Starting phenix.real_space_refine on Tue Jan 21 12:22:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yw1_39619/01_2025/8yw1_39619.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yw1_39619/01_2025/8yw1_39619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yw1_39619/01_2025/8yw1_39619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yw1_39619/01_2025/8yw1_39619.map" model { file = "/net/cci-nas-00/data/ceres_data/8yw1_39619/01_2025/8yw1_39619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yw1_39619/01_2025/8yw1_39619.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 sd= 0.123 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 554 5.16 5 C 42627 2.51 5 N 11653 2.21 5 O 12910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 67744 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3330 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "B" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "C" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 896 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "D" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1245 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "F" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3330 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "G" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3330 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "H" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3330 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "I" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "J" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 386} Chain: "K" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "L" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 46} Chain: "M" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 46} Chain: "N" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 46} Chain: "O" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1245 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "P" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1245 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "Q" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1245 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "S" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 46} Chain: "E" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3330 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "R" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "T" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1245 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "U" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3330 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "V" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3330 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "W" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3330 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "X" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "Y" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 386} Chain: "Z" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "a" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 46} Chain: "b" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 46} Chain: "c" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 46} Chain: "d" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1245 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "e" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1245 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "f" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1245 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "g" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 46} Chain: "h" 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: "i" 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: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 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: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 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: 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: "s" 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: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 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: "w" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 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: "z" 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: "0" 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: "1" 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: "2" 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: "3" 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: "4" 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 Time building chain proxies: 29.38, per 1000 atoms: 0.43 Number of scatterers: 67744 At special positions: 0 Unit cell: (325.42, 195.04, 206.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 554 16.00 O 12910 8.00 N 11653 7.00 C 42627 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=121, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.05 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.02 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 125 " distance=2.03 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 105 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 120 " - pdb=" SG CYS C 140 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 179 " distance=2.02 Simple disulfide: pdb=" SG CYS C 173 " - pdb=" SG CYS C 188 " distance=2.02 Simple disulfide: pdb=" SG CYS C 193 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 200 " - pdb=" SG CYS C 218 " distance=2.02 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 229 " distance=2.02 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 114 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 271 " distance=2.05 Simple disulfide: pdb=" SG CYS F 301 " - pdb=" SG CYS F 376 " distance=2.02 Simple disulfide: pdb=" SG CYS F 306 " - pdb=" SG CYS F 380 " distance=2.03 Simple disulfide: pdb=" SG CYS F 328 " - pdb=" SG CYS F 370 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.05 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS H 49 " - pdb=" SG CYS H 114 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 94 " distance=2.03 Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 259 " - pdb=" SG CYS H 271 " distance=2.05 Simple disulfide: pdb=" SG CYS H 301 " - pdb=" SG CYS H 376 " distance=2.03 Simple disulfide: pdb=" SG CYS H 306 " - pdb=" SG CYS H 380 " distance=2.03 Simple disulfide: pdb=" SG CYS H 328 " - pdb=" SG CYS H 370 " distance=2.02 Simple disulfide: pdb=" SG CYS I 19 " - pdb=" SG CYS I 125 " distance=2.03 Simple disulfide: pdb=" SG CYS I 91 " - pdb=" SG CYS I 105 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 225 " distance=2.03 Simple disulfide: pdb=" SG CYS I 203 " - pdb=" SG CYS I 220 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 125 " distance=2.03 Simple disulfide: pdb=" SG CYS J 91 " - pdb=" SG CYS J 105 " distance=2.02 Simple disulfide: pdb=" SG CYS J 201 " - pdb=" SG CYS J 225 " distance=2.03 Simple disulfide: pdb=" SG CYS J 203 " - pdb=" SG CYS J 220 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 125 " distance=2.03 Simple disulfide: pdb=" SG CYS K 91 " - pdb=" SG CYS K 105 " distance=2.02 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 225 " distance=2.03 Simple disulfide: pdb=" SG CYS K 203 " - pdb=" SG CYS K 220 " distance=2.03 Simple disulfide: pdb=" SG CYS L 9 " - pdb=" SG CYS L 18 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 27 " distance=2.03 Simple disulfide: pdb=" SG CYS L 26 " - pdb=" SG CYS L 58 " distance=2.03 Simple disulfide: pdb=" SG CYS M 9 " - pdb=" SG CYS M 18 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 27 " distance=2.03 Simple disulfide: pdb=" SG CYS M 26 " - pdb=" SG CYS M 58 " distance=2.03 Simple disulfide: pdb=" SG CYS N 9 " - pdb=" SG CYS N 18 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 27 " distance=2.03 Simple disulfide: pdb=" SG CYS N 26 " - pdb=" SG CYS N 58 " distance=2.03 Simple disulfide: pdb=" SG CYS S 9 " - pdb=" SG CYS S 18 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 27 " distance=2.03 Simple disulfide: pdb=" SG CYS S 26 " - pdb=" SG CYS S 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 114 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 94 " distance=2.03 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 271 " distance=2.05 Simple disulfide: pdb=" SG CYS E 301 " - pdb=" SG CYS E 376 " distance=2.02 Simple disulfide: pdb=" SG CYS E 306 " - pdb=" SG CYS E 380 " distance=2.03 Simple disulfide: pdb=" SG CYS E 328 " - pdb=" SG CYS E 370 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 125 " distance=2.03 Simple disulfide: pdb=" SG CYS R 91 " - pdb=" SG CYS R 105 " distance=2.03 Simple disulfide: pdb=" SG CYS R 201 " - pdb=" SG CYS R 225 " distance=2.03 Simple disulfide: pdb=" SG CYS R 203 " - pdb=" SG CYS R 220 " distance=2.03 Simple disulfide: pdb=" SG CYS U 49 " - pdb=" SG CYS U 114 " distance=2.03 Simple disulfide: pdb=" SG CYS U 62 " - pdb=" SG CYS U 94 " distance=2.03 Simple disulfide: pdb=" SG CYS U 63 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS U 259 " - pdb=" SG CYS U 271 " distance=2.05 Simple disulfide: pdb=" SG CYS U 301 " - pdb=" SG CYS U 376 " distance=2.03 Simple disulfide: pdb=" SG CYS U 306 " - pdb=" SG CYS U 380 " distance=2.03 Simple disulfide: pdb=" SG CYS U 328 " - pdb=" SG CYS U 370 " distance=2.03 Simple disulfide: pdb=" SG CYS V 49 " - pdb=" SG CYS V 114 " distance=2.03 Simple disulfide: pdb=" SG CYS V 62 " - pdb=" SG CYS V 94 " distance=2.03 Simple disulfide: pdb=" SG CYS V 63 " - pdb=" SG CYS V 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 259 " - pdb=" SG CYS V 271 " distance=2.05 Simple disulfide: pdb=" SG CYS V 301 " - pdb=" SG CYS V 376 " distance=2.03 Simple disulfide: pdb=" SG CYS V 306 " - pdb=" SG CYS V 380 " distance=2.03 Simple disulfide: pdb=" SG CYS V 328 " - pdb=" SG CYS V 370 " distance=2.02 Simple disulfide: pdb=" SG CYS W 49 " - pdb=" SG CYS W 114 " distance=2.03 Simple disulfide: pdb=" SG CYS W 62 " - pdb=" SG CYS W 94 " distance=2.03 Simple disulfide: pdb=" SG CYS W 63 " - pdb=" SG CYS W 96 " distance=2.03 Simple disulfide: pdb=" SG CYS W 259 " - pdb=" SG CYS W 271 " distance=2.05 Simple disulfide: pdb=" SG CYS W 301 " - pdb=" SG CYS W 376 " distance=2.03 Simple disulfide: pdb=" SG CYS W 306 " - pdb=" SG CYS W 380 " distance=2.03 Simple disulfide: pdb=" SG CYS W 328 " - pdb=" SG CYS W 370 " distance=2.02 Simple disulfide: pdb=" SG CYS X 19 " - pdb=" SG CYS X 125 " distance=2.03 Simple disulfide: pdb=" SG CYS X 91 " - pdb=" SG CYS X 105 " distance=2.03 Simple disulfide: pdb=" SG CYS X 201 " - pdb=" SG CYS X 225 " distance=2.03 Simple disulfide: pdb=" SG CYS X 203 " - pdb=" SG CYS X 220 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 19 " - pdb=" SG CYS Y 125 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 91 " - pdb=" SG CYS Y 105 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 201 " - pdb=" SG CYS Y 225 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 203 " - pdb=" SG CYS Y 220 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 19 " - pdb=" SG CYS Z 125 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 91 " - pdb=" SG CYS Z 105 " distance=2.02 Simple disulfide: pdb=" SG CYS Z 201 " - pdb=" SG CYS Z 225 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 203 " - pdb=" SG CYS Z 220 " distance=2.03 Simple disulfide: pdb=" SG CYS a 9 " - pdb=" SG CYS a 18 " distance=2.03 Simple disulfide: pdb=" SG CYS a 23 " - pdb=" SG CYS a 27 " distance=2.03 Simple disulfide: pdb=" SG CYS a 26 " - pdb=" SG CYS a 58 " distance=2.03 Simple disulfide: pdb=" SG CYS b 9 " - pdb=" SG CYS b 18 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 27 " distance=2.03 Simple disulfide: pdb=" SG CYS b 26 " - pdb=" SG CYS b 58 " distance=2.03 Simple disulfide: pdb=" SG CYS c 9 " - pdb=" SG CYS c 18 " distance=2.03 Simple disulfide: pdb=" SG CYS c 23 " - pdb=" SG CYS c 27 " distance=2.03 Simple disulfide: pdb=" SG CYS c 26 " - pdb=" SG CYS c 58 " distance=2.03 Simple disulfide: pdb=" SG CYS g 9 " - pdb=" SG CYS g 18 " distance=2.03 Simple disulfide: pdb=" SG CYS g 23 " - pdb=" SG CYS g 27 " distance=2.03 Simple disulfide: pdb=" SG CYS g 26 " - pdb=" SG CYS g 58 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG 0 1 " - " ASN X 200 " " NAG 1 1 " - " ASN Y 262 " " NAG 2 1 " - " ASN Y 200 " " NAG 3 1 " - " ASN Z 262 " " NAG 4 1 " - " ASN Z 200 " " NAG h 1 " - " ASN A 141 " " NAG i 1 " - " ASN B 262 " " NAG j 1 " - " ASN B 200 " " NAG k 1 " - " ASN F 141 " " NAG l 1 " - " ASN G 141 " " NAG m 1 " - " ASN H 141 " " NAG n 1 " - " ASN I 262 " " NAG o 1 " - " ASN I 200 " " NAG p 1 " - " ASN J 262 " " NAG q 1 " - " ASN J 200 " " NAG r 1 " - " ASN K 262 " " NAG s 1 " - " ASN K 200 " " NAG t 1 " - " ASN E 141 " " NAG u 1 " - " ASN R 262 " " NAG v 1 " - " ASN R 200 " " NAG w 1 " - " ASN U 141 " " NAG x 1 " - " ASN V 141 " " NAG y 1 " - " ASN W 141 " " NAG z 1 " - " ASN X 262 " Time building additional restraints: 13.18 Conformation dependent library (CDL) restraints added in 6.9 seconds 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16112 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 157 sheets defined 15.7% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.18 Creating SS restraints... Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.855A pdb=" N LYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 removed outlier: 4.155A pdb=" N GLY A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 259' Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.521A pdb=" N ALA A 286 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 287 " --> pdb=" O ASP A 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 283 through 287' Processing helix chain 'A' and resid 404 through 438 Processing helix chain 'B' and resid 7 through 11 Processing helix chain 'B' and resid 350 through 361 removed outlier: 3.669A pdb=" N VAL B 355 " --> pdb=" O PRO B 351 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN B 356 " --> pdb=" O HIS B 352 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 397 removed outlier: 4.048A pdb=" N SER B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 401 Processing helix chain 'B' and resid 407 through 414 removed outlier: 3.740A pdb=" N ILE B 413 " --> pdb=" O TRP B 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'D' and resid 108 through 119 Processing helix chain 'D' and resid 152 through 157 Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.566A pdb=" N MET D 177 " --> pdb=" O PRO D 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 246 removed outlier: 3.727A pdb=" N TYR F 242 " --> pdb=" O SER F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 259 removed outlier: 4.122A pdb=" N GLY F 258 " --> pdb=" O ALA F 255 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N CYS F 259 " --> pdb=" O PRO F 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 255 through 259' Processing helix chain 'F' and resid 404 through 438 removed outlier: 3.648A pdb=" N ARG F 438 " --> pdb=" O ILE F 434 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 247 removed outlier: 3.656A pdb=" N TYR G 242 " --> pdb=" O SER G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 259 removed outlier: 4.178A pdb=" N GLY G 258 " --> pdb=" O ALA G 255 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS G 259 " --> pdb=" O PRO G 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 255 through 259' Processing helix chain 'G' and resid 283 through 287 removed outlier: 3.672A pdb=" N ALA G 286 " --> pdb=" O PRO G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 293 Processing helix chain 'G' and resid 404 through 438 Processing helix chain 'H' and resid 238 through 247 removed outlier: 3.563A pdb=" N LYS H 245 " --> pdb=" O LYS H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 259 removed outlier: 4.030A pdb=" N GLY H 258 " --> pdb=" O ALA H 255 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS H 259 " --> pdb=" O PRO H 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 255 through 259' Processing helix chain 'H' and resid 404 through 438 Processing helix chain 'I' and resid 221 through 225 removed outlier: 3.894A pdb=" N GLN I 224 " --> pdb=" O LEU I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 361 removed outlier: 3.685A pdb=" N VAL I 355 " --> pdb=" O PRO I 351 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN I 356 " --> pdb=" O HIS I 352 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU I 361 " --> pdb=" O TYR I 357 " (cutoff:3.500A) Processing helix chain 'I' and resid 364 through 397 removed outlier: 4.097A pdb=" N SER I 368 " --> pdb=" O ALA I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 401 removed outlier: 3.799A pdb=" N LEU I 401 " --> pdb=" O PRO I 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 398 through 401' Processing helix chain 'I' and resid 407 through 414 removed outlier: 3.579A pdb=" N ILE I 413 " --> pdb=" O TRP I 409 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 12 removed outlier: 3.586A pdb=" N ALA J 11 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR J 12 " --> pdb=" O TYR J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 361 removed outlier: 3.709A pdb=" N VAL J 355 " --> pdb=" O PRO J 351 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN J 356 " --> pdb=" O HIS J 352 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU J 361 " --> pdb=" O TYR J 357 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 397 Processing helix chain 'J' and resid 398 through 401 Processing helix chain 'J' and resid 407 through 414 removed outlier: 3.727A pdb=" N ILE J 413 " --> pdb=" O TRP J 409 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 11 Processing helix chain 'K' and resid 350 through 361 removed outlier: 3.602A pdb=" N VAL K 355 " --> pdb=" O PRO K 351 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN K 356 " --> pdb=" O HIS K 352 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU K 361 " --> pdb=" O TYR K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 364 through 397 removed outlier: 4.164A pdb=" N SER K 368 " --> pdb=" O ALA K 364 " (cutoff:3.500A) Processing helix chain 'K' and resid 398 through 402 removed outlier: 3.921A pdb=" N THR K 402 " --> pdb=" O TYR K 399 " (cutoff:3.500A) Processing helix chain 'K' and resid 407 through 414 removed outlier: 3.679A pdb=" N ILE K 413 " --> pdb=" O TRP K 409 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 31 Processing helix chain 'L' and resid 31 through 40 Processing helix chain 'L' and resid 48 through 56 removed outlier: 3.622A pdb=" N LEU L 56 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 31 Processing helix chain 'M' and resid 31 through 42 removed outlier: 3.528A pdb=" N ASN M 42 " --> pdb=" O MET M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 56 removed outlier: 3.505A pdb=" N LEU M 56 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 31 Processing helix chain 'N' and resid 31 through 41 removed outlier: 3.809A pdb=" N ASP N 41 " --> pdb=" O ARG N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 55 Processing helix chain 'O' and resid 108 through 119 Processing helix chain 'O' and resid 152 through 158 removed outlier: 3.721A pdb=" N LYS O 157 " --> pdb=" O ALA O 153 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU O 158 " --> pdb=" O ASP O 154 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 181 removed outlier: 4.494A pdb=" N SER O 179 " --> pdb=" O HIS O 176 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA O 181 " --> pdb=" O ARG O 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 119 Processing helix chain 'P' and resid 152 through 157 removed outlier: 3.898A pdb=" N LYS P 157 " --> pdb=" O ALA P 153 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 181 removed outlier: 3.546A pdb=" N MET P 177 " --> pdb=" O PRO P 174 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N SER P 179 " --> pdb=" O HIS P 176 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA P 181 " --> pdb=" O ARG P 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 119 Processing helix chain 'Q' and resid 152 through 157 removed outlier: 3.606A pdb=" N LYS Q 157 " --> pdb=" O ALA Q 153 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 181 removed outlier: 5.187A pdb=" N SER Q 179 " --> pdb=" O HIS Q 176 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA Q 181 " --> pdb=" O ARG Q 178 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 31 Processing helix chain 'S' and resid 31 through 41 removed outlier: 3.697A pdb=" N ASP S 41 " --> pdb=" O ARG S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 56 Processing helix chain 'E' and resid 238 through 246 removed outlier: 3.853A pdb=" N LYS E 245 " --> pdb=" O LYS E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 259 removed outlier: 4.156A pdb=" N GLY E 258 " --> pdb=" O ALA E 255 