Starting phenix.real_space_refine on Sat Jul 4 10:02:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lx3_23565/07_2026/7lx3_23565.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lx3_23565/07_2026/7lx3_23565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7lx3_23565/07_2026/7lx3_23565.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lx3_23565/07_2026/7lx3_23565.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lx3_23565/07_2026/7lx3_23565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lx3_23565/07_2026/7lx3_23565.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lx3_23565/07_2026/7lx3_23565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lx3_23565/07_2026/7lx3_23565.map" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.144 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 12645 2.51 5 N 3279 2.21 5 O 4161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 5 Time building chain proxies: 5.07, per 1000 atoms: 0.25 Number of scatterers: 20196 At special positions: 0 Unit cell: (144.2, 153.47, 152.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4161 8.00 N 3279 7.00 C 12645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.14 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.10 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.05 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.15 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.09 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.02 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.18 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.05 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.15 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.09 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.18 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.05 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " " MAN W 4 " - " MAN W 5 " " MAN h 4 " - " MAN h 5 " " MAN h 5 " - " MAN h 6 " " MAN k 4 " - " MAN k 5 " " MAN v 4 " - " MAN v 5 " " MAN v 5 " - " MAN v 6 " " MAN y 4 " - " MAN y 5 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 8 " " BMA W 3 " - " MAN W 4 " " BMA c 3 " - " MAN c 4 " " MAN c 4 " - " MAN c 5 " " BMA h 3 " - " MAN h 4 " " MAN h 7 " - " MAN h 8 " " BMA k 3 " - " MAN k 4 " " BMA q 3 " - " MAN q 4 " " MAN q 4 " - " MAN q 5 " " BMA v 3 " - " MAN v 4 " " MAN v 7 " - " MAN v 8 " " BMA y 3 " - " MAN y 4 " ALPHA1-6 " BMA J 3 " - " MAN J 6 " " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 9 " " BMA W 3 " - " MAN W 6 " " BMA c 3 " - " MAN c 6 " " BMA h 3 " - " MAN h 7 " " MAN h 7 " - " MAN h 9 " " BMA k 3 " - " MAN k 6 " " BMA q 3 " - " MAN q 6 " " BMA v 3 " - " MAN v 7 " " MAN v 7 " - " MAN v 9 " " BMA y 3 " - " MAN y 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " NAG-ASN " NAG A 701 " - " ASN A 160 " " NAG A 702 " - " ASN A 190 " " NAG A 703 " - " ASN A 289 " " NAG A 704 " - " ASN A 339 " " NAG A 705 " - " ASN A 611 " " NAG B 701 " - " ASN B 160 " " NAG B 702 " - " ASN B 190 " " NAG B 703 " - " ASN B 289 " " NAG B 704 " - " ASN B 339 " " NAG B 705 " - " ASN B 611 " " NAG C 701 " - " ASN C 160 " " NAG C 702 " - " ASN C 190 " " NAG C 703 " - " ASN C 289 " " NAG C 704 " - " ASN C 339 " " NAG C 705 " - " ASN C 611 " " NAG D 1 " - " ASN A 88 " " NAG E 1 " - " ASN A 130 " " NAG F 1 " - " ASN A 197 " " NAG G 1 " - " ASN A 276 " " NAG I 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 262 " " NAG K 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 392 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 295 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 234 " " NAG V 1 " - " ASN A 241 " " NAG W 1 " - " ASN A 138 " " NAG X 1 " - " ASN B 88 " " NAG Y 1 " - " ASN B 130 " " NAG Z 1 " - " ASN B 197 " " NAG a 1 " - " ASN B 276 " " NAG b 1 " - " ASN B 301 " " NAG c 1 " - " ASN B 262 " " NAG d 1 " - " ASN B 386 " " NAG e 1 " - " ASN B 392 " " NAG f 1 " - " ASN B 448 " " NAG g 1 " - " ASN B 295 " " NAG h 1 " - " ASN B 332 " " NAG i 1 " - " ASN B 234 " " NAG j 1 " - " ASN B 241 " " NAG k 1 " - " ASN B 138 " " NAG l 1 " - " ASN C 88 " " NAG m 1 " - " ASN C 130 " " NAG n 1 " - " ASN C 197 " " NAG o 1 " - " ASN C 276 " " NAG p 1 " - " ASN C 301 " " NAG q 1 " - " ASN C 262 " " NAG r 1 " - " ASN C 386 " " NAG s 1 " - " ASN C 392 " " NAG t 1 " - " ASN C 448 " " NAG u 1 " - " ASN C 295 " " NAG v 1 " - " ASN C 332 " " NAG w 1 " - " ASN C 234 " " NAG x 1 " - " ASN C 241 " " NAG y 1 " - " ASN C 138 " Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 933.7 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: 52 helices and 45 sheets defined 20.8% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.292A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.993A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.803A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 528 removed outlier: 4.305A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 546 removed outlier: 3.806A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 597 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 650 removed outlier: 4.259A pdb=" N SER A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100D through 100H Processing helix chain 'B' and resid 98 through 116 removed outlier: 4.288A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.997A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.807A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.453A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.783A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 597 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 650 removed outlier: 4.199A pdb=" N SER B 644 " --> pdb=" O ASP B 640 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 100D through 100H Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.295A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.008A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.828A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 528 removed outlier: 4.444A pdb=" N GLY C 527 " --> pdb=" O GLY C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 546 removed outlier: 3.801A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C 544 " --> pdb=" O GLN C 540 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 597 Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 650 removed outlier: 4.255A pdb=" N SER C 644 " --> pdb=" O ASP C 640 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 52 through 56 removed outlier: 4.103A pdb=" N GLY P 55 " --> pdb=" O HIS P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 100D through 100H Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.672A pdb=" N VAL A 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.909A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 132 