Starting phenix.real_space_refine on Fri Mar 6 08:20:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n28_24128/03_2026/7n28_24128.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n28_24128/03_2026/7n28_24128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n28_24128/03_2026/7n28_24128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n28_24128/03_2026/7n28_24128.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n28_24128/03_2026/7n28_24128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n28_24128/03_2026/7n28_24128.map" } resolution = 4.2 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= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 143 5.16 5 C 18487 2.51 5 N 4838 2.21 5 O 5990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29461 Number of models: 1 Model: "" Number of chains: 58 Chain: "A" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3731 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 24, 'TRANS': 447} Chain: "C" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1676 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "D" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1603 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Chain: "F" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3731 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 24, 'TRANS': 447} Chain: "G" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3731 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 24, 'TRANS': 447} Chain: "J" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1676 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "K" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1603 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Chain: "S" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1676 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "U" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1603 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Chain: "X" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1684 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 209} Chain breaks: 1 Chain: "Y" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "M" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain breaks: 1 Chain: "B" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain breaks: 1 Chain: "N" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "O" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "n" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 117 Unusual residues: {'NAG': 8, 'PO4': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 150 Unusual residues: {'NAG': 10, 'PO4': 2} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.88, per 1000 atoms: 0.23 Number of scatterers: 29461 At special positions: 0 Unit cell: (184.62, 178.5, 181.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 143 16.00 P 3 15.00 O 5990 8.00 N 4838 7.00 C 18487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=52, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 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=2.03 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 B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.04 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.04 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS M 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS N 605 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 140 " - pdb=" SG CYS J 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS S 140 " - pdb=" SG CYS S 196 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=2.03 Simple disulfide: pdb=" SG CYS U 134 " - pdb=" SG CYS U 194 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.03 Simple disulfide: pdb=" SG CYS X 152 " - pdb=" SG CYS X 208 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 134 " - pdb=" SG CYS Y 194 " distance=2.03 Simple disulfide: pdb=" SG CYS M 598 " - pdb=" SG CYS M 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS N 598 " - pdb=" SG CYS N 604 " 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=1, symmetry=0 Links applied ALPHA1-2 " MAN L 4 " - " MAN L 5 " " MAN L 5 " - " MAN L 6 " " MAN m 4 " - " MAN m 5 " ALPHA1-3 " BMA L 3 " - " MAN L 4 " " MAN L 7 " - " MAN L 8 " " BMA O 3 " - " MAN O 7 " " MAN O 4 " - " MAN O 5 " " BMA e 3 " - " MAN e 7 " " MAN e 4 " - " MAN e 5 " " BMA k 3 " - " MAN k 6 " " BMA m 3 " - " MAN m 4 " " BMA n 3 " - " MAN n 4 " ALPHA1-6 " BMA L 3 " - " MAN L 7 " " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 6 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " " MAN e 4 " - " MAN e 6 " " BMA k 3 " - " MAN k 4 " " MAN k 4 " - " MAN k 5 " " BMA m 3 " - " MAN m 6 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 T 1 " - " NAG T 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 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 d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " 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 m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 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 u 1 " - " NAG u 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 392 " " NAG A 605 " - " ASN A 149 " " NAG A 606 " - " ASN A 355 " " NAG A 607 " - " ASN A 405 " " NAG A 608 " - " ASN A 339 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 616 " " NAG D 301 " - " ASN D 72 " " NAG E 1 " - " ASN A 156 " " NAG F 603 " - " ASN F 133 " " NAG F 604 " - " ASN F 234 " " NAG F 605 " - " ASN F 301 " " NAG F 606 " - " ASN F 392 " " NAG F 607 " - " ASN F 448 " " NAG F 608 " - " ASN F 149 " " NAG F 609 " - " ASN F 241 " " NAG F 610 " - " ASN F 355 " " NAG F 611 " - " ASN F 405 " " NAG F 612 " - " ASN F 339 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 160 " " NAG G 603 " - " ASN G 197 " " NAG G 604 " - " ASN G 234 " " NAG G 605 " - " ASN G 301 " " NAG G 606 " - " ASN G 392 " " NAG G 607 " - " ASN G 149 " " NAG G 608 " - " ASN G 355 " " NAG G 609 " - " ASN G 339 " " NAG H 1 " - " ASN A 160 " " NAG I 1 " - " ASN A 197 " " NAG K 301 " - " ASN K 72 " " NAG L 1 " - " ASN A 262 " " NAG M 701 " - " ASN M 611 " " NAG M 702 " - " ASN M 637 " " NAG M 703 " - " ASN M 616 " " NAG N 701 " - " ASN N 611 " " NAG N 702 " - " ASN N 637 " " NAG N 703 " - " ASN N 625 " " NAG O 1 " - " ASN A 276 " " NAG P 1 " - " ASN A 295 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 448 " " NAG T 1 " - " ASN A 88 " " NAG U 301 " - " ASN U 72 " " NAG V 1 " - " ASN A 334 " " NAG W 1 " - " ASN A 241 " " NAG Z 1 " - " ASN A 289 " " NAG a 1 " - " ASN M 625 " " NAG b 1 " - " ASN F 156 " " NAG c 1 " - " ASN F 197 " " NAG d 1 " - " ASN F 262 " " NAG e 1 " - " ASN F 276 " " NAG f 1 " - " ASN F 295 " " NAG g 1 " - " ASN F 386 " " NAG h 1 " - " ASN F 88 " " NAG i 1 " - " ASN F 334 " " NAG j 1 " - " ASN F 289 " " NAG k 1 " - " ASN F 160 " " NAG l 1 " - " ASN G 156 " " NAG m 1 " - " ASN G 262 " " NAG n 1 " - " ASN G 276 " " NAG o 1 " - " ASN G 295 " " NAG p 1 " - " ASN G 386 " " NAG q 1 " - " ASN G 448 " " NAG r 1 " - " ASN G 88 " " NAG s 1 " - " ASN G 334 " " NAG t 1 " - " ASN G 241 " " NAG u 1 " - " ASN G 289 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.2 seconds 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6588 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 78 sheets defined 13.5% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.733A pdb=" N GLN A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.677A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 353 removed outlier: 4.200A pdb=" N GLU A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N HIS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.919A pdb=" N ASN A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 121 through 127 removed outlier: 3.598A pdb=" N SER D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 187 removed outlier: 3.536A pdb=" N GLU D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 183 through 187' Processing helix chain 'F' and resid 98 through 115 removed outlier: 4.319A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 126 Processing helix chain 'F' and resid 335 through 351 removed outlier: 4.109A pdb=" N GLU F 351 " --> pdb=" O GLY F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 481 removed outlier: 3.979A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 115 removed outlier: 4.582A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN G 103 " --> pdb=" O ASN G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 353 removed outlier: 3.914A pdb=" N GLU G 351 " --> pdb=" O GLY G 347 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N HIS G 352 " --> pdb=" O LYS G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 476 through 481 Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.943A pdb=" N ASP J 86 " --> pdb=" O ARG J 83 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR J 87 " --> pdb=" O SER J 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 83 through 87' Processing helix chain 'J' and resid 185 through 189 Processing helix chain 'K' and resid 121 through 126 removed outlier: 3.654A pdb=" N LEU K 125 " --> pdb=" O SER K 121 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS K 126 " --> pdb=" O ASP K 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 121 through 126' Processing helix chain 'K' and resid 183 through 189 removed outlier: 3.692A pdb=" N GLU K 187 " --> pdb=" O LYS K 183 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N HIS K 189 " --> pdb=" O ASP K 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 156 through 158 No H-bonds generated for 'chain 'S' and resid 156 through 158' Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'U' and resid 122 through 127 removed outlier: 3.725A pdb=" N SER U 127 " --> pdb=" O GLU U 123 " (cutoff:3.500A) Processing helix chain 'U' and resid 183 through 188 removed outlier: 3.787A pdb=" N GLU U 187 " --> pdb=" O LYS U 183 " (cutoff:3.500A) Processing helix chain 'X' and resid 61 through 65 removed outlier: 3.651A pdb=" N THR X 65 " --> pdb=" O PRO X 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 91 removed outlier: 4.080A pdb=" N THR X 91 " --> pdb=" O ALA X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 168 through 170 No H-bonds generated for 'chain 'X' and resid 168 through 170' Processing helix chain 'Y' and resid 121 through 127 Processing helix chain 'M' and resid 529 through 534 removed outlier: 3.920A pdb=" N SER M 534 " --> pdb=" O MET M 530 " (cutoff:3.500A) Processing helix chain 'M' and resid 535 through 537 No H-bonds generated for 'chain 'M' and resid 535 through 537' Processing helix chain 'M' and resid 547 through 551 removed outlier: 3.517A pdb=" N GLN M 550 " --> pdb=" O GLY M 547 " (cutoff:3.500A) Processing helix chain 'M' and resid 569 through 597 removed outlier: 4.202A pdb=" N LEU M 576 " --> pdb=" O GLY M 572 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL M 589 " --> pdb=" O ARG M 585 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE M 592 " --> pdb=" O GLU M 588 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY M 597 " --> pdb=" O LEU M 593 " (cutoff:3.500A) Processing helix chain 'M' and resid 618 through 624 Processing helix chain 'M' and resid 627 through 635 removed outlier: 3.882A pdb=" N GLU M 632 " --> pdb=" O TRP M 628 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG M 633 " --> pdb=" O ILE M 629 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU M 634 " --> pdb=" O GLU M 630 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE M 635 " --> pdb=" O TRP M 631 " (cutoff:3.500A) Processing helix chain 'M' and resid 638 through 659 removed outlier: 4.230A pdb=" N ASP M 644 " --> pdb=" O SER M 640 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR M 647 " --> pdb=" O TYR M 643 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP M 654 " --> pdb=" O GLN M 650 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN M 656 " --> pdb=" O GLN M 652 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP M 659 " --> pdb=" O ILE M 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 534 removed outlier: 3.587A pdb=" N SER B 534 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.088A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 569 removed outlier: 3.507A pdb=" N THR B 569 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 4.470A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.672A pdb=" N ILE B 622 " --> pdb=" O SER B 618 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 659 removed outlier: 3.906A pdb=" N THR B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'N' and resid 531 through 535 removed outlier: 4.081A pdb=" N ASN N 535 " --> pdb=" O ALA N 532 " (cutoff:3.500A) Processing helix chain 'N' and resid 536 through 543 removed outlier: 4.295A pdb=" N GLN N 540 " --> pdb=" O THR N 536 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN N 543 " --> pdb=" O VAL N 539 " (cutoff:3.500A) Processing helix chain 'N' and resid 547 through 551 removed outlier: 3.724A pdb=" N GLN N 550 " --> pdb=" O GLY N 547 " (cutoff:3.500A) Processing helix chain 'N' and resid 569 through 596 removed outlier: 3.514A pdb=" N LYS N 574 " --> pdb=" O VAL N 570 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN N 575 " --> pdb=" O TRP N 571 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL N 589 " --> pdb=" O ARG N 585 " (cutoff:3.500A) Processing helix chain 'N' and resid 619 through 624 removed outlier: 3.552A pdb=" N ASN N 624 " --> pdb=" O GLU N 620 " (cutoff:3.500A) Processing helix chain 'N' and resid 627 through 636 removed outlier: 3.947A pdb=" N ARG N 633 " --> pdb=" O ILE N 629 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU N 634 " --> pdb=" O GLU N 630 " (cutoff:3.500A) Processing helix chain 'N' and resid 638 through 641 Processing helix chain 'N' and resid 642 through 659 removed outlier: 3.503A pdb=" N GLN N 650 " --> pdb=" O LEU N 646 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP N 659 " --> pdb=" O ILE N 655 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 38 removed outlier: 3.587A pdb=" N ALA A 497 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.737A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.629A pdb=" N PHE A 93 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.770A pdb=" N LYS A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 215 through 218 removed outlier: 4.502A pdb=" N TYR A 217 " --> pdb=" O HIS A 249 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N HIS A 249 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.741A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.697A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N LYS A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLY A 451 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS A 445 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.936A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 393 through 395 removed outlier: 4.187A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N SER A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 5 through 6 removed outlier: 3.637A pdb=" N LEU C 5 " --> pdb=" O GLU C 23 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA C 24 " --> pdb=" O TYR C 76 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.725A pdb=" N THR C 107 " --> pdb=" O TYR C 90 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 89 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 122 through 124 removed outlier: 5.871A pdb=" N GLY C 139 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL C 182 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU C 141 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N SER C 180 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LYS C 143 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU C 178 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 122 through 124 removed outlier: 5.871A pdb=" N GLY C 139 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL C 182 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU C 141 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N SER C 180 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LYS C 143 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU C 178 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 177 " --> pdb=" O VAL C 169 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 153 through 154 removed outlier: 4.804A pdb=" N TYR C 194 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL C 211 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.512A pdb=" N GLU D 70 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 72 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.822A pdb=" N TYR D 49 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE D 87 " --> pdb=" O TYR D 36 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 114 through 115 removed outlier: 4.000A pdb=" N CYS D 134 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER D 177 " --> pdb=" O CYS D 134 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 144 through 148 removed outlier: 4.192A pdb=" N TYR D 192 " --> pdb=" O PHE D 209 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE D 209 " --> pdb=" O TYR D 192 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS D 194 " --> pdb=" O LYS D 207 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL D 205 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 