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N CYS E 259 " --> pdb=" O PRO E 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 255 through 259' Processing helix chain 'E' and resid 283 through 287 removed outlier: 3.521A pdb=" N ALA E 286 " --> pdb=" O PRO E 283 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE E 287 " --> pdb=" O ASP E 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 283 through 287' Processing helix chain 'E' and resid 404 through 438 Processing helix chain 'R' and resid 7 through 11 Processing helix chain 'R' and resid 350 through 361 removed outlier: 3.668A pdb=" N VAL R 355 " --> pdb=" O PRO R 351 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN R 356 " --> pdb=" O HIS R 352 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU R 361 " --> pdb=" O TYR R 357 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 397 removed outlier: 4.049A pdb=" N SER R 368 " --> pdb=" O ALA R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 398 through 401 Processing helix chain 'R' and resid 407 through 414 removed outlier: 3.742A pdb=" N ILE R 413 " --> pdb=" O TRP R 409 " (cutoff:3.500A) Processing helix chain 'T' and resid 108 through 119 Processing helix chain 'T' and resid 152 through 157 Processing helix chain 'T' and resid 174 through 178 removed outlier: 3.566A pdb=" N MET T 177 " --> pdb=" O PRO T 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 238 through 246 removed outlier: 3.727A pdb=" N TYR U 242 " --> pdb=" O SER U 238 " (cutoff:3.500A) Processing helix chain 'U' and resid 255 through 259 removed outlier: 4.122A pdb=" N GLY U 258 " --> pdb=" O ALA U 255 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS U 259 " --> pdb=" O PRO U 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 255 through 259' Processing helix chain 'U' and resid 404 through 438 removed outlier: 3.648A pdb=" N ARG U 438 " --> pdb=" O ILE U 434 " (cutoff:3.500A) Processing helix chain 'V' and resid 238 through 247 removed outlier: 3.655A pdb=" N TYR V 242 " --> pdb=" O SER V 238 " (cutoff:3.500A) Processing helix chain 'V' and resid 255 through 259 removed outlier: 4.177A pdb=" N GLY V 258 " --> pdb=" O ALA V 255 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N CYS V 259 " --> pdb=" O PRO V 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 255 through 259' Processing helix chain 'V' and resid 283 through 287 removed outlier: 3.672A pdb=" N ALA V 286 " --> pdb=" O PRO V 283 " (cutoff:3.500A) Processing helix chain 'V' and resid 289 through 293 Processing helix chain 'V' and resid 404 through 438 Processing helix chain 'W' and resid 238 through 247 removed outlier: 3.564A pdb=" N LYS W 245 " --> pdb=" O LYS W 241 " (cutoff:3.500A) Processing helix chain 'W' and resid 255 through 259 removed outlier: 4.030A pdb=" N GLY W 258 " --> pdb=" O ALA W 255 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS W 259 " --> pdb=" O PRO W 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 255 through 259' Processing helix chain 'W' and resid 404 through 438 Processing helix chain 'X' and resid 221 through 225 removed outlier: 3.893A pdb=" N GLN X 224 " --> pdb=" O LEU X 221 " (cutoff:3.500A) Processing helix chain 'X' and resid 350 through 361 removed outlier: 3.685A pdb=" N VAL X 355 " --> pdb=" O PRO X 351 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN X 356 " --> pdb=" O HIS X 352 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU X 361 " --> pdb=" O TYR X 357 " (cutoff:3.500A) Processing helix chain 'X' and resid 364 through 397 removed outlier: 4.096A pdb=" N SER X 368 " --> pdb=" O ALA X 364 " (cutoff:3.500A) Processing helix chain 'X' and resid 398 through 401 removed outlier: 3.800A pdb=" N LEU X 401 " --> pdb=" O PRO X 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 398 through 401' Processing helix chain 'X' and resid 407 through 414 removed outlier: 3.579A pdb=" N ILE X 413 " --> pdb=" O TRP X 409 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 12 removed outlier: 3.588A pdb=" N ALA Y 11 " --> pdb=" O VAL Y 8 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR Y 12 " --> pdb=" O TYR Y 9 " (cutoff:3.500A) Processing helix chain 'Y' and resid 350 through 361 removed outlier: 3.709A pdb=" N VAL Y 355 " --> pdb=" O PRO Y 351 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN Y 356 " --> pdb=" O HIS Y 352 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU Y 361 " --> pdb=" O TYR Y 357 " (cutoff:3.500A) Processing helix chain 'Y' and resid 365 through 397 Processing helix chain 'Y' and resid 398 through 401 Processing helix chain 'Y' and resid 407 through 414 removed outlier: 3.727A pdb=" N ILE Y 413 " --> pdb=" O TRP Y 409 " (cutoff:3.500A) Processing helix chain 'Z' and resid 7 through 11 Processing helix chain 'Z' and resid 350 through 361 removed outlier: 3.602A pdb=" N VAL Z 355 " --> pdb=" O PRO Z 351 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN Z 356 " --> pdb=" O HIS Z 352 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU Z 361 " --> pdb=" O TYR Z 357 " (cutoff:3.500A) Processing helix chain 'Z' and resid 364 through 397 removed outlier: 4.163A pdb=" N SER Z 368 " --> pdb=" O ALA Z 364 " (cutoff:3.500A) Processing helix chain 'Z' and resid 398 through 402 removed outlier: 3.921A pdb=" N THR Z 402 " --> pdb=" O TYR Z 399 " (cutoff:3.500A) Processing helix chain 'Z' and resid 407 through 414 removed outlier: 3.679A pdb=" N ILE Z 413 " --> pdb=" O TRP Z 409 " (cutoff:3.500A) Processing helix chain 'a' and resid 26 through 31 Processing helix chain 'a' and resid 31 through 40 Processing helix chain 'a' and resid 48 through 56 removed outlier: 3.621A pdb=" N LEU a 56 " --> pdb=" O LEU a 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 26 through 31 Processing helix chain 'b' and resid 31 through 42 removed outlier: 3.528A pdb=" N ASN b 42 " --> pdb=" O MET b 38 " (cutoff:3.500A) Processing helix chain 'b' and resid 47 through 56 removed outlier: 3.504A pdb=" N LEU b 56 " --> pdb=" O LEU b 52 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 31 Processing helix chain 'c' and resid 31 through 41 removed outlier: 3.811A pdb=" N ASP c 41 " --> pdb=" O ARG c 37 " (cutoff:3.500A) Processing helix chain 'c' and resid 47 through 55 Processing helix chain 'd' and resid 108 through 119 Processing helix chain 'd' and resid 152 through 158 removed outlier: 3.720A pdb=" N LYS d 157 " --> pdb=" O ALA d 153 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU d 158 " --> pdb=" O ASP d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 174 through 181 removed outlier: 4.495A pdb=" N SER d 179 " --> pdb=" O HIS d 176 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA d 181 " --> pdb=" O ARG d 178 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 119 Processing helix chain 'e' and resid 152 through 157 removed outlier: 3.899A pdb=" N LYS e 157 " --> pdb=" O ALA e 153 " (cutoff:3.500A) Processing helix chain 'e' and resid 174 through 181 removed outlier: 3.546A pdb=" N MET e 177 " --> pdb=" O PRO e 174 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N SER e 179 " --> pdb=" O HIS e 176 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA e 181 " --> pdb=" O ARG e 178 " (cutoff:3.500A) Processing helix chain 'f' and resid 108 through 119 Processing helix chain 'f' and resid 152 through 157 removed outlier: 3.608A pdb=" N LYS f 157 " --> pdb=" O ALA f 153 " (cutoff:3.500A) Processing helix chain 'f' and resid 174 through 181 removed outlier: 5.189A pdb=" N SER f 179 " --> pdb=" O HIS f 176 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA f 181 " --> pdb=" O ARG f 178 " (cutoff:3.500A) Processing helix chain 'g' and resid 26 through 31 Processing helix chain 'g' and resid 31 through 41 removed outlier: 3.698A pdb=" N ASP g 41 " --> pdb=" O ARG g 37 " (cutoff:3.500A) Processing helix chain 'g' and resid 47 through 56 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.618A pdb=" N HIS A 3 " --> pdb=" O MET A 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 5.310A pdb=" N MET A 31 " --> pdb=" O MET A 136 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N MET A 136 " --> pdb=" O MET A 31 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N THR A 126 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ASN A 43 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ALA A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N GLU A 45 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N TYR A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE A 47 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N SER A 120 " --> pdb=" O ILE A 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 143 through 147 current: chain 'A' and resid 183 through 186 Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 51 through 54 current: chain 'A' and resid 101 through 110 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA5, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA6, first strand: chain 'A' and resid 260 through 262 Processing sheet with id=AA7, first strand: chain 'A' and resid 296 through 306 removed outlier: 5.751A pdb=" N ASP A 298 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS A 321 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL A 315 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AA9, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB1, first strand: chain 'B' and resid 17 through 19 removed outlier: 3.649A pdb=" N ALA B 17 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS B 19 " --> pdb=" O CYS B 28 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS B 28 " --> pdb=" O CYS B 19 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 75 through 79 removed outlier: 4.456A pdb=" N GLY B 55 " --> pdb=" O ASP B 63 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N THR B 65 " --> pdb=" O GLN B 53 " (cutoff:3.500A) removed outlier: 11.692A pdb=" N GLN B 53 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 11.637A pdb=" N ILE B 67 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 11.430A pdb=" N SER B 51 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 13.182A pdb=" N TYR B 69 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 16.587A pdb=" N GLN B 49 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 10.921A pdb=" N PHE B 50 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 11.803A pdb=" N LEU B 102 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 9.527A pdb=" N ALA B 52 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE B 100 