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.659A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.621A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.007A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.931A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.749A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 315 through 323 removed outlier: 6.572A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 393 through 395 Processing sheet with id=AB2, first strand: chain 'L' and resid 8 through 13 removed outlier: 6.400A pdb=" N THR L 8 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE L 105 " --> pdb=" O THR L 8 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL L 11 " --> pdb=" O ILE L 105 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.821A pdb=" N TYR H 33 " --> pdb=" O THR H 95 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB7, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.307A pdb=" N VAL B 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL B 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR B 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N TYR B 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N CYS B 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.047A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AC3, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AC4, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.665A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.617A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY B 451 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N GLU B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 11.888A pdb=" N LEU B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 11.998A pdb=" N LEU B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 10.935A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 315 through 323 removed outlier: 6.568A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE B 322 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASN B 301 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLU B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER B 334 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 393 through 395 Processing sheet with id=AC8, first strand: chain 'M' and resid 8 through 13 removed outlier: 6.399A pdb=" N THR M 8 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE M 105 " --> pdb=" O THR M 8 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL M 11 " --> pdb=" O ILE M 105 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLU M 100 " --> pdb=" O CYS M 88 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N CYS M 88 " --> pdb=" O GLU M 100 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP M 35 " --> pdb=" O ILE M 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 19 through 23 Processing sheet with id=AD1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.820A pdb=" N TYR N 33 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AD4, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.641A pdb=" N VAL C 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.047A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AD9, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AE1, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.687A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.611A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.917A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 12.060A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.796A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 315 through 323 removed outlier: 6.572A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 393 through 395 Processing sheet with id=AE5, first strand: chain 'O' and resid 8 through 13 removed outlier: 6.388A pdb=" N THR O 8 " --> pdb=" O THR O 103 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE O 105 " --> pdb=" O THR O 8 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL O 11 " --> pdb=" O ILE O 105 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP O 35 " --> pdb=" O ILE O 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 19 through 23 Processing sheet with id=AE7, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'P' and resid 11 through 12 removed outlier: 3.782A pdb=" N TYR P 33 " --> pdb=" O THR P 95 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY P 49 " --> pdb=" O TRP P 36 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 11 through 12 732 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.37 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 5563 1.33 - 1.48: 6744 1.48 - 1.63: 8159 1.63 - 1.78: 58 1.78 - 1.93: 83 Bond restraints: 20607 Sorted by residual: bond pdb=" CB CYS C 247 " pdb=" SG CYS C 247 " ideal model delta sigma weight residual 1.808 1.587 0.221 3.30e-02 9.18e+02 4.49e+01 bond pdb=" CB CYS B 247 " pdb=" SG CYS B 247 " ideal model delta sigma weight residual 1.808 1.588 0.220 3.30e-02 9.18e+02 4.45e+01 bond pdb=" CB HIS L 89 " pdb=" CG HIS L 89 " ideal model delta sigma weight residual 1.497 1.411 0.086 1.40e-02 5.10e+03 3.75e+01 bond pdb=" NE1 TRP C 427 " pdb=" CE2 TRP C 427 " ideal model delta sigma weight residual 1.370 1.305 0.065 1.10e-02 8.26e+03 3.49e+01 bond pdb=" CB CYS M 88 " pdb=" SG CYS M 88 " ideal model delta sigma weight residual 1.808 1.614 0.194 3.30e-02 9.18e+02 3.44e+01 ... (remaining 20602 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 23443 2.28 - 4.57: 3949 4.57 - 6.85: 532 6.85 - 9.14: 71 9.14 - 11.42: 16 Bond angle restraints: 28011 Sorted by residual: angle pdb=" C VAL A 75 " pdb=" N PRO A 76 " pdb=" CA PRO A 76 " ideal model delta sigma weight residual 120.03 128.16 -8.13 9.90e-01 1.02e+00 6.74e+01 angle pdb=" C VAL C 75 " pdb=" N PRO C 76 " pdb=" CA PRO C 76 " ideal model delta sigma weight residual 120.03 128.04 -8.01 9.90e-01 1.02e+00 6.55e+01 angle pdb=" C VAL B 75 " pdb=" N PRO B 76 " pdb=" CA PRO B 76 " ideal model delta sigma weight residual 120.03 128.00 -7.97 9.90e-01 1.02e+00 6.49e+01 angle pdb=" C ALA C 219 " pdb=" N PRO C 220 " pdb=" CA PRO C 220 " ideal model delta sigma weight residual 120.52 127.81 -7.29 9.90e-01 1.02e+00 5.42e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.87 127.52 -7.65 1.04e+00 9.25e-01 5.41e+01 ... (remaining 28006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10813 17.96 - 35.93: 285 35.93 - 53.89: 79 53.89 - 71.85: 32 71.85 - 89.81: 5 Dihedral angle restraints: 11214 sinusoidal: 4530 harmonic: 6684 Sorted by residual: dihedral pdb=" CB CYS C 218 " pdb=" SG CYS C 218 " pdb=" SG CYS C 247 " pdb=" CB CYS C 247 " ideal model delta sinusoidal sigma weight residual 93.00 43.89 49.11 1 1.00e+01 1.00e-02 3.32e+01 dihedral pdb=" CB CYS B 218 " pdb=" SG CYS B 218 " pdb=" SG CYS B 247 " pdb=" CB CYS B 247 " ideal model delta sinusoidal sigma weight residual 93.00 43.92 49.08 