35 through 40 removed outlier: 3.527A pdb=" N ALA F 497 " --> pdb=" O THR F 37 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'F' and resid 75 through 76 removed outlier: 7.229A pdb=" N CYS F 54 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR F 217 " --> pdb=" O HIS F 249 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N HIS F 249 " --> pdb=" O TYR F 217 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 120 through 121 removed outlier: 3.715A pdb=" N VAL F 120 " --> pdb=" O GLN F 203 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 130 through 132 removed outlier: 3.793A pdb=" N PHE F 176 " --> pdb=" O ARG F 155 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 160 through 161 removed outlier: 3.561A pdb=" N GLN F 170 " --> pdb=" O VAL F 161 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 181 through 182 Processing sheet with id=AD1, first strand: chain 'F' and resid 259 through 261 removed outlier: 3.684A pdb=" N GLY F 451 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N ASN F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.522A pdb=" N ILE F 294 " --> pdb=" O ASN F 444 " (cutoff:3.500A) removed outlier: 10.004A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N ASN F 448 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 10.748A pdb=" N LYS F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 304 through 308 removed outlier: 3.511A pdb=" N THR F 305 " --> pdb=" O ARG F 319 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 332 through 334 Processing sheet with id=AD4, first strand: chain 'F' and resid 393 through 395 removed outlier: 3.628A pdb=" N SER F 393 " --> pdb=" O PHE F 361 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE F 359 " --> pdb=" O TRP F 395 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 374 through 378 removed outlier: 4.083A pdb=" N PHE F 376 " --> pdb=" O PHE F 383 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS F 421 " --> pdb=" O PHE F 382 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 494 through 499 removed outlier: 3.543A pdb=" N ALA G 497 " --> pdb=" O THR G 37 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.561A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 91 through 93 removed outlier: 3.886A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE G 93 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 131 through 132 Processing sheet with id=AE1, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AE2, first strand: chain 'G' and resid 201 through 203 removed outlier: 3.828A pdb=" N TYR G 435 " --> pdb=" O LYS G 202 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 259 through 261 removed outlier: 3.746A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 10.120A pdb=" N ASN G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.055A pdb=" N ILE G 294 " --> pdb=" O ASN G 444 " (cutoff:3.500A) removed outlier: 9.973A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.226A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N ASN G 448 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 10.852A pdb=" N LYS G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE G 452 " --> pdb=" O VAL G 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 259 through 261 removed outlier: 3.746A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 10.120A pdb=" N ASN G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.055A pdb=" N ILE G 294 " --> pdb=" O ASN G 444 " (cutoff:3.500A) removed outlier: 9.973A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.226A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N ASN G 448 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 10.852A pdb=" N LYS G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE G 452 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N GLU G 293 " --> pdb=" O ASN G 334 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN G 334 " --> pdb=" O GLU G 293 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.420A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 393 through 395 removed outlier: 3.838A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE G 359 " --> pdb=" O TRP G 395 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N THR G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N PHE G 468 " --> pdb=" O THR G 358 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.511A pdb=" N ALA J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR J 107 " --> pdb=" O TYR J 90 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL J 89 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TRP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 18 through 24 removed outlier: 3.852A pdb=" N VAL J 20 " --> pdb=" O MET J 80 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 120 through 123 removed outlier: 3.512A pdb=" N SER J 120 " --> pdb=" O LYS J 143 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS J 143 " --> pdb=" O SER J 120 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR J 176 " --> pdb=" O ASP J 144 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 120 through 123 removed outlier: 3.512A pdb=" N SER J 120 " --> pdb=" O LYS J 143 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS J 143 " --> pdb=" O SER J 120 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR J 176 " --> pdb=" O ASP J 144 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 136 through 137 Processing sheet with id=AF3, first strand: chain 'J' and resid 150 through 154 removed outlier: 4.062A pdb=" N THR J 151 " --> pdb=" O ASN J 199 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN J 199 " --> pdb=" O THR J 151 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR J 194 " --> pdb=" O VAL J 211 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N CYS J 196 " --> pdb=" O LYS J 209 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS J 209 " --> pdb=" O CYS J 196 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL J 198 " --> pdb=" O VAL J 207 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL J 207 " --> pdb=" O VAL J 198 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 5 through 6 removed outlier: 3.731A pdb=" N GLN K 24 " --> pdb=" O THR K 5 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.947A pdb=" N LEU K 11 " --> pdb=" O ARG K 103 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.587A pdb=" N LYS K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 114 through 118 removed outlier: 3.550A pdb=" N ASN K 137 " --> pdb=" O SER K 114 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER K 177 " --> pdb=" O CYS K 134 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR K 178 " --> pdb=" O GLN K 160 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 144 through 145 Processing sheet with id=AF9, first strand: chain 'K' and resid 148 through 149 removed outlier: 4.060A pdb=" N TRP K 148 " --> pdb=" O GLN K 155 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'S' and resid 5 through 6 Processing sheet with id=AG2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.695A pdb=" N THR S 110 " --> pdb=" O ALA S 10 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL S 109 " --> pdb=" O ALA S 88 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL S 89 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE S 34 " --> pdb=" O TRP S 50 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TRP S 50 " --> pdb=" O ILE S 34 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.695A pdb=" N THR S 110 " --> pdb=" O ALA S 10 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL S 109 " --> pdb=" O ALA S 88 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL S 102 " --> pdb=" O ARG S 94 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'S' and resid 120 through 123 removed outlier: 3.944A pdb=" N SER S 120 " --> pdb=" O LYS S 143 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU S 141 " --> pdb=" O PHE S 122 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LYS S 143 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU S 178 " --> pdb=" O LYS S 143 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR S 145 " --> pdb=" O TYR S 176 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'S' and resid 150 through 154 removed outlier: 3.524A pdb=" N ASN S 199 " --> pdb=" O THR S 151 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR S 194 " --> pdb=" O VAL S 211 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL S 198 " --> pdb=" O VAL S 207 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL S 207 " --> pdb=" O VAL S 198 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'S' and resid 163 through 165 Processing sheet with id=AG7, first