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ILE B 56 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 13.102A pdb=" N THR B 96 " --> pdb=" O ILE B 56 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 84 through 86 removed outlier: 5.400A pdb=" N TYR B 129 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLN B 112 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE B 127 " --> pdb=" O GLN B 112 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N SER B 114 " --> pdb=" O CYS B 125 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N CYS B 125 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLN B 116 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ARG B 123 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 149 through 156 Processing sheet with id=AB5, first strand: chain 'B' and resid 175 through 177 removed outlier: 3.759A pdb=" N VAL B 227 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B 209 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB7, first strand: chain 'B' and resid 274 through 277 removed outlier: 3.545A pdb=" N LEU B 286 " --> pdb=" O VAL B 314 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 117 through 119 Processing sheet with id=AB9, first strand: chain 'C' and resid 158 through 160 Processing sheet with id=AC1, first strand: chain 'C' and resid 197 through 199 Processing sheet with id=AC2, first strand: chain 'D' and resid 149 through 150 removed outlier: 3.556A pdb=" N VAL D 149 " --> pdb=" O LYS D 124 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY D 131 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N HIS D 125 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL D 129 " --> pdb=" O HIS D 125 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N TYR D 132 " --> pdb=" O PRO D 143 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 191 through 195 removed outlier: 3.762A pdb=" N GLY D 191 " --> pdb=" O TYR D 202 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 206 through 209 current: chain 'D' and resid 230 through 240 removed outlier: 7.861A pdb=" N ALA D 232 " --> pdb=" O TRP D 251 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N TRP D 251 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL D 234 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL D 249 " --> pdb=" O VAL D 234 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 2 through 8 removed outlier: 3.709A pdb=" N HIS F 3 " --> pdb=" O MET F 280 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 27 through 42 current: chain 'F' and resid 119 through 136 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 143 through 147 current: chain 'F' and resid 183 through 186 Processing sheet with id=AC6, first strand: chain 'F' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 51 through 54 current: chain 'F' and resid 100 through 110 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 203 through 204 Processing sheet with id=AC8, first strand: chain 'F' and resid 220 through 221 Processing sheet with id=AC9, first strand: chain 'F' and resid 260 through 262 removed outlier: 3.521A pdb=" N ARG F 267 " --> pdb=" O LYS F 262 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 296 through 305 removed outlier: 5.730A pdb=" N ASP F 298 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS F 321 " --> pdb=" O ASP F 298 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL F 315 " --> pdb=" O ALA F 304 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 326 through 328 removed outlier: 3.505A pdb=" N VAL F 346 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 331 through 332 Processing sheet with id=AD4, first strand: chain 'F' and resid 387 through 388 Processing sheet with id=AD5, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AD6, first strand: chain 'G' and resid 15 through 19 removed outlier: 5.353A pdb=" N MET G 31 " --> pdb=" O MET G 136 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N MET G 136 " --> pdb=" O MET G 31 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N THR G 126 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASN G 43 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ALA G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE G 47 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N SER G 120 " --> pdb=" O ILE G 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 143 through 147 current: chain 'G' and resid 183 through 186 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 183 through 186 current: chain 'G' and resid 267 through 269 Processing sheet with id=AD7, first strand: chain 'G' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 51 through 54 current: chain 'G' and resid 100 through 110 No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'G' and resid 203 through 204 Processing sheet with id=AD9, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AE1, first strand: chain 'G' and resid 297 through 306 removed outlier: 5.722A pdb=" N ASP G 298 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS G 321 " --> pdb=" O ASP G 298 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL G 315 " --> pdb=" O ALA G 304 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 343 through 346 Processing sheet with id=AE3, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AE4, first strand: chain 'H' and resid 2 through 8 removed outlier: 3.582A pdb=" N HIS H 3 " --> pdb=" O MET H 280 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 27 through 42 current: chain 'H' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 140 through 147 current: chain 'H' and resid 183 through 185 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 183 through 185 current: chain 'H' and resid 267 through 269 Processing sheet with id=AE6, first strand: chain 'H' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 51 through 54 current: chain 'H' and resid 101 through 110 No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'H' and resid 203 through 204 Processing sheet with id=AE8, first strand: chain 'H' and resid 220 through 221 Processing sheet with id=AE9, first strand: chain 'H' and resid 296 through 305 removed outlier: 5.592A pdb=" N ASP H 298 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS H 321 " --> pdb=" O ASP H 298 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL H 315 " --> pdb=" O ALA H 304 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 326 through 328 removed outlier: 3.562A pdb=" N GLY H 326 " --> pdb=" O VAL H 346 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 331 through 332 Processing sheet with id=AF3, first strand: chain 'H' and resid 387 through 388 Processing sheet with id=AF4, first strand: chain 'I' and resid 17 through 18 Processing sheet with id=AF5, first strand: chain 'I' and resid 46 through 54 removed outlier: 11.359A pdb=" N ILE I 48 " --> pdb=" O LYS I 104 " (cutoff:3.500A) removed outlier: 10.773A pdb=" N LYS I 104 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 11.105A pdb=" N PHE I 50 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 11.545A pdb=" N LEU I 102 " --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 9.857A pdb=" N ALA I 52 " --> pdb=" O PHE I 100 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE I 100 " --> pdb=" O ALA I 52 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 66 through 70 Processing sheet with id=AF7, first strand: chain 'I' and resid 84 through 86 removed outlier: 4.088A pdb=" N GLU I 109 " --> pdb=" O TYR I 129 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 149 through 156 removed outlier: 3.559A pdb=" N VAL I 267 " --> pdb=" O LYS I 149 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 175 through 177 removed outlier: 3.752A pdb=" N VAL I 227 " --> pdb=" O ASP I 177 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY I 209 " --> pdb=" O TYR I 199 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AG2, first strand: chain 'I' and resid 274 through 277 Processing sheet with id=AG3, first strand: chain 'J' and resid 17 through 19 removed outlier: 3.583A pdb=" N CYS J 19 " --> pdb=" O CYS J 28 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS J 28 " --> pdb=" O CYS J 19 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 75 through 79 removed outlier: 4.738A pdb=" N GLY J 55 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N THR J 65 " --> pdb=" O GLN J 53 " (cutoff:3.500A) removed outlier: 12.066A pdb=" N GLN J 53 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 11.673A pdb=" N ILE J 67 " --> pdb=" O SER J 51 " (cutoff:3.500A) removed outlier: 11.396A pdb=" N SER J 51 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 13.224A pdb=" N TYR J 69 " --> pdb=" O GLN J 49 " (cutoff:3.500A) removed outlier: 16.702A pdb=" N GLN J 49 " --> pdb=" O TYR J 69 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N HIS J 99 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 9.608A pdb=" N ALA J 52 " --> pdb=" O MET J 97 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N MET J 97 " --> pdb=" O ALA J 52 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N ILE J 54 " --> pdb=" O GLY J 95 " (cutoff:3.500A) removed outlier: 10.905A pdb=" N GLY J 95 " --> pdb=" O ILE J 54 " (cutoff:3.500A) removed outlier: 15.374A pdb=" N ILE J 56 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 18.501A pdb=" N VAL J 93 " --> pdb=" O ILE J 56 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 84 through 86 removed outlier: 4.238A pdb=" N GLU J 109 " --> pdb=" O TYR J 129 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 149 through 152 Processing sheet with id=AG7, first strand: chain 'J' and resid 155 through 156 Processing sheet with id=AG8, first strand: chain 'J' and resid 167 through 169 Processing sheet with id=AG9, first strand: chain 'J' and resid 175 through 176 Processing sheet with id=AH1, first strand: chain 'J' and resid 181 through 183 Processing sheet with id=AH2, first strand: chain 'J' and resid 274 through 277 Processing sheet with id=AH3, first strand: chain 'K' and resid 17 through 19 removed outlier: 3.563A pdb=" N ALA K 17 " --> pdb=" O SER K 30 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS K 19 " --> pdb=" O CYS K 28 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N CYS K 28 " --> pdb=" O CYS K 19 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 37 through 38 removed outlier: 3.716A pdb=" N ARG K 38 " --> pdb=" O LYS K 47 " (cutoff:3.500A) removed outlier: 11.315A pdb=" N ILE K 48 " --> pdb=" O LYS K 104 " (cutoff:3.500A) removed outlier: 