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -132.14 46.14 1 1.00e+01 1.00e-02 2.95e+01 ... (remaining 11211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2524 0.108 - 0.217: 900 0.217 - 0.325: 133 0.325 - 0.433: 20 0.433 - 0.542: 2 Chirality restraints: 3579 Sorted by residual: chirality pdb=" C1 BMA v 3 " pdb=" O4 NAG v 2 " pdb=" C2 BMA v 3 " pdb=" O5 BMA v 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.96e+01 chirality pdb=" C1 BMA y 3 " pdb=" O4 NAG y 2 " pdb=" C2 BMA y 3 " pdb=" O5 BMA y 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.00e+01 ... (remaining 3576 not shown) Planarity restraints: 3393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 190 " 0.111 2.00e-02 2.50e+03 1.13e-01 1.61e+02 pdb=" CG ASN C 190 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN C 190 " -0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN C 190 " -0.175 2.00e-02 2.50e+03 pdb=" C1 NAG C 702 " 0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 190 " -0.107 2.00e-02 2.50e+03 1.09e-01 1.47e+02 pdb=" CG ASN A 190 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 190 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN A 190 " 0.167 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 190 " 0.106 2.00e-02 2.50e+03 1.08e-01 1.47e+02 pdb=" CG ASN B 190 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN B 190 " -0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN B 190 " -0.167 2.00e-02 2.50e+03 pdb=" C1 NAG B 702 " 0.130 2.00e-02 2.50e+03 ... (remaining 3390 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3190 2.74 - 3.28: 17887 3.28 - 3.82: 33184 3.82 - 4.36: 39825 4.36 - 4.90: 65381 Nonbonded interactions: 159467 Sorted by model distance: nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.198 3.040 nonbonded pdb=" O4 NAG C 704 " pdb=" O6 NAG C 704 " model vdw 2.248 3.040 nonbonded pdb=" O4 MAN T 9 " pdb=" O6 MAN T 9 " model vdw 2.265 3.040 nonbonded pdb=" O4 MAN h 9 " pdb=" O6 MAN h 9 " model vdw 2.269 3.040 nonbonded pdb=" O4 MAN v 9 " pdb=" O6 MAN v 9 " model vdw 2.299 3.040 ... (remaining 159462 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.160 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 0.221 20790 Z= 1.137 Angle : 1.777 11.918 28521 Z= 1.107 Chirality : 0.106 0.542 3579 Planarity : 0.009 0.047 3336 Dihedral : 9.570 89.815 6783 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.10 % Allowed : 0.34 % Favored : 99.56 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.17), residues: 2262 helix: -0.38 (0.25), residues: 354 sheet: 1.02 (0.19), residues: 684 loop : 1.01 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 31 TYR 0.050 0.007 TYR N 100O PHE 0.039 0.007 PHE L 67C TRP 0.039 0.009 TRP B 96 HIS 0.006 0.002 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.02074 / 1.10 (20607) covalent geometry : angle 1.73957 / 1.10 (28011) SS BOND : bond 0.04964 / 3.16 ( 39) SS BOND : angle 4.30291 / 2.73 ( 78) hydrogen bonds : bond 0.15800 / 10.45 ( 717) hydrogen bonds : angle 7.66935 / 5.34 ( 1866) link_ALPHA1-2 : bond 0.05633 / 3.03 ( 9) link_ALPHA1-2 : angle 2.83963 / 1.84 ( 27) link_ALPHA1-3 : bond 0.05726 / 3.66 ( 15) link_ALPHA1-3 : angle 2.77040 / 1.76 ( 45) link_ALPHA1-6 : bond 0.05708 / 3.58 ( 12) link_ALPHA1-6 : angle 2.74677 / 1.82 ( 36) link_BETA1-4 : bond 0.05424 / 3.61 ( 51) link_BETA1-4 : angle 3.77597 / 2.83 ( 153) link_NAG-ASN : bond 0.07843 / 5.08 ( 57) link_NAG-ASN : angle 2.19655 / 1.53 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 391 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 HIS cc_start: 0.6698 (t70) cc_final: 0.6400 (t-90) REVERT: H 91 TYR cc_start: 0.7703 (m-80) cc_final: 0.7449 (m-80) REVERT: B 180 ASP cc_start: 0.6989 (m-30) cc_final: 0.6787 (m-30) REVERT: M 49 TYR cc_start: 0.8053 (p90) cc_final: 0.7739 (p90) REVERT: M 104 LEU cc_start: 0.7808 (tp) cc_final: 0.7415 (tp) REVERT: N 24 VAL cc_start: 0.7996 (t) cc_final: 0.7698 (t) REVERT: N 91 TYR cc_start: 0.7558 (m-80) cc_final: 0.6873 (m-80) REVERT: N 92 CYS cc_start: 0.6264 (t) cc_final: 0.6014 (t) REVERT: C 180 ASP cc_start: 0.6995 (m-30) cc_final: 0.6787 (m-30) REVERT: O 37 GLN cc_start: 0.7963 (tt0) cc_final: 0.7717 (tt0) REVERT: O 49 TYR cc_start: 0.8086 (p90) cc_final: 0.7665 (p90) REVERT: O 52 ASN cc_start: 0.8730 (t0) cc_final: 0.8465 (t0) REVERT: O 78 VAL cc_start: 0.8416 (t) cc_final: 0.8176 (p) REVERT: O 79 GLU cc_start: 0.8091 (pt0) cc_final: 0.7827 (pm20) REVERT: P 91 TYR cc_start: 0.7735 (m-80) cc_final: 0.7470 (m-80) outliers start: 2 outliers final: 2 residues processed: 393 average time/residue: 0.1776 time to fit residues: 101.3638 Evaluate side-chains 194 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 192 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain C residue 138 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 HIS A 543 ASN B 105 HIS B 543 ASN N 32 ASN C 105 HIS C 478 ASN P 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.109590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.078745 restraints weight = 40926.739| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.61 r_work: 0.2962 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20790 Z= 0.170 Angle : 0.729 9.171 28521 Z= 0.361 Chirality : 0.047 0.243 3579 Planarity : 0.004 0.052 3336 Dihedral : 5.111 27.790 2482 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.06 % Favored : 98.85 % Rotamer: Outliers : 2.19 % Allowed : 6.38 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.17), residues: 2262 helix: 0.84 (0.26), residues: 363 sheet: 0.77 (0.18), residues: 690 loop : 0.61 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 476 TYR 0.024 0.002 TYR H 33 PHE 0.020 0.002 PHE A 383 TRP 0.027 0.002 TRP H 36 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (20607) covalent geometry : angle 0.68202 / 0.35 (28011) SS BOND : bond 0.00348 / 0.24 ( 39) SS BOND : angle 1.94582 / 1.23 ( 78) hydrogen bonds : bond 0.04743 / 3.15 ( 717) hydrogen bonds : angle 6.10959 / 4.31 ( 1866) link_ALPHA1-2 : bond 0.00462 / 0.22 ( 9) link_ALPHA1-2 : angle 1.66154 / 1.05 ( 27) link_ALPHA1-3 : bond 0.00693 / 0.44 ( 15) link_ALPHA1-3 : angle 1.53742 / 0.93 ( 45) link_ALPHA1-6 : bond 0.00609 / 0.38 ( 12) link_ALPHA1-6 : angle 1.65578 / 1.04 ( 36) link_BETA1-4 : bond 0.00712 / 0.47 ( 51) link_BETA1-4 : angle 2.48426 / 1.91 ( 153) link_NAG-ASN : bond 0.00306 / 0.20 ( 57) link_NAG-ASN : angle 1.88215 / 1.34 ( 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 303 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 258 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLN cc_start: 0.7323 (mm-40) cc_final: 0.6207 (mt0) REVERT: L 25 GLU cc_start: 0.7888 (tt0) cc_final: 0.7441 (tt0) REVERT: L 79 GLU cc_start: 0.7522 (pm20) cc_final: 0.7237 (pm20) REVERT: L 87 TYR cc_start: 0.8356 (m-80) cc_final: 0.8021 (m-80) REVERT: L 95 ARG cc_start: 0.7996 (mtt-85) cc_final: 0.7747 (mtt-85) REVERT: H 5 GLN cc_start: 0.8617 (tm-30) cc_final: 0.7718 (pm20) REVERT: H 6 GLU cc_start: 0.6289 (mp0) cc_final: 0.4458 (mp0) REVERT: H 13 LYS cc_start: 0.9089 (ttpt) cc_final: 0.8766 (ptpp) REVERT: H 64 LYS cc_start: 0.7007 (ttpp) cc_final: 0.6805 (ttpp) REVERT: H 100 ASP cc_start: 0.8380 (t0) cc_final: 0.8141 (t0) REVERT: H 103 LYS cc_start: 0.7347 (mmmt) cc_final: 0.7062 (mmmt) REVERT: B 54 CYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6929 (p) REVERT: B 82 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7323 (pm20) REVERT: B 180 ASP cc_start: 0.8196 (m-30) cc_final: 0.7974 (m-30) REVERT: M 17 GLN cc_start: 0.7387 (mm-40) cc_final: 0.6183 (mt0) REVERT: M 49 TYR cc_start: 0.8164 (p90) cc_final: 0.7546 (p90) REVERT: N 5 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8691 (tm-30) REVERT: N 13 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8543 (ttpt) REVERT: N 81 ARG cc_start: 0.8409 (ttp80) cc_final: 0.7626 (ttm-80) REVERT: C 54 CYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6425 (p) REVERT: C 69 TRP cc_start: 0.8206 (m-90) cc_final: 0.7056 (m-90) REVERT: C 82 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7527 (pm20) REVERT: C 180 ASP cc_start: 0.8332 (m-30) cc_final: 0.8096 (m-30) REVERT: O 17 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6232 (mt0) REVERT: O 36 TYR cc_start: 0.8638 (m-80) cc_final: 0.8190 (m-80) REVERT: O 49 TYR cc_start: 0.7878 (p90) cc_final: 0.7077 (p90) REVERT: O 87 TYR cc_start: 0.8270 (m-80) cc_final: 0.7951 (m-80) REVERT: P 5 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8614 (tm-30) REVERT: P 81 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7932 (ttp80) REVERT: P 91 TYR cc_start: 0.8155 (m-80) cc_final: 0.7705 (m-80) outliers start: 45 outliers final: 22 residues processed: 291 average time/residue: 0.1627 time to fit residues: 70.6502 Evaluate side-chains 236 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 18 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 211 optimal weight: 0.0770 chunk 54 optimal weight: 20.0000 chunk 77 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 206 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.110543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.080840 restraints weight = 40466.090| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.38 r_work: 0.2987 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20790 Z= 0.139 Angle : 0.630 7.940 28521 Z= 0.310 Chirality : 0.044 0.184 3579 Planarity : 0.004 0.042 3336 Dihedral : 4.804 26.341 2478 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.78 % Allowed : 7.80 % Favored : 89.42 % 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: 0.80 (0.17), residues: 2262 helix: 1.28 (0.27), residues: 366 sheet: 0.64 (0.19), residues: 702 loop : 0.36 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 476 TYR 0.022 0.001 TYR P 33 PHE 0.013 0.002 PHE H 100K TRP 0.031 0.002 TRP H 36 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (20607) covalent geometry : angle 0.59260 / 0.30 (28011) SS BOND : bond 0.00428 / 0.24 ( 39) SS BOND : angle 1.75488 / 1.09 ( 78) hydrogen bonds : bond 0.03916 / 2.59 ( 717) hydrogen bonds : angle 5.61680 / 3.99 ( 1866) link_ALPHA1-2 : bond 0.00561 / 0.28 ( 9) link_ALPHA1-2 : angle 1.58964 / 1.00 ( 27) link_ALPHA1-3 : bond 0.00642 / 0.41 ( 15) link_ALPHA1-3 : angle 1.49522 / 0.92 ( 45) link_ALPHA1-6 : bond 0.00593 / 0.37 ( 12) link_ALPHA1-6 : angle 1.46933 / 0.90 ( 36) link_BETA1-4 : bond 0.00673 / 0.45 ( 51) link_BETA1-4 : angle 2.08866 / 1.62 ( 153) link_NAG-ASN : bond 0.00175 / 0.11 ( 57) link_NAG-ASN : angle 1.38170 / 0.95 ( 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 305 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 248 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLN cc_start: 0.7700 (mm-40) cc_final: 0.6625 (mt0) REVERT: L 26 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8476 (pm20) REVERT: L 87 TYR cc_start: 0.8657 (m-80) cc_final: 0.8411 (m-80) REVERT: H 5 GLN cc_start: 0.8527 (tm-30) cc_final: 0.7815 (mp10) REVERT: H 31 ASP cc_start: 0.8891 (t0) cc_final: 0.8541 (t0) REVERT: H 46 GLU cc_start: 0.8408 (tp30) cc_final: 0.8140 (tp30) REVERT: H 81 ARG cc_start: 0.8419 (ttp80) cc_final: 0.7931 (ttm-80) REVERT: B 180 ASP cc_start: 0.7596 (m-30) cc_final: 0.7393 (m-30) REVERT: M 17 GLN cc_start: 0.7775 (mm-40) cc_final: 0.6645 (mt0) REVERT: M 49 TYR cc_start: 0.8199 (p90) cc_final: 0.7634 (p90) REVERT: M 75 ILE cc_start: 0.6874 (mt) cc_final: 0.6626 (mt) REVERT: N 81 ARG cc_start: 0.8342 (ttp80) cc_final: 0.7977 (ttp-110) REVERT: C 54 CYS cc_start: 0.7058 (OUTLIER) cc_final: 0.6839 (p) REVERT: C 82 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7648 (pm20) REVERT: C 180 ASP cc_start: 0.7808 (m-30) cc_final: 0.7581 (m-30) REVERT: O 17 GLN cc_start: 0.7653 (mm-40) cc_final: 0.6734 (mt0) REVERT: O 36 TYR cc_start: 0.8482 (m-80) cc_final: 0.8167 (m-80) REVERT: O 49 TYR cc_start: 0.7989 (p90) cc_final: 0.7414 (p90) REVERT: O 87 TYR cc_start: 0.8620 (m-80) cc_final: 0.8409 (m-80) REVERT: P 41 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8661 (mm) REVERT: P 91 TYR cc_start: 0.8002 (m-80) cc_final: 0.7439 (m-80) outliers start: 57 outliers final: 27 residues processed: 287 average time/residue: 0.1560 time to fit residues: 67.5048 Evaluate side-chains 239 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 18 LEU Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 92 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 153 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 223 optimal weight: 30.0000 chunk 182 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.109637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.079920 restraints weight = 40664.270| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.35 r_work: 0.2961 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20790 Z= 0.150 Angle : 0.617 7.954 28521 Z= 0.302 Chirality : 0.044 0.182 3579 Planarity : 0.004 0.040 3336 Dihedral : 4.709 31.520 2478 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.97 % Allowed : 7.94 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.17), residues: 2262 helix: 1.44 (0.28), residues: 366 sheet: 0.61 (0.19), residues: 687 loop : 0.15 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 30 TYR 0.019 0.001 TYR N 33 PHE 0.016 0.002 PHE H 100K TRP 0.042 0.002 TRP N 36 HIS 0.011 0.001 HIS P 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (20607) covalent geometry : angle 0.58057 / 0.29 (28011) SS BOND : bond 0.00385 / 0.22 ( 39) SS BOND : angle 1.69461 / 1.16 ( 78) hydrogen bonds : bond 0.03655 / 2.43 ( 717) hydrogen bonds : angle 5.44043 / 3.86 ( 1866) link_ALPHA1-2 : bond 0.00454 / 0.22 ( 9) link_ALPHA1-2 : angle 1.62368 / 1.03 ( 