strand: chain 'U' and resid 53 through 54 removed outlier: 5.232A pdb=" N LEU U 46 " --> pdb=" O GLN U 37 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLN U 37 " --> pdb=" O LEU U 46 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'U' and resid 114 through 117 removed outlier: 3.747A pdb=" N ASN U 137 " --> pdb=" O SER U 114 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA U 130 " --> pdb=" O LEU U 181 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TYR U 173 " --> pdb=" O ASN U 138 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'U' and resid 144 through 146 removed outlier: 3.636A pdb=" N THR U 197 " --> pdb=" O LYS U 145 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'U' and resid 149 through 150 removed outlier: 3.832A pdb=" N ALA U 193 " --> pdb=" O LYS U 149 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'X' and resid 4 through 5 removed outlier: 3.506A pdb=" N ILE X 79 " --> pdb=" O CYS X 22 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL X 80 " --> pdb=" O SER X 71 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'X' and resid 46 through 51 removed outlier: 4.832A pdb=" N TRP X 47 " --> pdb=" O ARG X 38 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ARG X 38 " --> pdb=" O TRP X 47 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLY X 49 " --> pdb=" O TRP X 36 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TRP X 36 " --> pdb=" O GLY X 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS X 34 " --> pdb=" O ILE X 51 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N SER X 114 " --> pdb=" O GLY X 98 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'X' and resid 46 through 51 removed outlier: 4.832A pdb=" N TRP X 47 " --> pdb=" O ARG X 38 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ARG X 38 " --> pdb=" O TRP X 47 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLY X 49 " --> pdb=" O TRP X 36 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TRP X 36 " --> pdb=" O GLY X 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS X 34 " --> pdb=" O ILE X 51 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU X 119 " --> pdb=" O TYR X 94 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'X' and resid 132 through 135 removed outlier: 3.808A pdb=" N LYS X 155 " --> pdb=" O LEU X 190 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU X 190 " --> pdb=" O LYS X 155 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR X 188 " --> pdb=" O TYR X 157 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL X 181 " --> pdb=" O SER X 189 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'X' and resid 163 through 166 removed outlier: 4.021A pdb=" N THR X 163 " --> pdb=" O ASN X 211 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Y' and resid 10 through 12 removed outlier: 6.859A pdb=" N VAL Y 11 " --> pdb=" O GLU Y 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'Y' and resid 20 through 24 removed outlier: 3.727A pdb=" N PHE Y 71 " --> pdb=" O CYS Y 23 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Y' and resid 33 through 34 Processing sheet with id=AI1, first strand: chain 'Y' and resid 45 through 46 removed outlier: 4.025A pdb=" N THR Y 85 " --> pdb=" O ALA Y 38 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Y' and resid 48 through 49 Processing sheet with id=AI3, first strand: chain 'Y' and resid 117 through 118 removed outlier: 3.907A pdb=" N VAL Y 133 " --> pdb=" O PHE Y 118 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Y' and resid 129 through 130 Processing sheet with id=AI5, first strand: chain 'Y' and resid 136 through 139 removed outlier: 5.583A pdb=" N TYR Y 173 " --> pdb=" O ASN Y 138 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Y' and resid 147 through 148 708 hydrogen bonds defined for protein. 1821 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: 5.81 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9090 1.34 - 1.46: 7631 1.46 - 1.59: 13203 1.59 - 1.71: 0 1.71 - 1.84: 180 Bond restraints: 30104 Sorted by residual: bond pdb=" C1 NAG A 607 " pdb=" O5 NAG A 607 " ideal model delta sigma weight residual 1.406 1.505 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C1 NAG A 604 " pdb=" O5 NAG A 604 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C1 NAG i 1 " pdb=" O5 NAG i 1 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C1 NAG A 603 " pdb=" O5 NAG A 603 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C1 NAG N 703 " pdb=" O5 NAG N 703 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.09e+00 ... (remaining 30099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 39690 1.94 - 3.88: 1058 3.88 - 5.82: 167 5.82 - 7.77: 48 7.77 - 9.71: 7 Bond angle restraints: 40970 Sorted by residual: angle pdb=" C ASN A 448 " pdb=" CA ASN A 448 " pdb=" CB ASN A 448 " ideal model delta sigma weight residual 111.70 121.41 -9.71 1.31e+00 5.83e-01 5.49e+01 angle pdb=" C ASN N 625 " pdb=" CA ASN N 625 " pdb=" CB ASN N 625 " ideal model delta sigma weight residual 109.16 117.38 -8.22 1.29e+00 6.01e-01 4.06e+01 angle pdb=" N ASN N 625 " pdb=" CA ASN N 625 " pdb=" CB ASN N 625 " ideal model delta sigma weight residual 111.15 104.15 7.00 1.46e+00 4.69e-01 2.30e+01 angle pdb=" C ASN N 624 " pdb=" N ASN N 625 " pdb=" CA ASN N 625 " ideal model delta sigma weight residual 121.52 113.31 8.21 1.74e+00 3.30e-01 2.23e+01 angle pdb=" N ASN A 448 " pdb=" CA ASN A 448 " pdb=" CB ASN A 448 " ideal model delta sigma weight residual 111.36 103.79 7.57 1.82e+00 3.02e-01 1.73e+01 ... (remaining 40965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.08: 18389 25.08 - 50.17: 1050 50.17 - 75.25: 205 75.25 - 100.34: 84 100.34 - 125.42: 48 Dihedral angle restraints: 19776 sinusoidal: 9553 harmonic: 10223 Sorted by residual: dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -170.36 84.36 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS G 378 " pdb=" SG CYS G 378 " pdb=" SG CYS G 445 " pdb=" CB CYS G 445 " ideal model delta sinusoidal sigma weight residual -86.00 -169.89 83.89 1 1.00e+01 1.00e-02 8.58e+01 dihedral pdb=" CB CYS D 134 " pdb=" SG CYS D 134 " pdb=" SG CYS D 194 " pdb=" CB CYS D 194 " ideal model delta sinusoidal sigma weight residual 93.00 175.90 -82.90 1 1.00e+01 1.00e-02 8.41e+01 ... (remaining 19773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.227: 4966 0.227 - 0.454: 23 0.454 - 0.681: 4 0.681 - 0.908: 1 0.908 - 1.135: 1 Chirality restraints: 4995 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN A 448 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.27 -1.13 2.00e-01 2.50e+01 3.22e+01 chirality pdb=" C1 NAG r 1 " pdb=" ND2 ASN G 88 " pdb=" C2 NAG r 1 " pdb=" O5 NAG r 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" C1 NAG N 703 " pdb=" ND2 ASN N 625 " pdb=" C2 NAG N 703 " pdb=" O5 NAG N 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.11e+01 ... (remaining 4992 not shown) Planarity restraints: 5118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 448 " -0.019 2.00e-02 2.50e+03 7.03e-02 6.18e+01 pdb=" CG ASN A 448 " 0.088 2.00e-02 2.50e+03 pdb=" OD1 ASN A 448 " -0.079 2.00e-02 2.50e+03 pdb=" ND2 ASN A 448 " 0.077 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN N 625 " -0.003 2.00e-02 2.50e+03 5.30e-02 3.51e+01 pdb=" CG ASN N 625 " -0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN N 625 " 0.063 2.00e-02 2.50e+03 pdb=" ND2 ASN N 625 " -0.060 2.00e-02 2.50e+03 pdb=" C1 NAG N 703 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 88 " -0.051 2.00e-02 2.50e+03 4.72e-02 2.78e+01 pdb=" CG ASN A 88 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 88 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 88 " 0.056 2.00e-02 2.50e+03 pdb=" C1 NAG T 1 " -0.053 2.00e-02 2.50e+03 ... (remaining 5115 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 708 2.66 - 3.22: 28764 3.22 - 3.78: 43922 3.78 - 4.34: 58196 4.34 - 4.90: 93408 Nonbonded interactions: 224998 Sorted by model distance: nonbonded pdb=" OG1 THR D 5 " pdb=" OE1 GLN D 24 " model vdw 2.103 3.040 nonbonded pdb=" OD1 ASN F 133 " pdb=" NH1 ARG F 155 " model vdw 2.119 3.120 nonbonded pdb=" O PRO X 135 " pdb=" NE2 GLN Y 124 " model vdw 2.137 3.120 nonbonded pdb=" O LEU D 106 " pdb=" OH TYR D 140 " model vdw 2.149 3.040 nonbonded pdb=" O CYS K 134 " pdb=" OG SER K 177 " model vdw 2.151 3.040 ... (remaining 224993 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 507 or resid 603 through 608)) selection = (chain 'F' and (resid 31 through 507 or resid 603 through 608)) selection = (chain 'G' and (resid 31 through 507 or resid 603 through 608)) } ncs_group { reference = (chain 'B' and resid 519 through 703) selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'J' selection = (chain 'S' and resid 1 through 213) } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'U' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' } ncs_group { reference = (chain 'L' and (resid 2 or resid 5 through 8)) selection = (chain 'O' and (resid 1 or resid 4 through 7)) selection = (chain 'e' and (resid 1 or resid 4 through 7)) } ncs_group { reference = chain 'd' selection = chain 'n' } ncs_group { reference = chain 'k' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.870 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: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 26.370 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 : 0.005 0.099 30292 Z= 0.231 Angle : 0.857 22.811 41479 Z= 0.379 Chirality : 0.059 1.135 4995 Planarity : 0.005 0.060 5045 Dihedral : 17.208 125.419 13032 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.16 % Allowed : 0.48 % Favored : 99.