10.834A pdb=" N LYS K 104 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 11.314A pdb=" N PHE K 50 " --> pdb=" O LEU K 102 " (cutoff:3.500A) removed outlier: 11.601A pdb=" N LEU K 102 " --> pdb=" O PHE K 50 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N ALA K 52 " --> pdb=" O PHE K 100 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE K 100 " --> pdb=" O ALA K 52 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 66 through 69 Processing sheet with id=AH6, first strand: chain 'K' and resid 84 through 86 removed outlier: 4.239A pdb=" N GLU K 109 " --> pdb=" O TYR K 129 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 149 through 152 Processing sheet with id=AH8, first strand: chain 'K' and resid 155 through 156 Processing sheet with id=AH9, first strand: chain 'K' and resid 175 through 176 removed outlier: 3.780A pdb=" N GLY K 209 " --> pdb=" O TYR K 199 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 182 through 183 Processing sheet with id=AI2, first strand: chain 'K' and resid 274 through 277 Processing sheet with id=AI3, first strand: chain 'O' and resid 149 through 150 removed outlier: 6.097A pdb=" N HIS O 125 " --> pdb=" O VAL O 129 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL O 129 " --> pdb=" O HIS O 125 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'O' and resid 191 through 195 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 206 through 209 current: chain 'O' and resid 230 through 240 removed outlier: 7.474A pdb=" N ALA O 232 " --> pdb=" O TRP O 251 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N TRP O 251 " --> pdb=" O ALA O 232 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL O 234 " --> pdb=" O VAL O 249 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL O 249 " --> pdb=" O VAL O 234 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'P' and resid 149 through 150 removed outlier: 4.230A pdb=" N GLY P 131 " --> pdb=" O VAL P 123 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N HIS P 125 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL P 129 " --> pdb=" O HIS P 125 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N TYR P 132 " --> pdb=" O PRO P 143 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU P 168 " --> pdb=" O SER P 163 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'P' and resid 191 through 195 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 206 through 209 current: chain 'P' and resid 230 through 240 removed outlier: 7.848A pdb=" N ALA P 232 " --> pdb=" O TRP P 251 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N TRP P 251 " --> pdb=" O ALA P 232 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL P 234 " --> pdb=" O VAL P 249 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL P 249 " --> pdb=" O VAL P 234 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Q' and resid 149 through 150 removed outlier: 3.571A pdb=" N VAL Q 149 " --> pdb=" O LYS Q 124 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE Q 121 " --> pdb=" O TYR Q 132 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N TYR Q 132 " --> pdb=" O PHE Q 121 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL Q 123 " --> pdb=" O THR Q 130 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N TYR Q 132 " --> pdb=" O PRO Q 143 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER Q 163 " --> pdb=" O LEU Q 168 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'Q' and resid 191 through 195 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 207 through 209 current: chain 'Q' and resid 230 through 240 removed outlier: 7.675A pdb=" N ALA Q 232 " --> pdb=" O TRP Q 251 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N TRP Q 251 " --> pdb=" O ALA Q 232 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N VAL Q 234 " --> pdb=" O VAL Q 249 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL Q 249 " --> pdb=" O VAL Q 234 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 2 through 8 removed outlier: 3.618A pdb=" N HIS E 3 " --> pdb=" O MET E 280 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 15 through 19 removed outlier: 5.310A pdb=" N MET E 31 " --> pdb=" O MET E 136 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N MET E 136 " --> pdb=" O MET E 31 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL E 33 " --> pdb=" O ARG E 134 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG E 134 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR E 41 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N THR E 126 " --> pdb=" O THR E 41 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ASN E 43 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ALA E 124 " --> pdb=" O ASN E 43 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N GLU E 45 " --> pdb=" O TYR E 122 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N TYR E 122 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE E 47 " --> pdb=" O SER E 120 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N SER E 120 " --> pdb=" O ILE E 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 143 through 147 current: chain 'E' and resid 183 through 186 Processing sheet with id=AJ2, first strand: chain 'E' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 51 through 54 current: chain 'E' and resid 101 through 110 No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'E' and resid 203 through 204 Processing sheet with id=AJ4, first strand: chain 'E' and resid 220 through 221 Processing sheet with id=AJ5, first strand: chain 'E' and resid 260 through 262 Processing sheet with id=AJ6, first strand: chain 'E' and resid 296 through 306 removed outlier: 5.751A pdb=" N ASP E 298 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS E 321 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL E 315 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'E' and resid 343 through 346 Processing sheet with id=AJ8, first strand: chain 'E' and resid 387 through 388 Processing sheet with id=AJ9, first strand: chain 'R' and resid 17 through 19 removed outlier: 3.650A pdb=" N ALA R 17 " --> pdb=" O SER R 30 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS R 19 " --> pdb=" O CYS R 28 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS R 28 " --> pdb=" O CYS R 19 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'R' and resid 75 through 79 removed outlier: 4.456A pdb=" N GLY R 55 " --> pdb=" O ASP R 63 " (cutoff:3.500A) removed outlier: 10.224A pdb=" N THR R 65 " --> pdb=" O GLN R 53 " (cutoff:3.500A) removed outlier: 11.692A pdb=" N GLN R 53 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 11.639A pdb=" N ILE R 67 " --> pdb=" O SER R 51 " (cutoff:3.500A) removed outlier: 11.430A pdb=" N SER R 51 " --> pdb=" O ILE R 67 " (cutoff:3.500A) removed outlier: 13.182A pdb=" N TYR R 69 " --> pdb=" O GLN R 49 " (cutoff:3.500A) removed outlier: 16.587A pdb=" N GLN R 49 " --> pdb=" O TYR R 69 " (cutoff:3.500A) removed outlier: 10.920A pdb=" N PHE R 50 " --> pdb=" O LEU R 102 " (cutoff:3.500A) removed outlier: 11.802A pdb=" N LEU R 102 " --> pdb=" O PHE R 50 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N ALA R 52 " --> pdb=" O PHE R 100 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE R 100 " --> pdb=" O ALA R 52 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ILE R 56 " --> pdb=" O THR R 96 " (cutoff:3.500A) removed outlier: 13.102A pdb=" N THR R 96 " --> pdb=" O ILE R 56 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'R' and resid 84 through 86 removed outlier: 5.401A pdb=" N TYR R 129 " --> pdb=" O PHE R 110 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLN R 112 " --> pdb=" O ILE R 127 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE R 127 " --> pdb=" O GLN R 112 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N SER R 114 " --> pdb=" O CYS R 125 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N CYS R 125 " --> pdb=" O SER R 114 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLN R 116 " --> pdb=" O ARG R 123 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ARG R 123 " --> pdb=" O GLN R 116 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'R' and resid 149 through 156 Processing sheet with id=AK4, first strand: chain 'R' and resid 175 through 177 removed outlier: 3.758A pdb=" N VAL R 227 " --> pdb=" O ASP R 177 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY R 209 " --> pdb=" O TYR R 199 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'R' and resid 181 through 183 Processing sheet with id=AK6, first strand: chain 'R' and resid 274 through 277 removed outlier: 3.546A pdb=" N LEU R 286 " --> pdb=" O VAL R 314 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'T' and resid 149 through 150 removed outlier: 3.555A pdb=" N VAL T 149 " --> pdb=" O LYS T 124 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY T 131 " --> pdb=" O VAL T 123 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N HIS T 125 " --> pdb=" O VAL T 129 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL T 129 " --> pdb=" O HIS T 125 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N TYR T 132 " --> pdb=" O PRO T 143 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'T' and resid 191 through 195 removed outlier: 3.761A pdb=" N GLY T 191 " --> pdb=" O TYR T 202 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 206 through 209 current: chain 'T' and resid 230 through 240 removed outlier: 7.860A pdb=" N ALA T 232 " --> pdb=" O TRP T 251 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N TRP T 251 " --> pdb=" O ALA T 232 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL T 234 " --> pdb=" O VAL T 249 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL T 249 " --> pdb=" O VAL T 234 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'U' and resid 2 through 8 removed outlier: 3.709A pdb=" N HIS U 3 " --> pdb=" O MET U 280 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'U' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 27 through 42 current: chain 'U' and resid 119 through 136 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 143 through 147 current: chain 'U' and resid 183 through 186 Processing sheet with id=AL2, first strand: chain 'U' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 51 through 54 current: chain 'U' and resid 100 through 110 No H-bonds generated for sheet with id=AL2 Processing sheet with id=AL3, first strand: chain 'U' and resid 203 through 204 Processing sheet with id=AL4, first strand: chain 'U' and resid 220 through 221 Processing