t0) cc_final: 0.7679 (t0) REVERT: L 95 ASN cc_start: 0.7607 (m-40) cc_final: 0.7208 (t0) REVERT: H 28 LEU cc_start: 0.7738 (tp) cc_final: 0.7504 (tp) REVERT: H 80 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7476 (tp) REVERT: B 95 MET cc_start: 0.8981 (ptm) cc_final: 0.8592 (ptm) REVERT: B 246 GLN cc_start: 0.8518 (mt0) cc_final: 0.7984 (tp-100) REVERT: B 475 MET cc_start: 0.7574 (mmt) cc_final: 0.7211 (mmt) REVERT: B 620 ASP cc_start: 0.8390 (t0) cc_final: 0.7803 (t0) REVERT: N 99 ARG cc_start: 0.8194 (ttp-110) cc_final: 0.7740 (ttp80) REVERT: N 100 LYS cc_start: 0.8403 (mttt) cc_final: 0.7747 (mmtt) REVERT: C 246 GLN cc_start: 0.8525 (mt0) cc_final: 0.7929 (tp-100) REVERT: C 475 MET cc_start: 0.7642 (mmt) cc_final: 0.7245 (mmt) REVERT: C 581 LEU cc_start: 0.8514 (mt) cc_final: 0.8233 (mt) REVERT: O 31 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.7626 (mtp180) REVERT: P 100 LYS cc_start: 0.8301 (mttp) cc_final: 0.7976 (mmtt) outliers start: 36 outliers final: 31 residues processed: 196 average time/residue: 0.1563 time to fit residues: 46.8644 Evaluate side-chains 191 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 92 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 16 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 139 optimal weight: 20.0000 chunk 112 optimal weight: 0.0010 chunk 171 optimal weight: 2.9990 chunk 65 optimal weight: 30.0000 chunk 70 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 chunk 176 optimal weight: 0.6980 chunk 168 optimal weight: 0.8980 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.148745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.107263 restraints weight = 27171.321| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.18 r_work: 0.3239 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20790 Z= 0.106 Angle : 0.561 7.958 28521 Z= 0.269 Chirality : 0.044 0.180 3579 Planarity : 0.003 0.031 3336 Dihedral : 7.598 74.485 5412 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.71 % Allowed : 9.65 % Favored : 88.65 % 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: 0.50 (0.18), residues: 2262 helix: 1.52 (0.28), residues: 387 sheet: 0.53 (0.19), residues: 708 loop : -0.12 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 95 TYR 0.016 0.001 TYR L 87 PHE 0.012 0.001 PHE B 53 TRP 0.013 0.001 TRP B 427 HIS 0.009 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00246 (20607) covalent geometry : angle 0.52198 (28011) SS BOND : bond 0.00354 ( 39) SS BOND : angle 1.60135 ( 78) hydrogen bonds : bond 0.02892 ( 707) hydrogen bonds : angle 4.86484 ( 1941) link_ALPHA1-2 : bond 0.00596 ( 9) link_ALPHA1-2 : angle 1.58130 ( 27) link_ALPHA1-3 : bond 0.00802 ( 15) link_ALPHA1-3 : angle 1.54827 ( 45) link_ALPHA1-6 : bond 0.00770 ( 12) link_ALPHA1-6 : angle 1.42547 ( 36) link_BETA1-4 : bond 0.00629 ( 51) link_BETA1-4 : angle 1.99215 ( 153) link_NAG-ASN : bond 0.00166 ( 57) link_NAG-ASN : angle 1.27649 ( 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 204 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7737 (tpp) cc_final: 0.7256 (mmp) REVERT: A 620 ASP cc_start: 0.8383 (t0) cc_final: 0.7754 (t0) REVERT: L 95 ASN cc_start: 0.7565 (m-40) cc_final: 0.7174 (t0) REVERT: H 28 LEU cc_start: 0.7783 (tp) cc_final: 0.7581 (tp) REVERT: H 80 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7615 (tp) REVERT: B 95 MET cc_start: 0.9037 (ptm) cc_final: 0.8681 (ptm) REVERT: B 246 GLN cc_start: 0.8546 (mt0) cc_final: 0.8080 (tp-100) REVERT: B 620 ASP cc_start: 0.8471 (t0) cc_final: 0.7883 (t0) REVERT: N 99 ARG cc_start: 0.8166 (ttp-110) cc_final: 0.7761 (ttp80) REVERT: N 100 LYS cc_start: 0.8514 (mttt) cc_final: 0.8024 (mmmt) REVERT: C 246 GLN cc_start: 0.8527 (mt0) cc_final: 0.8033 (tp-100) REVERT: C 475 MET cc_start: 0.7690 (mmt) cc_final: 0.7340 (mmt) REVERT: C 581 LEU cc_start: 0.8614 (mt) cc_final: 0.8356 (mt) REVERT: P 5 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8000 (mm110) REVERT: P 100 LYS cc_start: 0.8453 (mttp) cc_final: 0.8128 (mmtt) outliers start: 35 outliers final: 24 residues processed: 200 average time/residue: 0.1538 time to fit residues: 47.0657 Evaluate side-chains 187 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 92 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 44 optimal weight: 6.9990 chunk 176 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 156 optimal weight: 0.3980 chunk 57 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 225 optimal weight: 8.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.146478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.104838 restraints weight = 27176.655| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.18 r_work: 0.3209 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20790 Z= 0.167 Angle : 0.610 9.704 28521 Z= 0.294 Chirality : 0.045 0.175 3579 Planarity : 0.003 0.037 3336 Dihedral : 7.736 76.938 5412 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.36 % Allowed : 10.38 % 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: 0.41 (0.18), residues: 2262 helix: 1.40 (0.28), residues: 387 sheet: 0.48 (0.19), residues: 708 loop : -0.17 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 95 TYR 0.013 0.001 TYR P 100M PHE 0.015 0.002 PHE C 53 TRP 0.019 0.001 TRP B 427 HIS 0.009 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00408 (20607) covalent geometry : angle 0.56600 (28011) SS BOND : bond 0.00436 ( 39) SS BOND : angle 2.21021 ( 78) hydrogen bonds : bond 0.03250 ( 707) hydrogen bonds : angle 5.00037 ( 1941) link_ALPHA1-2 : bond 0.00518 ( 9) link_ALPHA1-2 : angle 1.59445 ( 27) link_ALPHA1-3 : bond 0.00725 ( 15) link_ALPHA1-3 : angle 1.50474 ( 45) link_ALPHA1-6 : bond 0.00672 ( 12) link_ALPHA1-6 : angle 1.43741 ( 36) link_BETA1-4 : bond 0.00608 ( 51) link_BETA1-4 : angle 2.07762 ( 153) link_NAG-ASN : bond 0.00202 ( 57) link_NAG-ASN : angle 1.42836 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4168.79 seconds wall clock time: 72 minutes 31.74 seconds (4351.74 seconds total)