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 7.95 % 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: -1.88 (0.14), residues: 3481 helix: -1.20 (0.25), residues: 406 sheet: -0.53 (0.17), residues: 982 loop : -1.66 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 56 TYR 0.023 0.001 TYR X 111 PHE 0.009 0.001 PHE Y 118 TRP 0.039 0.002 TRP G 69 HIS 0.014 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00474 (30104) covalent geometry : angle 0.73540 (40970) SS BOND : bond 0.00324 ( 52) SS BOND : angle 1.40030 ( 104) hydrogen bonds : bond 0.27878 ( 674) hydrogen bonds : angle 10.51430 ( 1821) Misc. bond : bond 0.00344 ( 1) link_ALPHA1-2 : bond 0.00148 ( 3) link_ALPHA1-2 : angle 2.26070 ( 9) link_ALPHA1-3 : bond 0.00482 ( 9) link_ALPHA1-3 : angle 1.76947 ( 27) link_ALPHA1-6 : bond 0.00356 ( 9) link_ALPHA1-6 : angle 1.85411 ( 27) link_BETA1-4 : bond 0.00633 ( 41) link_BETA1-4 : angle 1.78992 ( 123) link_NAG-ASN : bond 0.00989 ( 73) link_NAG-ASN : angle 5.83586 ( 219) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 210 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8767 (ppp) cc_final: 0.8336 (tmm) REVERT: A 318 TYR cc_start: 0.7790 (m-80) cc_final: 0.7539 (m-80) REVERT: D 175 LEU cc_start: 0.9110 (tp) cc_final: 0.8886 (tp) REVERT: F 66 HIS cc_start: 0.8263 (m90) cc_final: 0.7855 (m90) REVERT: G 117 LYS cc_start: 0.8732 (tmtt) cc_final: 0.8374 (tptm) REVERT: G 282 LYS cc_start: 0.8971 (mptt) cc_final: 0.8752 (mmtm) REVERT: J 32 TYR cc_start: 0.8975 (m-10) cc_final: 0.8652 (m-10) REVERT: K 204 PRO cc_start: 0.6563 (Cg_exo) cc_final: 0.6315 (Cg_endo) REVERT: X 70 MET cc_start: 0.6154 (ppp) cc_final: 0.5749 (ptp) REVERT: X 94 TYR cc_start: 0.6717 (m-80) cc_final: 0.4271 (m-80) REVERT: X 109 GLN cc_start: 0.8843 (mp10) cc_final: 0.8308 (mp10) REVERT: B 520 PHE cc_start: 0.7775 (m-80) cc_final: 0.7480 (m-10) outliers start: 5 outliers final: 1 residues processed: 215 average time/residue: 0.1881 time to fit residues: 66.1402 Evaluate side-chains 156 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 146 ASN C 3 GLN C 6 GLN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 478 ASN F 490 GLN ** G 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 39 GLN J 62 GLN K 38 GLN K 152 ASN S 3 GLN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 199 GLN ** M 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.081309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.065078 restraints weight = 127177.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.065191 restraints weight = 86215.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.065537 restraints weight = 75827.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.065726 restraints weight = 67133.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.065785 restraints weight = 61821.510| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 30292 Z= 0.213 Angle : 0.783 19.906 41479 Z= 0.365 Chirality : 0.050 0.413 4995 Planarity : 0.005 0.061 5045 Dihedral : 13.550 113.523 6579 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.16 % Allowed : 7.34 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % 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: -1.86 (0.14), residues: 3481 helix: -0.73 (0.25), residues: 412 sheet: -0.63 (0.16), residues: 1028 loop : -1.70 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 155 TYR 0.020 0.002 TYR X 111 PHE 0.024 0.002 PHE M 651 TRP 0.021 0.002 TRP F 479 HIS 0.009 0.001 HIS X 212 Details of bonding type rmsd covalent geometry : bond 0.00480 (30104) covalent geometry : angle 0.69659 (40970) SS BOND : bond 0.00422 ( 52) SS BOND : angle 1.32903 ( 104) hydrogen bonds : bond 0.05493 ( 674) hydrogen bonds : angle 7.40134 ( 1821) Misc. bond : bond 0.00084 ( 1) link_ALPHA1-2 : bond 0.00342 ( 3) link_ALPHA1-2 : angle 2.25491 ( 9) link_ALPHA1-3 : bond 0.00813 ( 9) link_ALPHA1-3 : angle 2.66153 ( 27) link_ALPHA1-6 : bond 0.00465 ( 9) link_ALPHA1-6 : angle 2.62017 ( 27) link_BETA1-4 : bond 0.00537 ( 41) link_BETA1-4 : angle 1.86071 ( 123) link_NAG-ASN : bond 0.00739 ( 73) link_NAG-ASN : angle 4.53627 ( 219) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 197 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8828 (mtm) cc_final: 0.8362 (mtm) REVERT: A 104 MET cc_start: 0.8871 (ppp) cc_final: 0.8522 (tmm) REVERT: C 36 TRP cc_start: 0.9101 (m100) cc_final: 0.8823 (m-10) REVERT: D 91 TYR cc_start: 0.7897 (m-80) cc_final: 0.7692 (m-80) REVERT: F 66 HIS cc_start: 0.8395 (m90) cc_final: 0.7964 (m90) REVERT: F 373 MET cc_start: 0.8639 (tpp) cc_final: 0.8361 (tpp) REVERT: F 434 MET cc_start: 0.8533 (tmm) cc_final: 0.8198 (tmm) REVERT: G 104 MET cc_start: 0.8957 (tmm) cc_final: 0.8609 (tmm) REVERT: G 117 LYS cc_start: 0.8903 (tmtt) cc_final: 0.8595 (tptm) REVERT: J 72 ASP cc_start: 0.8686 (m-30) cc_final: 0.8247 (m-30) REVERT: K 204 PRO cc_start: 0.6589 (Cg_exo) cc_final: 0.6341 (Cg_endo) REVERT: S 100 ASP cc_start: 0.8405 (p0) cc_final: 0.8159 (p0) REVERT: U 81 GLU cc_start: 0.6615 (pp20) cc_final: 0.5990 (pm20) REVERT: X 70 MET cc_start: 0.6000 (ppp) cc_final: 0.5706 (ppp) REVERT: X 109 GLN cc_start: 0.8889 (mp10) cc_final: 0.8494 (mp10) REVERT: Y 165 GLU cc_start: 0.7945 (tp30) cc_final: 0.7702 (tp30) REVERT: B 520 PHE cc_start: 0.7808 (m-80) cc_final: 0.7432 (m-10) REVERT: B 530 MET cc_start: 0.8091 (ttm) cc_final: 0.7832 (ttp) outliers start: 5 outliers final: 1 residues processed: 202 average time/residue: 0.1886 time to fit residues: 61.3577 Evaluate side-chains 159 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 274 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 306 optimal weight: 10.0000 chunk 178 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 175 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 235 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN C 58 ASN F 490 GLN G 183 GLN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 490 GLN J 3 GLN J 62 GLN K 152 ASN S 3 GLN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 199 GLN ** N 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.082628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.066506 restraints weight = 124992.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.066673 restraints weight = 83447.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.067066 restraints weight = 73143.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.067265 restraints weight = 63172.