sheet with id=AL5, first strand: chain 'U' and resid 260 through 262 removed outlier: 3.520A pdb=" N ARG U 267 " --> pdb=" O LYS U 262 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'U' and resid 296 through 305 removed outlier: 5.730A pdb=" N ASP U 298 " --> pdb=" O LYS U 321 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS U 321 " --> pdb=" O ASP U 298 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL U 315 " --> pdb=" O ALA U 304 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'U' and resid 326 through 328 removed outlier: 3.506A pdb=" N VAL U 346 " --> pdb=" O GLY U 326 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'U' and resid 331 through 332 Processing sheet with id=AL9, first strand: chain 'U' and resid 387 through 388 Processing sheet with id=AM1, first strand: chain 'V' and resid 2 through 8 Processing sheet with id=AM2, first strand: chain 'V' and resid 15 through 19 removed outlier: 5.352A pdb=" N MET V 31 " --> pdb=" O MET V 136 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N MET V 136 " --> pdb=" O MET V 31 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL V 33 " --> pdb=" O ARG V 134 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG V 134 " --> pdb=" O VAL V 33 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR V 41 " --> pdb=" O THR V 126 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N THR V 126 " --> pdb=" O THR V 41 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASN V 43 " --> pdb=" O ALA V 124 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ALA V 124 " --> pdb=" O ASN V 43 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLU V 45 " --> pdb=" O TYR V 122 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N TYR V 122 " --> pdb=" O GLU V 45 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE V 47 " --> pdb=" O SER V 120 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N SER V 120 " --> pdb=" O ILE V 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 143 through 147 current: chain 'V' and resid 183 through 186 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 183 through 186 current: chain 'V' and resid 267 through 269 Processing sheet with id=AM3, first strand: chain 'V' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 51 through 54 current: chain 'V' and resid 100 through 110 No H-bonds generated for sheet with id=AM3 Processing sheet with id=AM4, first strand: chain 'V' and resid 203 through 204 Processing sheet with id=AM5, first strand: chain 'V' and resid 220 through 221 Processing sheet with id=AM6, first strand: chain 'V' and resid 297 through 306 removed outlier: 5.723A pdb=" N ASP V 298 " --> pdb=" O LYS V 321 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS V 321 " --> pdb=" O ASP V 298 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL V 315 " --> pdb=" O ALA V 304 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'V' and resid 343 through 346 Processing sheet with id=AM8, first strand: chain 'V' and resid 387 through 388 Processing sheet with id=AM9, first strand: chain 'W' and resid 2 through 8 removed outlier: 3.581A pdb=" N HIS W 3 " --> pdb=" O MET W 280 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'W' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 27 through 42 current: chain 'W' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 140 through 147 current: chain 'W' and resid 183 through 185 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 183 through 185 current: chain 'W' and resid 267 through 269 Processing sheet with id=AN2, first strand: chain 'W' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 51 through 54 current: chain 'W' and resid 101 through 110 No H-bonds generated for sheet with id=AN2 Processing sheet with id=AN3, first strand: chain 'W' and resid 203 through 204 Processing sheet with id=AN4, first strand: chain 'W' and resid 220 through 221 Processing sheet with id=AN5, first strand: chain 'W' and resid 296 through 305 removed outlier: 5.593A pdb=" N ASP W 298 " --> pdb=" O LYS W 321 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS W 321 " --> pdb=" O ASP W 298 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL W 315 " --> pdb=" O ALA W 304 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'W' and resid 326 through 328 removed outlier: 3.563A pdb=" N GLY W 326 " --> pdb=" O VAL W 346 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'W' and resid 331 through 332 Processing sheet with id=AN8, first strand: chain 'W' and resid 387 through 388 Processing sheet with id=AN9, first strand: chain 'X' and resid 17 through 18 Processing sheet with id=AO1, first strand: chain 'X' and resid 46 through 54 removed outlier: 11.358A pdb=" N ILE X 48 " --> pdb=" O LYS X 104 " (cutoff:3.500A) removed outlier: 10.774A pdb=" N LYS X 104 " --> pdb=" O ILE X 48 " (cutoff:3.500A) removed outlier: 11.104A pdb=" N PHE X 50 " --> pdb=" O LEU X 102 " (cutoff:3.500A) removed outlier: 11.545A pdb=" N LEU X 102 " --> pdb=" O PHE X 50 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N ALA X 52 " --> pdb=" O PHE X 100 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE X 100 " --> pdb=" O ALA X 52 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'X' and resid 66 through 70 Processing sheet with id=AO3, first strand: chain 'X' and resid 84 through 86 removed outlier: 4.089A pdb=" N GLU X 109 " --> pdb=" O TYR X 129 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'X' and resid 149 through 156 removed outlier: 3.558A pdb=" N VAL X 267 " --> pdb=" O LYS X 149 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'X' and resid 175 through 177 removed outlier: 3.752A pdb=" N VAL X 227 " --> pdb=" O ASP X 177 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY X 209 " --> pdb=" O TYR X 199 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'X' and resid 181 through 183 Processing sheet with id=AO7, first strand: chain 'X' and resid 274 through 277 Processing sheet with id=AO8, first strand: chain 'Y' and resid 17 through 19 removed outlier: 3.584A pdb=" N CYS Y 19 " --> pdb=" O CYS Y 28 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS Y 28 " --> pdb=" O CYS Y 19 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'Y' and resid 75 through 79 removed outlier: 4.739A pdb=" N GLY Y 55 " --> pdb=" O ASP Y 63 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N THR Y 65 " --> pdb=" O GLN Y 53 " (cutoff:3.500A) removed outlier: 12.065A pdb=" N GLN Y 53 " --> pdb=" O THR Y 65 " (cutoff:3.500A) removed outlier: 11.673A pdb=" N ILE Y 67 " --> pdb=" O SER Y 51 " (cutoff:3.500A) removed outlier: 11.396A pdb=" N SER Y 51 " --> pdb=" O ILE Y 67 " (cutoff:3.500A) removed outlier: 13.224A pdb=" N TYR Y 69 " --> pdb=" O GLN Y 49 " (cutoff:3.500A) removed outlier: 16.701A pdb=" N GLN Y 49 " --> pdb=" O TYR Y 69 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N HIS Y 99 " --> pdb=" O PHE Y 50 " (cutoff:3.500A) removed outlier: 9.606A pdb=" N ALA Y 52 " --> pdb=" O MET Y 97 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N MET Y 97 " --> pdb=" O ALA Y 52 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N ILE Y 54 " --> pdb=" O GLY Y 95 " (cutoff:3.500A) removed outlier: 10.907A pdb=" N GLY Y 95 " --> pdb=" O ILE Y 54 " (cutoff:3.500A) removed outlier: 15.375A pdb=" N ILE Y 56 " --> pdb=" O VAL Y 93 " (cutoff:3.500A) removed outlier: 18.501A pdb=" N VAL Y 93 " --> pdb=" O ILE Y 56 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'Y' and resid 84 through 86 removed outlier: 4.239A pdb=" N GLU Y 109 " --> pdb=" O TYR Y 129 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'Y' and resid 149 through 152 Processing sheet with id=AP3, first strand: chain 'Y' and resid 155 through 156 Processing sheet with id=AP4, first strand: chain 'Y' and resid 167 through 169 Processing sheet with id=AP5, first strand: chain 'Y' and resid 175 through 176 Processing sheet with id=AP6, first strand: chain 'Y' and resid 181 through 183 Processing sheet with id=AP7, first strand: chain 'Y' and resid 274 through 277 Processing sheet with id=AP8, first strand: chain 'Z' and resid 17 through 19 removed outlier: 3.564A pdb=" N ALA Z 17 " --> pdb=" O SER Z 30 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS Z 19 " --> pdb=" O CYS Z 28 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N CYS Z 28 " --> pdb=" O CYS Z 19 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'Z' and resid 37 through 38 removed outlier: 3.715A pdb=" N ARG Z 38 " --> pdb=" O LYS Z 47 " (cutoff:3.500A) removed outlier: 11.313A pdb=" N ILE Z 48 " --> pdb=" O LYS Z 104 " (cutoff:3.500A) removed outlier: 10.834A pdb=" N LYS Z 104 " --> pdb=" O ILE Z 48 " (cutoff:3.500A) removed outlier: 11.313A pdb=" N PHE Z 50 " --> pdb=" O LEU Z 102 " (cutoff:3.500A) removed outlier: 11.601A pdb=" N LEU Z 102 " --> pdb=" O PHE Z 50 " (cutoff:3.500A) removed outlier: 9.769A pdb=" N ALA Z 52 " --> pdb=" O PHE Z 100 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE Z 100 " --> pdb=" O ALA Z 52 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'Z' and resid 66 through 69 Processing sheet with id=AQ2, first strand: chain 'Z' and resid 84 through 86 removed outlier: 4.240A pdb=" N GLU Z 109 " --> pdb=" O TYR Z 129 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'Z' and resid 149 through 152 Processing sheet with id=AQ4, first strand: chain 'Z' and resid 155 through 156 Processing sheet with id=AQ5, first strand: chain 'Z' and resid 175 through 176 removed outlier: 3.780A pdb=" N GLY Z 209 " --> pdb=" O TYR Z 199 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'Z' and resid 182 through 183 Processing sheet with id=AQ7, first strand: chain 'Z' and resid 274 through 277 Processing sheet with id=AQ8, first strand: chain 'd' and resid 149 through 150 removed outlier: 6.096A pdb=" N HIS d 125 " --> pdb=" O VAL d 129 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N VAL d 129 " --> pdb=" O HIS d 125 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'd' and resid 191 through 195 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 206 through 209 current: chain 'd' and resid 230 through 240 removed outlier: 7.474A pdb=" N ALA d 232 " --> pdb=" O TRP d 251 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N TRP d 251 " --> pdb=" O ALA d 232 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL d 234 " --> pdb=" O VAL d 249 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL d 249 " --> pdb=" O VAL d 234 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 'e' and