27) link_ALPHA1-3 : bond 0.00517 / 0.32 ( 15) link_ALPHA1-3 : angle 1.52904 / 0.95 ( 45) link_ALPHA1-6 : bond 0.00500 / 0.31 ( 12) link_ALPHA1-6 : angle 1.53899 / 0.95 ( 36) link_BETA1-4 : bond 0.00621 / 0.41 ( 51) link_BETA1-4 : angle 2.02681 / 1.56 ( 153) link_NAG-ASN : bond 0.00194 / 0.12 ( 57) link_NAG-ASN : angle 1.29446 / 0.90 ( 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 282 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 221 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLN cc_start: 0.7928 (mm-40) cc_final: 0.6962 (pt0) REVERT: L 26 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8397 (pm20) REVERT: H 5 GLN cc_start: 0.8592 (tm-30) cc_final: 0.7754 (mp10) REVERT: H 6 GLU cc_start: 0.6073 (mp0) cc_final: 0.5854 (mp0) REVERT: H 81 ARG cc_start: 0.8387 (ttp80) cc_final: 0.8039 (mtm110) REVERT: M 49 TYR cc_start: 0.8196 (p90) cc_final: 0.7601 (p90) REVERT: M 75 ILE cc_start: 0.6945 (mt) cc_final: 0.6687 (mt) REVERT: N 5 GLN cc_start: 0.8806 (tm-30) cc_final: 0.7840 (pm20) REVERT: N 6 GLU cc_start: 0.7087 (mp0) cc_final: 0.5219 (mp0) REVERT: N 81 ARG cc_start: 0.8358 (ttp80) cc_final: 0.8035 (ttp-110) REVERT: C 54 CYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6783 (p) REVERT: C 82 GLN cc_start: 0.7998 (pt0) cc_final: 0.7735 (pm20) REVERT: C 95 MET cc_start: 0.9145 (ptm) cc_final: 0.8706 (ttp) REVERT: O 17 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7176 (mt0) REVERT: O 36 TYR cc_start: 0.8443 (m-80) cc_final: 0.8121 (m-80) REVERT: O 49 TYR cc_start: 0.8013 (p90) cc_final: 0.7435 (p90) REVERT: P 41 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8697 (mm) REVERT: P 81 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7700 (ttm-80) REVERT: P 91 TYR cc_start: 0.7974 (m-80) cc_final: 0.7521 (m-80) outliers start: 61 outliers final: 39 residues processed: 260 average time/residue: 0.1632 time to fit residues: 63.8768 Evaluate side-chains 237 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 18 LEU Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 89 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 136 optimal weight: 9.9990 chunk 217 optimal weight: 30.0000 chunk 130 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 92 optimal weight: 0.7980 chunk 141 optimal weight: 20.0000 chunk 32 optimal weight: 0.2980 chunk 173 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 37 GLN N 97 HIS O 109 GLN P 97 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.109609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.080050 restraints weight = 40146.491| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.36 r_work: 0.2974 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20790 Z= 0.126 Angle : 0.595 7.373 28521 Z= 0.291 Chirality : 0.044 0.174 3579 Planarity : 0.004 0.038 3336 Dihedral : 4.722 30.674 2478 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.58 % Allowed : 8.53 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.17), residues: 2262 helix: 1.57 (0.28), residues: 366 sheet: 0.67 (0.19), residues: 666 loop : 0.10 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 61 TYR 0.016 0.001 TYR N 33 PHE 0.015 0.001 PHE M 9 TRP 0.041 0.001 TRP P 36 HIS 0.012 0.001 HIS N 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (20607) covalent geometry : angle 0.55655 / 0.28 (28011) SS BOND : bond 0.00425 / 0.23 ( 39) SS BOND : angle 2.08639 / 1.34 ( 78) hydrogen bonds : bond 0.03373 / 2.22 ( 717) hydrogen bonds : angle 5.23995 / 3.72 ( 1866) link_ALPHA1-2 : bond 0.00513 / 0.25 ( 9) link_ALPHA1-2 : angle 1.60197 / 1.02 ( 27) link_ALPHA1-3 : bond 0.00549 / 0.35 ( 15) link_ALPHA1-3 : angle 1.51206 / 0.94 ( 45) link_ALPHA1-6 : bond 0.00512 / 0.31 ( 12) link_ALPHA1-6 : angle 1.49092 / 0.92 ( 36) link_BETA1-4 : bond 0.00637 / 0.42 ( 51) link_BETA1-4 : angle 1.95670 / 1.51 ( 153) link_NAG-ASN : bond 0.00153 / 0.10 ( 57) link_NAG-ASN : angle 1.18028 / 0.82 ( 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 265 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 212 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 HIS cc_start: 0.8190 (m90) cc_final: 0.7961 (m170) REVERT: L 17 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7002 (pt0) REVERT: H 5 GLN cc_start: 0.8708 (tm-30) cc_final: 0.7841 (mp10) REVERT: H 6 GLU cc_start: 0.6060 (mp0) cc_final: 0.5834 (mp0) REVERT: H 46 GLU cc_start: 0.8310 (tp30) cc_final: 0.8067 (tp30) REVERT: H 81 ARG cc_start: 0.8384 (ttp80) cc_final: 0.8050 (mtm110) REVERT: M 17 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7026 (mt0) REVERT: M 49 TYR cc_start: 0.8212 (p90) cc_final: 0.7599 (p90) REVERT: M 75 ILE cc_start: 0.6895 (mt) cc_final: 0.6683 (mt) REVERT: N 5 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8016 (mp10) REVERT: N 81 ARG cc_start: 0.8343 (ttp80) cc_final: 0.8030 (ttp-110) REVERT: C 82 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7740 (pm20) REVERT: C 95 MET cc_start: 0.9171 (ptm) cc_final: 0.8748 (ttp) REVERT: O 13 VAL cc_start: 0.8785 (m) cc_final: 0.8440 (t) REVERT: O 17 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7102 (mt0) REVERT: O 36 TYR cc_start: 0.8461 (m-80) cc_final: 0.8080 (m-80) REVERT: O 49 TYR cc_start: 0.7949 (p90) cc_final: 0.7424 (p90) REVERT: P 5 GLN cc_start: 0.8690 (tm-30) cc_final: 0.7989 (mp10) REVERT: P 6 GLU cc_start: 0.6917 (mp0) cc_final: 0.6588 (mp0) REVERT: P 41 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8703 (mm) REVERT: P 81 ARG cc_start: 0.8349 (ttp80) cc_final: 0.7823 (ttm-80) REVERT: P 91 TYR cc_start: 0.7951 (m-80) cc_final: 0.7692 (m-80) outliers start: 53 outliers final: 35 residues processed: 245 average time/residue: 0.1506 time to fit residues: 55.2227 Evaluate side-chains 225 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 18 LEU Chi-restraints excluded: chain P residue 41 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 12 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 217 optimal weight: 40.0000 chunk 156 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 163 optimal weight: 0.0770 chunk 199 optimal weight: 8.9990 chunk 204 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 97 optimal weight: 0.0010 overall best weight: 2.6150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 97 HIS P 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.108422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.078738 restraints weight = 40413.003| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.34 r_work: 0.2939 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20790 Z= 0.163 Angle : 0.616 7.948 28521 Z= 0.299 Chirality : 0.044 0.179 3579 Planarity : 0.004 0.039 3336 Dihedral : 4.624 27.599 2478 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.63 % Allowed : 9.55 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.18), residues: 2262 