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.067324 restraints weight = 58463.684| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30292 Z= 0.146 Angle : 0.732 20.313 41479 Z= 0.335 Chirality : 0.049 0.388 4995 Planarity : 0.004 0.055 5045 Dihedral : 12.126 112.928 6579 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.13 % Allowed : 5.50 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.79 (0.14), residues: 3481 helix: -0.51 (0.26), residues: 397 sheet: -0.61 (0.16), residues: 1003 loop : -1.67 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 61 TYR 0.021 0.001 TYR X 111 PHE 0.028 0.001 PHE M 651 TRP 0.014 0.001 TRP M 628 HIS 0.007 0.001 HIS X 212 Details of bonding type rmsd covalent geometry : bond 0.00326 (30104) covalent geometry : angle 0.64322 (40970) SS BOND : bond 0.00381 ( 52) SS BOND : angle 1.21793 ( 104) hydrogen bonds : bond 0.04584 ( 674) hydrogen bonds : angle 6.59258 ( 1821) Misc. bond : bond 0.00066 ( 1) link_ALPHA1-2 : bond 0.00226 ( 3) link_ALPHA1-2 : angle 2.02635 ( 9) link_ALPHA1-3 : bond 0.00937 ( 9) link_ALPHA1-3 : angle 2.20957 ( 27) link_ALPHA1-6 : bond 0.00540 ( 9) link_ALPHA1-6 : angle 2.27054 ( 27) link_BETA1-4 : bond 0.00530 ( 41) link_BETA1-4 : angle 1.74371 ( 123) link_NAG-ASN : bond 0.00756 ( 73) link_NAG-ASN : angle 4.50561 ( 219) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 204 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8809 (ppp) cc_final: 0.8421 (tmm) REVERT: C 36 TRP cc_start: 0.9021 (m100) cc_final: 0.8797 (m-10) REVERT: D 175 LEU cc_start: 0.9224 (tp) cc_final: 0.8981 (tp) REVERT: F 66 HIS cc_start: 0.8328 (m90) cc_final: 0.7937 (m90) REVERT: F 373 MET cc_start: 0.8662 (tpp) cc_final: 0.7757 (mmt) REVERT: F 434 MET cc_start: 0.8538 (tmm) cc_final: 0.8328 (tmm) REVERT: G 373 MET cc_start: 0.8524 (tpp) cc_final: 0.8280 (tpp) REVERT: J 72 ASP cc_start: 0.8713 (m-30) cc_final: 0.8191 (m-30) REVERT: K 204 PRO cc_start: 0.6567 (Cg_exo) cc_final: 0.6302 (Cg_endo) REVERT: S 100 ASP cc_start: 0.8392 (p0) cc_final: 0.8062 (p0) REVERT: X 191 SER cc_start: 0.8053 (p) cc_final: 0.7628 (m) REVERT: Y 165 GLU cc_start: 0.7946 (tp30) cc_final: 0.7700 (tp30) REVERT: B 520 PHE cc_start: 0.7797 (m-80) cc_final: 0.7426 (m-10) REVERT: B 530 MET cc_start: 0.7974 (ttm) cc_final: 0.7675 (ttp) outliers start: 4 outliers final: 0 residues processed: 208 average time/residue: 0.2032 time to fit residues: 67.3748 Evaluate side-chains 154 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 289 optimal weight: 10.0000 chunk 246 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 301 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 244 optimal weight: 0.6980 chunk 33 optimal weight: 0.0470 chunk 202 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 338 optimal weight: 2.9990 overall best weight: 1.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 3 GLN F 478 ASN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 490 GLN J 3 GLN J 62 GLN K 152 ASN S 3 GLN ** S 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 199 GLN ** N 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.082266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.066081 restraints weight = 124169.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.066257 restraints weight = 85968.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.066650 restraints weight = 74663.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.066769 restraints weight = 65629.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.066834 restraints weight = 61032.200| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30292 Z= 0.169 Angle : 0.747 20.290 41479 Z= 0.342 Chirality : 0.049 0.392 4995 Planarity : 0.004 0.055 5045 Dihedral : 11.471 112.446 6579 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 0.16 % Allowed : 4.02 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % 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: -1.78 (0.14), residues: 3481 helix: -0.39 (0.26), residues: 397 sheet: -0.62 (0.16), residues: 1033 loop : -1.68 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 56 TYR 0.022 0.001 TYR X 111 PHE 0.025 0.001 PHE M 651 TRP 0.042 0.001 TRP M 631 HIS 0.007 0.001 HIS X 212 Details of bonding type rmsd covalent geometry : bond 0.00380 (30104) covalent geometry : angle 0.66023 (40970) SS BOND : bond 0.00409 ( 52) SS BOND : angle 1.31492 ( 104) hydrogen bonds : bond 0.04280 ( 674) hydrogen bonds : angle 6.37774 ( 1821) Misc. bond : bond 0.00029 ( 1) link_ALPHA1-2 : bond 0.00245 ( 3) link_ALPHA1-2 : angle 2.00646 ( 9) link_ALPHA1-3 : bond 0.00898 ( 9) link_ALPHA1-3 : angle 2.36703 ( 27) link_ALPHA1-6 : bond 0.00648 ( 9) link_ALPHA1-6 : angle 2.34261 ( 27) link_BETA1-4 : bond 0.00505 ( 41) link_BETA1-4 : angle 1.68864 ( 123) link_NAG-ASN : bond 0.00736 ( 73) link_NAG-ASN : angle 4.48524 ( 219) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 189 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9015 (mtp) cc_final: 0.8606 (mtm) REVERT: A 104 MET cc_start: 0.8841 (ppp) cc_final: 0.8475 (tmm) REVERT: A 317 PHE cc_start: 0.7709 (t80) cc_final: 0.7489 (t80) REVERT: C 36 TRP cc_start: 0.9062 (m100) cc_final: 0.8855 (m-10) REVERT: F 100 MET cc_start: 0.7674 (mtp) cc_final: 0.7352 (mtm) REVERT: F 373 MET cc_start: 0.8761 (tpp) cc_final: 0.7776 (mmt) REVERT: F 434 MET cc_start: 0.8538 (tmm) cc_final: 0.7990 (tmm) REVERT: K 204 PRO cc_start: 0.6542 (Cg_exo) cc_final: 0.6279 (Cg_endo) REVERT: U 140 TYR cc_start: 0.6152 (t80) cc_final: 0.5649 (t80) outliers start: 5 outliers final: 0 residues processed: 194 average time/residue: 0.1919 time to fit residues: 60.6290 Evaluate side-chains 148 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 195 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 265 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 3 GLN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 490 GLN J 3 GLN J 62 GLN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 152 ASN S 3 GLN ** S 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 199 GLN B 656 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.081349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.065198 restraints weight = 125366.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.065262 restraints weight = 85258.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.065646 restraints weight = 74975.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.065793 restraints weight = 66968.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.065865 restraints weight = 61536.865| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30292 Z= 0.201 Angle : 0.759 20.129 41479 Z= 0.351 Chirality : 0.049 0.393 4995 Planarity : 0.005 0.056 5045 Dihedral : 11.119 112.192 6579 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.13 % Allowed : 3.44 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.85 (0.14), residues: 3481 helix: -0.54 (0.25), residues: 405 sheet: -0.65 (0.16), residues: 1008 loop : -1.71 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 166 TYR 0.024 0.001 TYR X 111 PHE 0.024 0.002 PHE M 522 TRP 0.033 0.002 TRP M 631 HIS 0.007 0.001 HIS X 212 Details of bonding type rmsd covalent geometry : bond 0.00459 (30104) covalent geometry : angle 0.68110 (40970) SS BOND : bond 0.00552 ( 52) SS BOND : angle 1.30555 ( 104) hydrogen bonds : bond 0.04285 ( 674) hydrogen bonds : angle 6.26322 ( 1821) Misc. bond : bond 0.00017 ( 1) link_ALPHA1-2 : bond 0.00332 ( 3) link_ALPHA1-2 : angle 2.05151 ( 9) link_ALPHA1-3 : bond 0.00931 ( 9) link_ALPHA1-3 : angle 2.50299 ( 27) link_ALPHA1-6 : bond 0.00620 ( 9) link_ALPHA1-6 : angle 2.39921 ( 27) link_BETA1-4 : bond 0.00450 ( 41) link_BETA1-4 : angle 1.63018 ( 123) link_NAG-ASN : bond 0.00690 ( 73) link_NAG-ASN : angle 4.28472 ( 219) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 184 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9047 (mtp) cc_final: 0.8761 (mtm) REVERT: A 104 MET cc_start: 0.8934 (ppp) cc_final: 0.8502 (tmm) REVERT: C 36 TRP cc_start: 0.9118 (m100) cc_final: 0.8891 (m-10) REVERT: D 165 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7969 (tm-30) REVERT: F 100 MET cc_start: 0.7691 (mtp) cc_final: 0.7379 (mtm) REVERT: F 434 MET cc_start: 0.8492 (tmm) cc_final: 0.7971 (tmm) REVERT: J 72 ASP cc_start: 0.8662 (m-30) cc_final: 0.8244 (m-30) REVERT: S 100 ASP cc_start: 0.8343 (p0) cc_final: 0.7947 (p0) REVERT: U 140 TYR cc_start: 0.6438 (t80) cc_final: 0.6135 (t80) REVERT: X 191 SER cc_start: 0.8119 (p) cc_final: 0.7810 (m) REVERT: B 530 MET cc_start: 0.8110 (ttm) cc_final: 0.7827 (ttp) outliers start: 4 outliers final: 1 residues processed: 188 average time/residue: 0.1893 time to fit residues: 58.5909 Evaluate side-chains 138 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 149 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 302 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 chunk 168 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 3 GLN D 124 GLN F 490 GLN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 62 GLN K 152 ASN S 3 GLN ** S 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 192 GLN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.080038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.064086 restraints weight = 126480.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.064067 restraints weight = 91384.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.064505 restraints weight = 83184.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.064750 restraints weight = 68931.