resid 149 through 150 removed outlier: 4.229A pdb=" N GLY e 131 " --> pdb=" O VAL e 123 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N HIS e 125 " --> pdb=" O VAL e 129 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N VAL e 129 " --> pdb=" O HIS e 125 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N TYR e 132 " --> pdb=" O PRO e 143 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU e 168 " --> pdb=" O SER e 163 " (cutoff:3.500A) Processing sheet with id=AR2, first strand: chain 'e' and resid 191 through 195 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 206 through 209 current: chain 'e' and resid 230 through 240 removed outlier: 7.848A pdb=" N ALA e 232 " --> pdb=" O TRP e 251 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N TRP e 251 " --> pdb=" O ALA e 232 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL e 234 " --> pdb=" O VAL e 249 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL e 249 " --> pdb=" O VAL e 234 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'f' and resid 149 through 150 removed outlier: 3.570A pdb=" N VAL f 149 " --> pdb=" O LYS f 124 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE f 121 " --> pdb=" O TYR f 132 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TYR f 132 " --> pdb=" O PHE f 121 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL f 123 " --> pdb=" O THR f 130 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N TYR f 132 " --> pdb=" O PRO f 143 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER f 163 " --> pdb=" O LEU f 168 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'f' and resid 191 through 195 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 207 through 209 current: chain 'f' and resid 230 through 240 removed outlier: 7.675A pdb=" N ALA f 232 " --> pdb=" O TRP f 251 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N TRP f 251 " --> pdb=" O ALA f 232 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N VAL f 234 " --> pdb=" O VAL f 249 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL f 249 " --> pdb=" O VAL f 234 " (cutoff:3.500A) 2014 hydrogen bonds defined for protein. 5208 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: 31.00 Time building geometry restraints manager: 15.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 20377 1.33 - 1.46: 16921 1.46 - 1.59: 31450 1.59 - 1.71: 0 1.71 - 1.84: 746 Bond restraints: 69494 Sorted by residual: bond pdb=" C GLU R 247 " pdb=" N PRO R 248 " ideal model delta sigma weight residual 1.331 1.358 -0.026 7.90e-03 1.60e+04 1.10e+01 bond pdb=" C GLU B 247 " pdb=" N PRO B 248 " ideal model delta sigma weight residual 1.331 1.358 -0.026 7.90e-03 1.60e+04 1.10e+01 bond pdb=" CA GLN R 304 " pdb=" CB GLN R 304 " ideal model delta sigma weight residual 1.530 1.484 0.047 1.50e-02 4.44e+03 9.61e+00 bond pdb=" CA GLN B 304 " pdb=" CB GLN B 304 " ideal model delta sigma weight residual 1.530 1.485 0.046 1.50e-02 4.44e+03 9.33e+00 bond pdb=" N CYS C 193 " pdb=" CA CYS C 193 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.22e-02 6.72e+03 8.68e+00 ... (remaining 69489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 92726 2.44 - 4.87: 1718 4.87 - 7.31: 161 7.31 - 9.75: 28 9.75 - 12.18: 8 Bond angle restraints: 94641 Sorted by residual: angle pdb=" OE1 GLN C 176 " pdb=" CD GLN C 176 " pdb=" NE2 GLN C 176 " ideal model delta sigma weight residual 122.60 117.08 5.52 1.00e+00 1.00e+00 3.05e+01 angle pdb=" OD1 ASN C 138 " pdb=" CG ASN C 138 " pdb=" ND2 ASN C 138 " ideal model delta sigma weight residual 122.60 117.45 5.15 1.00e+00 1.00e+00 2.65e+01 angle pdb=" N ASN I 212 " pdb=" CA ASN I 212 " pdb=" C ASN I 212 " ideal model delta sigma weight residual 114.75 108.70 6.05 1.26e+00 6.30e-01 2.30e+01 angle pdb=" N ASN X 212 " pdb=" CA ASN X 212 " pdb=" C ASN X 212 " ideal model delta sigma weight residual 114.75 108.72 6.03 1.26e+00 6.30e-01 2.29e+01 angle pdb=" C SER C 222 " pdb=" N ASP C 223 " pdb=" CA ASP C 223 " ideal model delta sigma weight residual 120.28 126.63 -6.35 1.34e+00 5.57e-01 2.25e+01 ... (remaining 94636 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 39913 22.35 - 44.70: 2308 44.70 - 67.06: 254 67.06 - 89.41: 174 89.41 - 111.76: 100 Dihedral angle restraints: 42749 sinusoidal: 17621 harmonic: 25128 Sorted by residual: dihedral pdb=" CA GLU K 247 " pdb=" C GLU K 247 " pdb=" N PRO K 248 " pdb=" CA PRO K 248 " ideal model delta harmonic sigma weight residual 180.00 137.63 42.37 0 5.00e+00 4.00e-02 7.18e+01 dihedral pdb=" CA GLU Z 247 " pdb=" C GLU Z 247 " pdb=" N PRO Z 248 " pdb=" CA PRO Z 248 " ideal model delta harmonic sigma weight residual 180.00 137.75 42.25 0 5.00e+00 4.00e-02 7.14e+01 dihedral pdb=" CB CYS X 203 " pdb=" SG CYS X 203 " pdb=" SG CYS X 220 " pdb=" CB CYS X 220 " ideal model delta sinusoidal sigma weight residual -86.00 -11.28 -74.72 1 1.00e+01 1.00e-02 7.07e+01 ... (remaining 42746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 9661 0.086 - 0.172: 999 0.172 - 0.258: 36 0.258 - 0.343: 23 0.343 - 0.429: 3 Chirality restraints: 10722 Sorted by residual: chirality pdb=" C1 BMA q 3 " pdb=" O4 NAG q 2 " pdb=" C2 BMA q 3 " pdb=" O5 BMA q 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 6.82e+00 chirality pdb=" C1 BMA 2 3 " pdb=" O4 NAG 2 2 " pdb=" C2 BMA 2 3 " pdb=" O5 BMA 2 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 5.81e+00 chirality pdb=" CA SER C 203 " pdb=" N SER C 203 " pdb=" C SER C 203 " pdb=" CB SER C 203 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 ... (remaining 10719 not shown) Planarity restraints: 12183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 132 " -0.005 2.00e-02 2.50e+03 4.64e-02 5.38e+01 pdb=" CG TRP C 132 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP C 132 " -0.078 2.00e-02 2.50e+03 pdb=" CD2 TRP C 132 " 0.053 2.00e-02 2.50e+03 pdb=" NE1 TRP C 132 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TRP C 132 " 0.049 2.00e-02 2.50e+03 pdb=" CE3 TRP C 132 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 132 " 0.036 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 132 " -0.052 2.00e-02 2.50e+03 pdb=" CH2 TRP C 132 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 210 " -0.033 2.00e-02 2.50e+03 3.15e-02 2.49e+01 pdb=" CG TRP C 210 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP C 210 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP C 210 " -0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP C 210 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 210 " -0.018 2.00e-02 2.50e+03 pdb=" CE3 TRP C 210 " 0.029 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 210 " -0.030 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 210 " 0.035 2.00e-02 2.50e+03 pdb=" CH2 TRP C 210 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 187 " -0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C ASP C 187 " 0.073 2.00e-02 2.50e+03 pdb=" O ASP C 187 " -0.028 2.00e-02 2.50e+03 pdb=" N CYS C 188 " -0.024 2.00e-02 2.50e+03 ... (remaining 12180 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.09: 11 2.09 - 2.79: 15938 2.79 - 3.49: 85459 3.49 - 4.20: 145034 4.20 - 4.90: 259721 Nonbonded interactions: 506163 Sorted by model distance: nonbonded pdb=" NH2 ARG D 206 " pdb=" NH1 ARG f 178 " model vdw 1.384 3.200 nonbonded pdb=" OH TYR H 242 " pdb=" ND1 HIS Z 287 " model vdw 1.526 3.120 nonbonded pdb=" CG ASN C 138 " pdb=" OD1 ASP C 157 " model vdw 1.643 3.270 nonbonded pdb=" OH TYR H 242 " pdb=" CE1 HIS Z 287 " model vdw 1.780 3.260 nonbonded pdb=" OD1 ASN C 138 " pdb=" OD1 ASP C 157 " model vdw 1.800 3.040 ... (remaining 506158 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 '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'R' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'D' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'd' selection = chain 'e' selection = chain 'f' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'S' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 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: 0.070 Extract box with map and model: 2.100 Check model and map are aligned: 0.390 Set scattering table: 0.470 Process input model: 122.950 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.890 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: 0.010 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 69494 Z= 0.456 Angle : 0.770 12.184 94641 Z= 0.406 Chirality : 0.052 0.429 10722 Planarity : 0.006 0.095 12159 Dihedral : 15.534 111.759 26274 Min Nonbonded Distance : 1.384 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.74 % Favored : 91.99 % Rotamer: Outliers : 0.18 % Allowed : 0.38 % Favored : 99.44 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.09), residues: 8607 helix: 2.52 (0.17), residues: 1022 sheet: -0.86 (0.10), residues: 2648 loop : -1.49 (0.09), residues: 4937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.002 TRP C 132 HIS 0.010 0.002 HIS H 230 PHE 0.032 0.002 PHE J 50 TYR 0.031 0.002 TYR W 93 ARG 0.011 0.001 ARG W 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1729 residues out of total 7348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 1716 time to evaluate : 5.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 THR cc_start: 0.8304 (p) cc_final: 0.7965 (p) REVERT: B 374 SER cc_start: 0.7795 (t) cc_final: 0.7475 (t) REVERT: B 376 LEU cc_start: 0.7928 (tp) cc_final: 0.7699 (tt) REVERT: D 177 MET cc_start: 0.8454 (mpp) cc_final: 0.8131 (mpp) REVERT: D 183 LYS cc_start: 0.6496 (pptt) cc_final: 0.6154 (ptmt) REVERT: F 47 ILE cc_start: 0.8776 (mm) cc_final: 0.8545 (tt) REVERT: F 95 PHE cc_start: 0.6513 (t80) cc_final: 0.5406 (m-10) REVERT: F 182 ASP cc_start: 0.7143 (t0) cc_final: 0.6940 (t0) REVERT: H 280 MET cc_start: 0.7924 (mtm) cc_final: 0.7661 (mtt) REVERT: I 76 GLU cc_start: 0.7750 (mp0) cc_final: 0.7528 (mp0) REVERT: I 169 MET cc_start: 0.8172 (mmt) cc_final: 0.7852 (mmt) REVERT: I 381 ILE cc_start: 0.8824 (tt) cc_final: 0.8605 (tt) REVERT: J 196 LYS cc_start: 0.8413 (ptmm) cc_final: 0.8002 (pttt) REVERT: J 199 TYR cc_start: 0.6344 (p90) cc_final: 0.6143 (p90) REVERT: J 326 GLU cc_start: 0.8301 (pt0) cc_final: 0.7955 (pt0) REVERT: K 269 MET cc_start: 0.7708 (mmm) cc_final: 0.7333 (mtm) REVERT: K 325 MET cc_start: 0.7019 (ppp) cc_final: 0.6205 (ptt) REVERT: O 120 ILE cc_start: 0.8644 (mt) cc_final: 0.8422 (mp) REVERT: O 252 ASN cc_start: 0.7863 (t0) cc_final: 0.7340 (m-40) REVERT: E 45 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6847 (mm-30) REVERT: E 81 TYR cc_start: 0.8305 (m-80) cc_final: 0.8105 (m-80) REVERT: E 364 SER cc_start: 0.7776 (t) cc_final: 0.7365 (p) REVERT: T 142 LYS cc_start: 0.8111 (ttpt) cc_final: 0.7172 (tttp) REVERT: V 51 TYR cc_start: 0.8386 (p90) cc_final: 0.7728 (p90) REVERT: V 145 ASP cc_start: 0.7231 (p0) cc_final: 0.6888 (p0) REVERT: V 242 TYR cc_start: 0.6258 (m-10) cc_final: 0.6053 (m-10) REVERT: W 151 ASP cc_start: 0.6887 (p0) cc_final: 0.6660 (p0) REVERT: X 224 GLN cc_start: 0.7084 (mt0) cc_final: 0.6715 (mt0) REVERT: Z 169 MET cc_start: 0.7638 (mmt) cc_final: 0.7177 (mmt) REVERT: Z 295 SER cc_start: 0.7884 (p) cc_final: 0.7676 (p) REVERT: d 139 LYS cc_start: 0.6745 (mttt) cc_final: 0.6162 (pttt) REVERT: d 202 TYR cc_start: 0.8105 (t80) cc_final: 0.7838 (t80) REVERT: e 124 LYS cc_start: 0.8075 (mmmt) cc_final: 0.7687 (mmtp) REVERT: e 147 LYS cc_start: 0.8084 (ptpp) cc_final: 0.7592 (mmtt) REVERT: e 227 LYS cc_start: 0.7095 (mmtm) cc_final: 0.6892 (mppt) REVERT: e 255 MET cc_start: 0.6407 (mmp) cc_final: 0.6103 (mmp) outliers start: 13 outliers final: 3 residues processed: 1728 average time/residue: 0.6286 time to fit residues: 1854.9856 Evaluate side-chains 1057 residues out of total 7348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1054 time to evaluate : 5.