helix: 1.88 (0.28), residues: 348 sheet: 0.67 (0.20), residues: 678 loop : 0.04 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 95 TYR 0.015 0.001 TYR N 33 PHE 0.016 0.002 PHE P 100K TRP 0.041 0.002 TRP N 36 HIS 0.012 0.001 HIS P 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (20607) covalent geometry : angle 0.58126 / 0.29 (28011) SS BOND : bond 0.00403 / 0.22 ( 39) SS BOND : angle 1.67462 / 1.10 ( 78) hydrogen bonds : bond 0.03476 / 2.28 ( 717) hydrogen bonds : angle 5.26655 / 3.75 ( 1866) link_ALPHA1-2 : bond 0.00470 / 0.22 ( 9) link_ALPHA1-2 : angle 1.60888 / 1.02 ( 27) link_ALPHA1-3 : bond 0.00441 / 0.28 ( 15) link_ALPHA1-3 : angle 1.57307 / 0.98 ( 45) link_ALPHA1-6 : bond 0.00434 / 0.26 ( 12) link_ALPHA1-6 : angle 1.55773 / 0.95 ( 36) link_BETA1-4 : bond 0.00600 / 0.40 ( 51) link_BETA1-4 : angle 1.98387 / 1.52 ( 153) link_NAG-ASN : bond 0.00195 / 0.13 ( 57) link_NAG-ASN : angle 1.28529 / 0.89 ( 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 247 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 193 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 HIS cc_start: 0.8234 (m90) cc_final: 0.7998 (m170) REVERT: A 434 MET cc_start: 0.8874 (ttp) cc_final: 0.8615 (ttt) REVERT: L 17 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7097 (pt0) REVERT: H 5 GLN cc_start: 0.8773 (tm-30) cc_final: 0.7942 (mp10) REVERT: H 46 GLU cc_start: 0.8364 (tp30) cc_final: 0.8007 (tp30) REVERT: H 81 ARG cc_start: 0.8356 (ttp80) cc_final: 0.8017 (mtm110) REVERT: M 17 GLN cc_start: 0.7955 (mm-40) cc_final: 0.6902 (mt0) REVERT: M 49 TYR cc_start: 0.8254 (p90) cc_final: 0.7736 (p90) REVERT: N 5 GLN cc_start: 0.8963 (tm-30) cc_final: 0.7897 (mp10) REVERT: N 6 GLU cc_start: 0.6785 (mp0) cc_final: 0.6328 (mp0) REVERT: N 81 ARG cc_start: 0.8309 (ttp80) cc_final: 0.8008 (ttp-110) REVERT: C 82 GLN cc_start: 0.8068 (pt0) cc_final: 0.7784 (pm20) REVERT: C 95 MET cc_start: 0.9278 (ptm) cc_final: 0.8908 (ttp) REVERT: O 17 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7182 (mt0) REVERT: O 49 TYR cc_start: 0.8031 (p90) cc_final: 0.7630 (p90) REVERT: O 105 ILE cc_start: 0.7568 (mt) cc_final: 0.7226 (mm) REVERT: P 5 GLN cc_start: 0.8668 (tm-30) cc_final: 0.7982 (mp10) REVERT: P 41 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8738 (mm) REVERT: P 81 ARG cc_start: 0.8325 (ttp80) cc_final: 0.7795 (ttm-80) REVERT: P 91 TYR cc_start: 0.7915 (m-80) cc_final: 0.7593 (m-80) outliers start: 54 outliers final: 39 residues processed: 226 average time/residue: 0.1616 time to fit residues: 55.5124 Evaluate side-chains 220 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 89 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 76 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 213 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 ASN A 543 ASN B 543 ASN N 97 HIS P 97 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.104384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.073481 restraints weight = 41597.639| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 4.02 r_work: 0.2847 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 20790 Z= 0.240 Angle : 0.680 7.741 28521 Z= 0.328 Chirality : 0.046 0.196 3579 Planarity : 0.005 0.050 3336 Dihedral : 4.802 29.403 2478 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.92 % Allowed : 9.45 % Favored : 87.62 % 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: 0.45 (0.18), residues: 2262 helix: 1.60 (0.28), residues: 348 sheet: 0.34 (0.19), residues: 696 loop : -0.03 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 95 TYR 0.020 0.002 TYR N 100M PHE 0.022 0.002 PHE P 100K TRP 0.046 0.002 TRP H 36 HIS 0.012 0.002 HIS P 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.24 (20607) covalent geometry : angle 0.64364 / 0.32 (28011) SS BOND : bond 0.00488 / 0.31 ( 39) SS BOND : angle 1.72737 / 1.11 ( 78) hydrogen bonds : bond 0.03884 / 2.56 ( 717) hydrogen bonds : angle 5.45504 / 3.88 ( 1866) link_ALPHA1-2 : bond 0.00381 / 0.18 ( 9) link_ALPHA1-2 : angle 1.63836 / 1.06 ( 27) link_ALPHA1-3 : bond 0.00297 / 0.18 ( 15) link_ALPHA1-3 : angle 1.66918 / 1.05 ( 45) link_ALPHA1-6 : bond 0.00351 / 0.21 ( 12) link_ALPHA1-6 : angle 1.70655 / 1.04 ( 36) link_BETA1-4 : bond 0.00581 / 0.39 ( 51) link_BETA1-4 : angle 2.07841 / 1.59 ( 153) link_NAG-ASN : bond 0.00323 / 0.22 ( 57) link_NAG-ASN : angle 1.50190 / 1.04 ( 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 262 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 202 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASN cc_start: 0.7915 (m110) cc_final: 0.7705 (m-40) REVERT: A 202 THR cc_start: 0.9182 (m) cc_final: 0.8955 (t) REVERT: A 352 HIS cc_start: 0.8456 (m90) cc_final: 0.8230 (m170) REVERT: A 434 MET cc_start: 0.9017 (ttp) cc_final: 0.8498 (ttt) REVERT: L 25 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7573 (tm-30) REVERT: L 26 GLU cc_start: 0.8486 (mp0) cc_final: 0.7994 (pm20) REVERT: L 42 GLN cc_start: 0.7455 (mt0) cc_final: 0.7114 (mp10) REVERT: L 83 GLU cc_start: 0.7569 (tp30) cc_final: 0.7293 (tp30) REVERT: H 5 GLN cc_start: 0.8936 (tm-30) cc_final: 0.7733 (mp10) REVERT: H 46 GLU cc_start: 0.8466 (tp30) cc_final: 0.8219 (tp30) REVERT: H 81 ARG cc_start: 0.8429 (ttp80) cc_final: 0.8050 (mtm110) REVERT: B 475 MET cc_start: 0.8834 (mmm) cc_final: 0.8361 (mmp) REVERT: N 5 GLN cc_start: 0.9010 (tm-30) cc_final: 0.7903 (mp10) REVERT: N 6 GLU cc_start: 0.6623 (mp0) cc_final: 0.5916 (mp0) REVERT: N 43 LYS cc_start: 0.8517 (mmmm) cc_final: 0.8316 (mmmm) REVERT: N 81 ARG cc_start: 0.8371 (ttp80) cc_final: 0.8024 (ttp-110) REVERT: C 82 GLN cc_start: 0.8346 (pt0) cc_final: 0.7681 (pm20) REVERT: C 202 THR cc_start: 0.9173 (m) cc_final: 0.8912 (t) REVERT: O 60 ASP cc_start: 0.8535 (m-30) cc_final: 0.8261 (t0) REVERT: P 5 GLN cc_start: 0.8806 (tm-30) cc_final: 0.7873 (mp10) REVERT: P 6 GLU cc_start: 0.7156 (mp0) cc_final: 0.6136 (mp0) REVERT: P 41 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8771 (mm) REVERT: P 81 ARG cc_start: 0.8348 (ttp80) cc_final: 0.7796 (ttm-80) REVERT: P 91 TYR cc_start: 0.8161 (m-80) cc_final: 0.7724 (m-80) outliers start: 60 outliers final: 40 residues processed: 238 average time/residue: 0.1556 time to fit residues: 56.4549 Evaluate side-chains 224 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 89 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 110 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 217 optimal weight: 40.0000 chunk 197 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 97 HIS M 17 GLN N 97 HIS O 17 GLN P 97 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.105988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.075528 restraints weight = 41148.304| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.90 r_work: 0.2886 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20790 