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.064782 restraints weight = 62791.787| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 30292 Z= 0.269 Angle : 0.833 19.958 41479 Z= 0.387 Chirality : 0.052 0.553 4995 Planarity : 0.005 0.061 5045 Dihedral : 11.218 111.323 6579 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.10 % Allowed : 3.99 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.01 (0.14), residues: 3481 helix: -0.69 (0.25), residues: 405 sheet: -0.74 (0.16), residues: 977 loop : -1.82 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 166 TYR 0.024 0.002 TYR X 111 PHE 0.020 0.002 PHE M 522 TRP 0.045 0.002 TRP A 69 HIS 0.007 0.001 HIS Y 90 Details of bonding type rmsd covalent geometry : bond 0.00610 (30104) covalent geometry : angle 0.75179 (40970) SS BOND : bond 0.00478 ( 52) SS BOND : angle 1.53959 ( 104) hydrogen bonds : bond 0.04617 ( 674) hydrogen bonds : angle 6.43753 ( 1821) Misc. bond : bond 0.00071 ( 1) link_ALPHA1-2 : bond 0.00595 ( 3) link_ALPHA1-2 : angle 2.16887 ( 9) link_ALPHA1-3 : bond 0.00668 ( 9) link_ALPHA1-3 : angle 2.62186 ( 27) link_ALPHA1-6 : bond 0.00764 ( 9) link_ALPHA1-6 : angle 2.41288 ( 27) link_BETA1-4 : bond 0.00506 ( 41) link_BETA1-4 : angle 1.71930 ( 123) link_NAG-ASN : bond 0.00792 ( 73) link_NAG-ASN : angle 4.60433 ( 219) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 185 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9010 (mtp) cc_final: 0.8786 (mtm) REVERT: A 104 MET cc_start: 0.9067 (ppp) cc_final: 0.8546 (tmm) REVERT: C 36 TRP cc_start: 0.9171 (m100) cc_final: 0.8958 (m-10) REVERT: F 100 MET cc_start: 0.7781 (mtp) cc_final: 0.7553 (mtm) REVERT: F 373 MET cc_start: 0.8728 (tpp) cc_final: 0.7785 (mmt) REVERT: F 434 MET cc_start: 0.8476 (tmm) cc_final: 0.8028 (tmm) REVERT: G 69 TRP cc_start: 0.8306 (m100) cc_final: 0.7613 (m100) REVERT: G 117 LYS cc_start: 0.8618 (tptt) cc_final: 0.8273 (tptm) REVERT: G 373 MET cc_start: 0.8635 (tpp) cc_final: 0.8222 (tpp) REVERT: S 100 ASP cc_start: 0.8476 (p0) cc_final: 0.8077 (p0) REVERT: U 140 TYR cc_start: 0.6506 (t80) cc_final: 0.6198 (t80) REVERT: X 191 SER cc_start: 0.8028 (p) cc_final: 0.7623 (m) outliers start: 3 outliers final: 0 residues processed: 188 average time/residue: 0.1863 time to fit residues: 57.7328 Evaluate side-chains 140 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 240 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 257 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 241 optimal weight: 9.9990 chunk 328 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 318 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 490 GLN J 3 GLN J 62 GLN K 37 GLN K 152 ASN S 3 GLN S 59 ASN S 64 GLN U 124 GLN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 199 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.081365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.065288 restraints weight = 126085.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.065450 restraints weight = 85305.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.065850 restraints weight = 73958.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.066014 restraints weight = 65009.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.066079 restraints weight = 59772.945| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30292 Z= 0.172 Angle : 0.761 20.265 41479 Z= 0.352 Chirality : 0.049 0.413 4995 Planarity : 0.005 0.060 5045 Dihedral : 10.777 112.038 6579 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.13 % Allowed : 1.93 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.97 (0.14), residues: 3481 helix: -0.56 (0.26), residues: 409 sheet: -0.64 (0.17), residues: 942 loop : -1.85 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 633 TYR 0.021 0.001 TYR F 217 PHE 0.015 0.001 PHE M 522 TRP 0.047 0.002 TRP A 69 HIS 0.009 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00391 (30104) covalent geometry : angle 0.67989 (40970) SS BOND : bond 0.00510 ( 52) SS BOND : angle 1.61654 ( 104) hydrogen bonds : bond 0.04120 ( 674) hydrogen bonds : angle 6.14112 ( 1821) Misc. bond : bond 0.00020 ( 1) link_ALPHA1-2 : bond 0.00210 ( 3) link_ALPHA1-2 : angle 2.14345 ( 9) link_ALPHA1-3 : bond 0.00965 ( 9) link_ALPHA1-3 : angle 2.36351 ( 27) link_ALPHA1-6 : bond 0.00714 ( 9) link_ALPHA1-6 : angle 2.17289 ( 27) link_BETA1-4 : bond 0.00465 ( 41) link_BETA1-4 : angle 1.62131 ( 123) link_NAG-ASN : bond 0.00674 ( 73) link_NAG-ASN : angle 4.36110 ( 219) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 196 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8965 (mtp) cc_final: 0.8592 (mtm) REVERT: A 104 MET cc_start: 0.8969 (ppp) cc_final: 0.8644 (tmm) REVERT: A 111 LEU cc_start: 0.9249 (mm) cc_final: 0.8867 (mt) REVERT: C 36 TRP cc_start: 0.9114 (m100) cc_final: 0.8867 (m-10) REVERT: D 175 LEU cc_start: 0.9148 (tp) cc_final: 0.8833 (tp) REVERT: F 100 MET cc_start: 0.7840 (mtp) cc_final: 0.7570 (mtm) REVERT: F 373 MET cc_start: 0.8724 (tpp) cc_final: 0.7741 (mmt) REVERT: F 434 MET cc_start: 0.8461 (tmm) cc_final: 0.8003 (tmm) REVERT: G 117 LYS cc_start: 0.8551 (tptt) cc_final: 0.8199 (tptm) REVERT: J 72 ASP cc_start: 0.8704 (m-30) cc_final: 0.8238 (m-30) REVERT: S 100 ASP cc_start: 0.8378 (p0) cc_final: 0.7964 (p0) REVERT: U 140 TYR cc_start: 0.6576 (t80) cc_final: 0.6257 (t80) REVERT: X 191 SER cc_start: 0.7945 (p) cc_final: 0.7702 (m) outliers start: 4 outliers final: 1 residues processed: 199 average time/residue: 0.1776 time to fit residues: 57.1150 Evaluate side-chains 147 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 325 optimal weight: 0.9990 chunk 242 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 317 optimal weight: 6.9990 chunk 294 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 236 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 490 GLN J 3 GLN J 62 GLN K 37 GLN K 152 ASN S 3 GLN U 79 GLN U 124 GLN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.081575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.065507 restraints weight = 124633.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.065870 restraints weight = 86795.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.066171 restraints weight = 74722.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.066401 restraints weight = 63708.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.066448 restraints weight = 58492.200| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30292 Z= 0.171 Angle : 0.756 20.135 41479 Z= 0.349 Chirality : 0.049 0.410 4995 Planarity : 0.005 0.060 5045 Dihedral : 10.506 111.021 6579 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 0.10 % Allowed : 1.35 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.91 (0.14), residues: 3481 helix: -0.36 (0.26), residues: 395 sheet: -0.65 (0.17), residues: 959 loop : -1.81 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 61 TYR 0.019 0.001 TYR J 176 PHE 0.018 0.001 PHE M 651 TRP 0.054 0.001 TRP A 69 HIS 0.006 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00389 (30104) covalent geometry : angle 0.67629 (40970) SS BOND : bond 0.00389 ( 52) SS BOND : angle 1.48446 ( 104) hydrogen bonds : bond 0.03988 ( 674) hydrogen bonds : angle 6.04148 ( 1821) Misc. bond : bond 0.00014 ( 1) link_ALPHA1-2 : bond 0.00249 ( 3) link_ALPHA1-2 : angle 2.09662 ( 9) link_ALPHA1-3 : bond 0.01016 ( 9) link_ALPHA1-3 : angle 2.37557 ( 27) link_ALPHA1-6 : bond 0.00802 ( 9) link_ALPHA1-6 : angle 2.11355 ( 27) link_BETA1-4 : bond 0.00461 ( 41) link_BETA1-4 : angle 1.61861 ( 123) link_NAG-ASN : bond 0.00664 ( 73) link_NAG-ASN : angle 4.31283 ( 219) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 188 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8958 (mtp) cc_final: 0.8613 (mtm) REVERT: A 111 LEU cc_start: 0.9228 (mm) cc_final: 0.8933 (mt) REVERT: A 175 LEU cc_start: 0.9034 (tp) cc_final: 0.8828 (tp) REVERT: C 36 TRP cc_start: 0.9116 (m100) cc_final: 0.8861 (m-10) REVERT: F 100 MET cc_start: 0.7720 (mtp) cc_final: 0.7498 (mtm) REVERT: F 373 MET cc_start: 0.8735 (tpp) cc_final: 0.7754 (mmt) REVERT: F 434 MET cc_start: 0.8472 (tmm) cc_final: 0.8003 (tmm) REVERT: G 117 LYS cc_start: 0.8552 (tptt) cc_final: 0.8191 (tptm) REVERT: G 373 MET cc_start: 0.8568 (tpp) cc_final: 0.8345 (tpp) REVERT: U 140 TYR cc_start: 0.6360 (t80) cc_final: 0.6078 (t80) REVERT: X 191 SER cc_start: 0.7963 (p) cc_final: 0.7756 (m) REVERT: M 654 ASP cc_start: 0.8886 (p0) cc_final: 0.8232 (p0) outliers start: 3 outliers final: 1 residues processed: 191 average time/residue: 0.1819 time to fit residues: 57.4094 Evaluate side-chains 147 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 281 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 322 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 139 optimal weight: 0.0010 chunk 303 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 308 optimal weight: 4.9990 chunk 317 optimal weight: 0.6980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN G 99 ASN G 490 GLN J 3 GLN J 62 GLN K 37 GLN K 147 GLN K 152 ASN S 3 GLN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 199 GLN ** N 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.082368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.066055 restraints weight = 124820.