Z= 0.144 Angle : 0.629 10.218 28521 Z= 0.306 Chirality : 0.044 0.184 3579 Planarity : 0.004 0.058 3336 Dihedral : 4.875 32.935 2478 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.58 % Allowed : 9.89 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.18), residues: 2262 helix: 1.80 (0.29), residues: 348 sheet: 0.44 (0.19), residues: 690 loop : -0.09 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 95 TYR 0.015 0.001 TYR N 50 PHE 0.014 0.001 PHE H 100K TRP 0.047 0.001 TRP H 36 HIS 0.013 0.001 HIS H 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (20607) covalent geometry : angle 0.58882 / 0.30 (28011) SS BOND : bond 0.00424 / 0.29 ( 39) SS BOND : angle 2.32488 / 1.44 ( 78) hydrogen bonds : bond 0.03410 / 2.23 ( 717) hydrogen bonds : angle 5.26007 / 3.75 ( 1866) link_ALPHA1-2 : bond 0.00483 / 0.23 ( 9) link_ALPHA1-2 : angle 1.66759 / 1.07 ( 27) link_ALPHA1-3 : bond 0.00446 / 0.28 ( 15) link_ALPHA1-3 : angle 1.52149 / 0.96 ( 45) link_ALPHA1-6 : bond 0.00453 / 0.27 ( 12) link_ALPHA1-6 : angle 1.54439 / 0.95 ( 36) link_BETA1-4 : bond 0.00603 / 0.40 ( 51) link_BETA1-4 : angle 1.94336 / 1.51 ( 153) link_NAG-ASN : bond 0.00164 / 0.11 ( 57) link_NAG-ASN : angle 1.30457 / 0.90 ( 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 251 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 198 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 THR cc_start: 0.9068 (m) cc_final: 0.8850 (t) REVERT: A 352 HIS cc_start: 0.8477 (m90) cc_final: 0.8257 (m170) REVERT: A 434 MET cc_start: 0.8944 (ttp) cc_final: 0.8456 (ttt) REVERT: L 17 GLN cc_start: 0.7956 (mp10) cc_final: 0.7124 (pt0) REVERT: L 42 GLN cc_start: 0.7426 (mt0) cc_final: 0.7109 (mp10) REVERT: L 83 GLU cc_start: 0.7577 (tp30) cc_final: 0.7287 (tp30) REVERT: L 87 TYR cc_start: 0.8097 (m-80) cc_final: 0.7872 (m-80) REVERT: H 5 GLN cc_start: 0.8763 (tm-30) cc_final: 0.7656 (mp10) REVERT: H 46 GLU cc_start: 0.8475 (tp30) cc_final: 0.8016 (tp30) REVERT: H 81 ARG cc_start: 0.8417 (ttp80) cc_final: 0.8073 (mtm110) REVERT: B 475 MET cc_start: 0.8770 (mmm) cc_final: 0.8194 (mmp) REVERT: M 17 GLN cc_start: 0.8049 (mm110) cc_final: 0.6785 (pt0) REVERT: N 5 GLN cc_start: 0.8999 (tm-30) cc_final: 0.7872 (mp10) REVERT: N 6 GLU cc_start: 0.6377 (mp0) cc_final: 0.5711 (mp0) REVERT: N 43 LYS cc_start: 0.8568 (mmmm) cc_final: 0.8330 (mmmm) REVERT: N 81 ARG cc_start: 0.8350 (ttp80) cc_final: 0.7997 (ttp-110) REVERT: C 54 CYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7281 (p) REVERT: C 66 ARG cc_start: 0.7044 (mtp85) cc_final: 0.6694 (mmt180) REVERT: C 82 GLN cc_start: 0.8368 (pt0) cc_final: 0.7673 (pm20) REVERT: C 202 THR cc_start: 0.9085 (m) cc_final: 0.8822 (t) REVERT: C 626 MET cc_start: 0.8042 (mtp) cc_final: 0.7717 (ttm) REVERT: O 31 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8555 (mtp85) REVERT: O 60 ASP cc_start: 0.8504 (m-30) cc_final: 0.8212 (t0) REVERT: P 5 GLN cc_start: 0.8785 (tm-30) cc_final: 0.7734 (mp10) REVERT: P 6 GLU cc_start: 0.7137 (mp0) cc_final: 0.6031 (mp0) REVERT: P 41 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8760 (mm) REVERT: P 81 ARG cc_start: 0.8331 (ttp80) cc_final: 0.7859 (ttp-110) REVERT: P 91 TYR cc_start: 0.8155 (m-80) cc_final: 0.7698 (m-80) outliers start: 53 outliers final: 38 residues processed: 236 average time/residue: 0.1456 time to fit residues: 52.6734 Evaluate side-chains 227 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 97 HIS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 89 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 85 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 208 optimal weight: 30.0000 chunk 148 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 201 optimal weight: 0.0470 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 97 HIS N 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.106751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.076535 restraints weight = 41049.336| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 4.10 r_work: 0.2893 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20790 Z= 0.122 Angle : 0.601 8.161 28521 Z= 0.294 Chirality : 0.043 0.172 3579 Planarity : 0.004 0.049 3336 Dihedral : 4.749 30.624 2478 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.39 % Allowed : 9.99 % Favored : 87.62 % 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: 0.58 (0.18), residues: 2262 helix: 1.95 (0.29), residues: 348 sheet: 0.55 (0.20), residues: 672 loop : -0.11 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 100 TYR 0.016 0.001 TYR N 50 PHE 0.012 0.001 PHE P 100K TRP 0.042 0.001 TRP N 36 HIS 0.025 0.001 HIS N 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (20607) covalent geometry : angle 0.56208 / 0.28 (28011) SS BOND : bond 0.00455 / 0.26 ( 39) SS BOND : angle 2.26665 / 1.40 ( 78) hydrogen bonds : bond 0.03197 / 2.08 ( 717) hydrogen bonds : angle 5.10179 / 3.65 ( 1866) link_ALPHA1-2 : bond 0.00518 / 0.25 ( 9) link_ALPHA1-2 : angle 1.66681 / 1.07 ( 27) link_ALPHA1-3 : bond 0.00484 / 0.30 ( 15) link_ALPHA1-3 : angle 1.50344 / 0.94 ( 45) link_ALPHA1-6 : bond 0.00470 / 0.27 ( 12) link_ALPHA1-6 : angle 1.49210 / 0.92 ( 36) link_BETA1-4 : bond 0.00614 / 0.41 ( 51) link_BETA1-4 : angle 1.89790 / 1.47 ( 153) link_NAG-ASN : bond 0.00145 / 0.09 ( 57) link_NAG-ASN : angle 1.22436 / 0.84 ( 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 251 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.6981 (mtp85) cc_final: 0.6637 (mmt180) REVERT: A 352 HIS cc_start: 0.8470 (m90) cc_final: 0.8251 (m170) REVERT: A 434 MET cc_start: 0.8921 (ttp) cc_final: 0.8427 (ttt) REVERT: A 626 MET cc_start: 0.8133 (mtp) cc_final: 0.7808 (ttm) REVERT: L 13 VAL cc_start: 0.8529 (t) cc_final: 0.8321 (t) REVERT: L 17 GLN cc_start: 0.8061 (mp10) cc_final: 0.7206 (pt0) REVERT: L 26 GLU cc_start: 0.8656 (pt0) cc_final: 0.8238 (pm20) REVERT: L 42 GLN cc_start: 0.7392 (mt0) cc_final: 0.7047 (mp10) REVERT: L 83 GLU cc_start: 0.7624 (tp30) cc_final: 0.7308 (tp30) REVERT: H 5 GLN cc_start: 0.8735 (tm-30) cc_final: 0.7627 (mp10) REVERT: H 46 GLU cc_start: 0.8445 (tp30) cc_final: 0.8169 (tp30) REVERT: H 81 ARG cc_start: 0.8387 (ttp80) cc_final: 0.8076 (mtm110) REVERT: B 66 ARG cc_start: 0.7020 (mtp85) cc_final: 0.6662 (mmt180) REVERT: B 475 MET cc_start: 0.8679 (mmm) cc_final: 0.8139 (mmp) REVERT: M 17 GLN cc_start: 0.8022 (mm110) cc_final: 0.6747 (pt0) REVERT: N 5 GLN cc_start: 0.8989 (tm-30) cc_final: 0.7860 (mp10) REVERT: N 6 GLU cc_start: 0.6219 (mp0) cc_final: 0.5567 (mp0) REVERT: N 38 ARG cc_start: 0.7109 (ptm-80) cc_final: 0.6897 (ptm-80) REVERT: N 43 LYS cc_start: 0.8547 (mmmm) cc_final: 0.8304 (mmmm) REVERT: N 81 ARG cc_start: 0.8307 (ttp80) cc_final: 0.8012 (ttp-110) REVERT: C 66 ARG cc_start: 0.7098 (mtp85) cc_final: 0.6741 (mmt180) REVERT: C 82 GLN cc_start: 0.8330 (pt0) cc_final: 0.7640 (pm20) REVERT: C 202 THR cc_start: 0.9016 (m) cc_final: 0.8736 (t) REVERT: C 626 MET cc_start: 0.8040 (mtp) cc_final: 0.7703 (ttm) REVERT: O 60 ASP cc_start: 0.8516 (m-30) cc_final: 0.8235 (t0) REVERT: P 5 GLN cc_start: 0.8766 (tm-30) cc_final: 0.7698 (mp10) REVERT: P 6 GLU cc_start: 0.7166 (mp0) cc_final: 0.5914 (mp0) REVERT: P 41 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8757 (mm) REVERT: P 81 ARG cc_start: 0.8353 (ttp80) cc_final: 0.7902 (ttp-110) REVERT: P 91 TYR cc_start: 0.8166 (m-80) cc_final: 0.7686 (m-80) outliers start: 49 outliers final: 36 residues processed: 236 average time/residue: 0.1481 time to fit residues: 53.1536 Evaluate side-chains 231 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 97 HIS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 89 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 16 optimal weight: 7.9990 chunk 187 optimal weight: 0.6980 chunk 139 optimal weight: 30.0000 chunk 112 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 168 optimal weight: 0.0670 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 97 HIS N 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.107042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.076267 restraints weight = 41452.680| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.98 r_work: 0.2899 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20790 Z= 0.125 Angle : 0.604 8.302 28521 Z= 0.295 Chirality : 0.043 0.168 3579 Planarity : 0.004 0.047 3336 Dihedral : 4.704 29.136 2478 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.10 % Allowed : 10.33 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 2262 helix: 2.03 (0.29), residues: 348 sheet: 0.52 (0.20), residues: 678 loop : -0.10 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 61 TYR 0.016 0.001 TYR N 50 PHE 0.013 0.001 PHE H 100K TRP 0.069 0.002 TRP P 36 HIS 0.024 0.001 HIS N 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (20607) covalent geometry : angle 0.56648 / 0.28 (28011) SS BOND : bond 0.00390 / 0.22 ( 39) SS BOND : angle 2.20792 / 1.37 ( 78) hydrogen bonds : bond 0.03166 / 2.06 ( 717) hydrogen bonds : angle 5.05435 / 3.62 ( 1866) link_ALPHA1-2 : bond 0.00511 / 0.24 ( 9) link_ALPHA1-2 : angle 1.64896 / 1.05 ( 27) link_ALPHA1-3 : bond 0.00513 / 0.33 ( 15) link_ALPHA1-3 : angle 1.51890 / 0.95 ( 45) link_ALPHA1-6 : bond 0.00488 / 0.30 ( 12) link_ALPHA1-6 : angle 1.49992 / 0.92 ( 36) link_BETA1-4 : bond 0.00609 / 0.41 ( 51) link_BETA1-4 : angle 1.89051 / 1.46 ( 153) link_NAG-ASN : bond 0.00142 / 0.09 ( 57) link_NAG-ASN : angle 1.20353 / 0.83 ( 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 240 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7036 (mtp85) cc_final: 0.6713 (mmt180) REVERT: A 103 GLN cc_start: 0.8745 (tp40) cc_final: 0.8232 (tt0) REVERT: A 352 HIS cc_start: 0.8454 (m90) cc_final: 0.8238 (m170) REVERT: A 434 MET cc_start: 0.8917 (ttp) cc_final: 0.8392 (ttt) REVERT: A 626 MET cc_start: 0.8105 (mtp) cc_final: 0.7823 (ttm) REVERT: L 17 GLN cc_start: 0.8109 (mp10) cc_final: 0.7152 (pt0) REVERT: L 26 GLU cc_start: 0.8662 (pt0) cc_final: 0.8254 (pm20) REVERT: H 5 GLN cc_start: 0.8730 (tm-30) cc_final: 0.7640 (mp10) REVERT: H 46 GLU cc_start: 0.8499 (tp30) cc_final: 0.8018 (tp30) REVERT: H 81 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8121 (mtm110) REVERT: B 66 ARG cc_start: 0.7055 (mtp85) cc_final: 0.6714 (mmt180) REVERT: B 475 MET cc_start: 0.8664 (mmm) cc_final: 0.8197 (mmp) REVERT: M 17 GLN cc_start: 0.8117 (mm110) cc_final: 0.6815 (pt0) REVERT: M 60 ASP cc_start: 0.8368 (m-30) cc_final: 0.8101 (t0) REVERT: N 5 GLN cc_start: 0.8920 (tm-30) cc_final: 0.7803 (mp10) REVERT: N 6 GLU cc_start: 0.6306 (mp0) cc_final: 0.5721 (mp0) REVERT: N 43 LYS cc_start: 0.8533 (mmmm) cc_final: 0.8289 (mmmm) REVERT: N 81 ARG cc_start: 0.8302 (ttp80) cc_final: 0.8030 (ttp-110) REVERT: C 66 ARG cc_start: 0.7135 (mtp85) cc_final: 0.6760 (mmt180) REVERT: C 82 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7702 (pm20) REVERT: C 103 GLN cc_start: 0.8720 (tp40) cc_final: 0.8322 (tt0) REVERT: C 202 THR cc_start: 0.8971 (m) cc_final: 0.8692 (t) REVERT: C 626 MET cc_start: 0.8030 (mtp) cc_final: 0.7806 (ttm) REVERT: O 60 ASP cc_start: 0.8411 (m-30) cc_final: 0.8171 (t0) REVERT: O 95 ARG cc_start: 0.8296 (mmt90) cc_final: 0.7998 (mtt-85) REVERT: P 5 GLN cc_start: 0.8761 (tm-30) cc_final: 0.7763 (mp10) REVERT: P 41 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8759 (mm) REVERT: P 81 ARG cc_start: 0.8338 (ttp80) cc_final: 0.7905 (ttp-110) REVERT: P 91 TYR cc_start: 0.8157 (m-80) cc_final: 0.7859 (m-80) outliers start: 43 outliers final: 35 residues processed: 225 average time/residue: 0.1529 time to fit residues: 52.2835 Evaluate side-chains 231 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 89 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 44 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 156 optimal weight: 4.9990 chunk 57 optimal weight: 0.0000 chunk 35 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 0.0770 chunk 225 optimal weight: 2.9990 overall best weight: 0.9746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 97 HIS N 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.107910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.077653 restraints weight = 40828.645| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.89 r_work: 0.2935 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20790 Z= 0.109 Angle : 0.582 8.222 28521 Z= 0.286 Chirality : 0.043 0.163 3579 Planarity : 0.004 0.042 3336 Dihedral : 4.567 27.087 2478 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.80 % Allowed : 10.82 % Favored : 87.38 % 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: 0.72 (0.18), residues: 2262 helix: 2.50 (0.29), residues: 330 sheet: 0.61 (0.20), residues: 672 loop : -0.09 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 30 TYR 0.017 0.001 TYR N 50 PHE 0.013 0.001 PHE C 53 TRP 0.058 0.001 TRP P 36 HIS 0.015 0.001 HIS N 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (20607) covalent geometry : angle 0.54746 / 0.28 (28011) SS BOND : bond 0.00386 / 0.24 ( 39) SS BOND : angle 1.96411 / 1.23 ( 78) hydrogen bonds : bond 0.02935 / 1.90 ( 717) hydrogen bonds : angle 4.88248 / 3.50 ( 1866) link_ALPHA1-2 : bond 0.00554 / 0.27 ( 9) link_ALPHA1-2 : angle 1.62512 / 1.04 ( 27) link_ALPHA1-3 : bond 0.00558 / 0.36 ( 15) link_ALPHA1-3 : angle 1.50114 / 0.94 ( 45) link_ALPHA1-6 : bond 0.00513 / 0.31 ( 12) link_ALPHA1-6 : angle 1.45473 / 0.90 ( 36) link_BETA1-4 : bond 0.00629 / 0.42 ( 51) link_BETA1-4 : angle 1.83904 / 1.42 ( 153) link_NAG-ASN : bond 0.00145 / 0.09 ( 57) link_NAG-ASN : angle 1.11067 / 0.77 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4140.66 seconds wall clock time: 72 minutes 11.81 seconds (4331.81 seconds total)