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.066312 restraints weight = 83329.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.066656 restraints weight = 73105.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.066931 restraints weight = 62945.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.066985 restraints weight = 56684.761| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30292 Z= 0.131 Angle : 0.734 20.200 41479 Z= 0.337 Chirality : 0.048 0.404 4995 Planarity : 0.004 0.059 5045 Dihedral : 10.064 110.623 6579 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.13 % Allowed : 0.51 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.79 (0.14), residues: 3481 helix: -0.29 (0.26), residues: 397 sheet: -0.54 (0.17), residues: 951 loop : -1.74 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 633 TYR 0.015 0.001 TYR J 176 PHE 0.023 0.001 PHE A 317 TRP 0.055 0.001 TRP G 69 HIS 0.005 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00291 (30104) covalent geometry : angle 0.65304 (40970) SS BOND : bond 0.00428 ( 52) SS BOND : angle 1.36306 ( 104) hydrogen bonds : bond 0.03694 ( 674) hydrogen bonds : angle 5.79446 ( 1821) Misc. bond : bond 0.00025 ( 1) link_ALPHA1-2 : bond 0.00186 ( 3) link_ALPHA1-2 : angle 2.00368 ( 9) link_ALPHA1-3 : bond 0.01196 ( 9) link_ALPHA1-3 : angle 2.26829 ( 27) link_ALPHA1-6 : bond 0.00906 ( 9) link_ALPHA1-6 : angle 2.04791 ( 27) link_BETA1-4 : bond 0.00497 ( 41) link_BETA1-4 : angle 1.57092 ( 123) link_NAG-ASN : bond 0.00668 ( 73) link_NAG-ASN : angle 4.33626 ( 219) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 198 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8824 (mtp) cc_final: 0.8523 (mtm) REVERT: A 111 LEU cc_start: 0.9216 (mm) cc_final: 0.8877 (mt) REVERT: C 36 TRP cc_start: 0.9077 (m100) cc_final: 0.8841 (m-10) REVERT: C 72 ASP cc_start: 0.8181 (p0) cc_final: 0.7852 (p0) REVERT: D 124 GLN cc_start: 0.7624 (tt0) cc_final: 0.7197 (tt0) REVERT: F 100 MET cc_start: 0.7645 (mtp) cc_final: 0.7336 (mtm) REVERT: F 373 MET cc_start: 0.8711 (tpp) cc_final: 0.7695 (mmt) REVERT: F 434 MET cc_start: 0.8469 (tmm) cc_final: 0.7992 (tmm) REVERT: G 117 LYS cc_start: 0.8491 (tptt) cc_final: 0.8093 (tptm) REVERT: G 373 MET cc_start: 0.8515 (tpp) cc_final: 0.8302 (tpp) REVERT: J 72 ASP cc_start: 0.8631 (m-30) cc_final: 0.8176 (m-30) REVERT: S 76 TYR cc_start: 0.8831 (m-80) cc_final: 0.8425 (m-80) REVERT: S 100 ASP cc_start: 0.8293 (p0) cc_final: 0.7861 (p0) REVERT: U 140 TYR cc_start: 0.6502 (t80) cc_final: 0.6197 (t80) REVERT: X 191 SER cc_start: 0.8070 (p) cc_final: 0.7535 (m) REVERT: Y 165 GLU cc_start: 0.7872 (tp30) cc_final: 0.7619 (tp30) REVERT: B 530 MET cc_start: 0.7990 (ttm) cc_final: 0.7709 (ttp) REVERT: N 530 MET cc_start: 0.7786 (mmm) cc_final: 0.6812 (tmm) outliers start: 4 outliers final: 1 residues processed: 201 average time/residue: 0.1845 time to fit residues: 61.3447 Evaluate side-chains 156 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 229 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 281 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 chunk 168 optimal weight: 0.8980 chunk 159 optimal weight: 0.5980 chunk 244 optimal weight: 0.8980 chunk 221 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN D 69 GLN F 183 GLN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 490 GLN J 3 GLN J 62 GLN K 152 ASN S 3 GLN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 199 GLN ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.082659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.066381 restraints weight = 123977.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.066461 restraints weight = 84495.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.066924 restraints weight = 74310.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.067068 restraints weight = 63507.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.067170 restraints weight = 58498.446| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30292 Z= 0.127 Angle : 0.721 20.097 41479 Z= 0.330 Chirality : 0.048 0.401 4995 Planarity : 0.004 0.059 5045 Dihedral : 9.630 109.178 6579 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 0.16 % Allowed : 0.42 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.71 (0.14), residues: 3481 helix: -0.23 (0.26), residues: 397 sheet: -0.48 (0.16), residues: 995 loop : -1.71 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 633 TYR 0.014 0.001 TYR U 49 PHE 0.026 0.001 PHE D 97 TRP 0.017 0.001 TRP M 631 HIS 0.006 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00283 (30104) covalent geometry : angle 0.64349 (40970) SS BOND : bond 0.00360 ( 52) SS BOND : angle 1.26807 ( 104) hydrogen bonds : bond 0.03508 ( 674) hydrogen bonds : angle 5.63524 ( 1821) Misc. bond : bond 0.00034 ( 1) link_ALPHA1-2 : bond 0.00175 ( 3) link_ALPHA1-2 : angle 1.94015 ( 9) link_ALPHA1-3 : bond 0.01219 ( 9) link_ALPHA1-3 : angle 2.17714 ( 27) link_ALPHA1-6 : bond 0.00919 ( 9) link_ALPHA1-6 : angle 2.00654 ( 27) link_BETA1-4 : bond 0.00485 ( 41) link_BETA1-4 : angle 1.51291 ( 123) link_NAG-ASN : bond 0.00656 ( 73) link_NAG-ASN : angle 4.20273 ( 219) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 189 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8827 (mtp) cc_final: 0.8524 (mtm) REVERT: A 175 LEU cc_start: 0.9090 (tp) cc_final: 0.8876 (tp) REVERT: C 36 TRP cc_start: 0.9062 (m100) cc_final: 0.8819 (m-10) REVERT: D 4 MET cc_start: 0.8516 (tpp) cc_final: 0.8180 (tpt) REVERT: D 124 GLN cc_start: 0.7471 (tt0) cc_final: 0.7192 (tt0) REVERT: F 100 MET cc_start: 0.7628 (mtp) cc_final: 0.7339 (mtm) REVERT: F 373 MET cc_start: 0.8705 (tpp) cc_final: 0.7673 (mmt) REVERT: F 434 MET cc_start: 0.8464 (tmm) cc_final: 0.7976 (tmm) REVERT: G 117 LYS cc_start: 0.8433 (tptt) cc_final: 0.7997 (tptm) REVERT: S 76 TYR cc_start: 0.8819 (m-80) cc_final: 0.8471 (m-80) REVERT: S 100 ASP cc_start: 0.8327 (p0) cc_final: 0.7918 (p0) REVERT: U 140 TYR cc_start: 0.6411 (t80) cc_final: 0.5979 (t80) REVERT: X 156 ASP cc_start: 0.7604 (t70) cc_final: 0.7255 (t0) REVERT: X 191 SER cc_start: 0.8185 (p) cc_final: 0.7710 (m) REVERT: Y 165 GLU cc_start: 0.7875 (tp30) cc_final: 0.7635 (tp30) REVERT: B 530 MET cc_start: 0.7913 (ttm) cc_final: 0.7603 (ttp) outliers start: 5 outliers final: 2 residues processed: 193 average time/residue: 0.1876 time to fit residues: 59.4910 Evaluate side-chains 153 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 73 optimal weight: 2.9990 chunk 330 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 63 optimal weight: 0.0030 chunk 65 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 266 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 490 GLN J 62 GLN K 152 ASN S 3 GLN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.082070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.065753 restraints weight = 125137.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.065914 restraints weight = 85990.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.066261 restraints weight = 75536.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.066428 restraints weight = 65319.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.066528 restraints weight = 60017.793| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30292 Z= 0.156 Angle : 0.734 20.039 41479 Z= 0.338 Chirality : 0.049 0.584 4995 Planarity : 0.004 0.063 5045 Dihedral : 9.597 108.060 6579 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.06 % Allowed : 0.29 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.72 (0.14), residues: 3481 helix: -0.25 (0.26), residues: 397 sheet: -0.47 (0.16), residues: 983 loop : -1.72 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 633 TYR 0.027 0.001 TYR S 32 PHE 0.023 0.001 PHE A 317 TRP 0.022 0.001 TRP M 631 HIS 0.007 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00353 (30104) covalent geometry : angle 0.65660 (40970) SS BOND : bond 0.00361 ( 52) SS BOND : angle 1.28825 ( 104) hydrogen bonds : bond 0.03689 ( 674) hydrogen bonds : angle 5.64637 ( 1821) Misc. bond : bond 0.00007 ( 1) link_ALPHA1-2 : bond 0.00199 ( 3) link_ALPHA1-2 : angle 1.95638 ( 9) link_ALPHA1-3 : bond 0.01134 ( 9) link_ALPHA1-3 : angle 2.23928 ( 27) link_ALPHA1-6 : bond 0.00805 ( 9) link_ALPHA1-6 : angle 2.01647 ( 27) link_BETA1-4 : bond 0.00444 ( 41) link_BETA1-4 : angle 1.51516 ( 123) link_NAG-ASN : bond 0.00647 ( 73) link_NAG-ASN : angle 4.24366 ( 219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4017.49 seconds wall clock time: 71 minutes 32.38 seconds (4292.38 seconds total)