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 226 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 719 optimal weight: 0.5980 chunk 645 optimal weight: 1.9990 chunk 358 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 435 optimal weight: 9.9990 chunk 345 optimal weight: 2.9990 chunk 667 optimal weight: 4.9990 chunk 258 optimal weight: 10.0000 chunk 406 optimal weight: 8.9990 chunk 497 optimal weight: 9.9990 chunk 773 optimal weight: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN B 304 GLN B 348 HIS C 170 ASN D 196 HIS D 197 HIS G 340 GLN ** H 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 264 ASN I 170 HIS ** J 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 GLN J 331 ASN K 62 HIS K 131 HIS L 53 GLN O 176 HIS E 211 ASN E 396 ASN R 232 HIS ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 204 GLN W 186 ASN W 196 GLN W 235 GLN X 7 ASN X 53 GLN X 120 ASN X 238 ASN X 348 HIS Y 53 GLN Y 170 HIS Y 236 GLN ** Z 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 348 HIS ** e 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.190074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.147108 restraints weight = 91112.694| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.77 r_work: 0.3389 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 69494 Z= 0.212 Angle : 0.657 12.503 94641 Z= 0.329 Chirality : 0.047 0.574 10722 Planarity : 0.005 0.066 12159 Dihedral : 9.292 70.244 10858 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.37 % Favored : 94.39 % Rotamer: Outliers : 2.15 % Allowed : 10.04 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.09), residues: 8607 helix: 2.45 (0.16), residues: 1038 sheet: -0.65 (0.10), residues: 2496 loop : -1.44 (0.08), residues: 5073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 329 HIS 0.013 0.001 HIS P 176 PHE 0.024 0.001 PHE P 121 TYR 0.038 0.002 TYR U 93 ARG 0.018 0.001 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1283 residues out of total 7348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1125 time to evaluate : 5.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8824 (m-80) cc_final: 0.8612 (m-80) REVERT: A 99 GLU cc_start: 0.7763 (pm20) cc_final: 0.7223 (pm20) REVERT: A 305 THR cc_start: 0.8594 (p) cc_final: 0.8235 (p) REVERT: A 385 ASP cc_start: 0.8787 (m-30) cc_final: 0.8534 (m-30) REVERT: B 53 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7225 (pt0) REVERT: B 71 ASP cc_start: 0.8443 (t0) cc_final: 0.8228 (t0) REVERT: B 232 HIS cc_start: 0.8151 (OUTLIER) cc_final: 0.7889 (t-90) REVERT: D 177 MET cc_start: 0.8371 (mpp) cc_final: 0.8041 (mpp) REVERT: F 47 ILE cc_start: 0.9294 (mm) cc_final: 0.8940 (tt) REVERT: F 95 PHE cc_start: 0.6767 (t80) cc_final: 0.5461 (m-10) REVERT: F 167 SER cc_start: 0.8751 (t) cc_final: 0.8257 (p) REVERT: F 182 ASP cc_start: 0.8498 (t0) cc_final: 0.8189 (t0) REVERT: H 115 ARG cc_start: 0.8336 (ttp-110) cc_final: 0.8104 (ptt90) REVERT: H 139 ASN cc_start: 0.8941 (t0) cc_final: 0.8729 (t0) REVERT: I 101 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8190 (pt) REVERT: I 169 MET cc_start: 0.8387 (mmt) cc_final: 0.7456 (mmt) REVERT: I 199 TYR cc_start: 0.7072 (p90) cc_final: 0.6488 (p90) REVERT: J 196 LYS cc_start: 0.7550 (ptmm) cc_final: 0.7227 (pttt) REVERT: J 224 GLN cc_start: 0.6055 (OUTLIER) cc_final: 0.5833 (tp40) REVERT: K 269 MET cc_start: 0.8147 (mmm) cc_final: 0.7860 (mtm) REVERT: K 344 GLU cc_start: 0.8149 (pm20) cc_final: 0.7931 (pm20) REVERT: O 120 ILE cc_start: 0.8548 (mt) cc_final: 0.8241 (mp) REVERT: O 141 MET cc_start: 0.7446 (mtt) cc_final: 0.7129 (mtp) REVERT: O 162 LYS cc_start: 0.8785 (tmtt) cc_final: 0.8406 (ttpt) REVERT: O 169 GLU cc_start: 0.6726 (mp0) cc_final: 0.6522 (mp0) REVERT: O 252 ASN cc_start: 0.7999 (t0) cc_final: 0.7542 (m-40) REVERT: O 255 MET cc_start: 0.6835 (mmm) cc_final: 0.6535 (mmm) REVERT: P 147 LYS cc_start: 0.8240 (pptt) cc_final: 0.7928 (pptt) REVERT: E 32 GLN cc_start: 0.8445 (tt0) cc_final: 0.8175 (mt0) REVERT: E 95 PHE cc_start: 0.6615 (t80) cc_final: 0.6240 (t80) REVERT: E 245 LYS cc_start: 0.8948 (ptpt) cc_final: 0.8598 (pttm) REVERT: E 364 SER cc_start: 0.7727 (t) cc_final: 0.7282 (p) REVERT: R 13 ARG cc_start: 0.8449 (ptm-80) cc_final: 0.8230 (ptm160) REVERT: R 28 CYS cc_start: 0.8248 (p) cc_final: 0.8020 (p) REVERT: R 199 TYR cc_start: 0.7416 (p90) cc_final: 0.7021 (p90) REVERT: T 183 LYS cc_start: 0.6717 (ttpp) cc_final: 0.6468 (tmmt) REVERT: T 188 LYS cc_start: 0.6250 (mtmm) cc_final: 0.6044 (mtmm) REVERT: U 67 GLU cc_start: 0.7973 (tp30) cc_final: 0.7369 (pm20) REVERT: U 182 ASP cc_start: 0.8685 (p0) cc_final: 0.8437 (p0) REVERT: V 46 TYR cc_start: 0.9223 (p90) cc_final: 0.8883 (p90) REVERT: V 99 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7016 (mp0) REVERT: V 402 MET cc_start: 0.6146 (mmt) cc_final: 0.5935 (mmt) REVERT: X 61 ASN cc_start: 0.7352 (m-40) cc_final: 0.7047 (m-40) REVERT: Z 7 ASN cc_start: 0.7575 (t0) cc_final: 0.6981 (t0) REVERT: Z 169 MET cc_start: 0.7857 (mmt) cc_final: 0.6984 (mmt) REVERT: Z 250 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7341 (mtp-110) REVERT: Z 251 LYS cc_start: 0.8365 (ptmm) cc_final: 0.7981 (mtmm) REVERT: Z 253 LYS cc_start: 0.7529 (mttm) cc_final: 0.7289 (ttmm) REVERT: c 40 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6144 (mp0) REVERT: d 139 LYS cc_start: 0.5622 (mttt) cc_final: 0.4850 (pttt) REVERT: d 157 LYS cc_start: 0.8766 (pttt) cc_final: 0.8429 (pttp) REVERT: d 252 ASN cc_start: 0.7506 (t0) cc_final: 0.7229 (t0) REVERT: e 124 LYS cc_start: 0.8061 (mmmt) cc_final: 0.7800 (mmtp) REVERT: e 147 LYS cc_start: 0.8164 (ptpp) cc_final: 0.7714 (mmtt) REVERT: e 162 LYS cc_start: 0.8730 (tttm) cc_final: 0.8319 (mtpp) REVERT: e 227 LYS cc_start: 0.7423 (mmtm) cc_final: 0.6956 (mttp) REVERT: e 255 MET cc_start: 0.7066 (mmp) cc_final: 0.6713 (mmp) REVERT: f 190 GLU cc_start: 0.6581 (mm-30) cc_final: 0.6380 (tp30) REVERT: f 252 ASN cc_start: 0.7436 (t0) cc_final: 0.7096 (t0) outliers start: 158 outliers final: 105 residues processed: 1224 average time/residue: 0.6100 time to fit residues: 1291.4497 Evaluate side-chains 1070 residues out of total 7348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 959 time to evaluate : 5.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain F residue 62 CYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 142 GLN Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 395 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 238 SER Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain J residue 224 GLN Chi-restraints excluded: chain J residue 263 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 362 TYR Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 307 GLU Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain O residue 251 TRP Chi-restraints excluded: chain O residue 265 GLU Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain Q residue 230 VAL Chi-restraints excluded: chain Q residue 231 VAL Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain T residue 251 TRP Chi-restraints excluded: chain T residue 257 THR Chi-restraints excluded: chain U residue 4 SER Chi-restraints excluded: chain U residue 62 CYS Chi-restraints excluded: chain U residue 280 MET Chi-restraints excluded: chain U residue 300 THR Chi-restraints excluded: chain U residue 395 SER Chi-restraints excluded: chain U residue 425 ILE Chi-restraints excluded: chain V residue 96 CYS Chi-restraints excluded: chain V residue 98 SER Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 211 ASN Chi-restraints excluded: chain W residue 2 GLU Chi-restraints excluded: chain W residue 120 SER Chi-restraints excluded: chain W residue 178 VAL Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 295 THR Chi-restraints excluded: chain W residue 303 VAL Chi-restraints excluded: chain X residue 143 ILE Chi-restraints excluded: chain X residue 175 THR Chi-restraints excluded: chain X residue 197 VAL Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 305 TYR Chi-restraints excluded: chain Y residue 97 MET Chi-restraints excluded: chain Y residue 122 VAL Chi-restraints excluded: chain Y residue 256 ILE Chi-restraints excluded: chain Y residue 260 LEU Chi-restraints excluded: chain Y residue 263 ILE Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 367 VAL Chi-restraints excluded: chain Z residue 90 ASP Chi-restraints excluded: chain Z residue 136 VAL Chi-restraints excluded: chain Z residue 250 ARG Chi-restraints excluded: chain Z residue 284 LEU Chi-restraints excluded: chain Z residue 290 HIS Chi-restraints excluded: chain Z residue 299 LEU Chi-restraints excluded: chain Z residue 362 TYR Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain b residue 43 VAL Chi-restraints excluded: chain c residue 40 GLU Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 200 VAL Chi-restraints excluded: chain d residue 251 TRP Chi-restraints excluded: chain e residue 208 THR Chi-restraints excluded: chain f residue 255 MET Chi-restraints excluded: chain f residue 257 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 742 optimal weight: 10.0000 chunk 362 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 609 optimal weight: 20.0000 chunk 597 optimal weight: 9.9990 chunk 500 optimal weight: 9.9990 chunk 689 optimal weight: 8.9990 chunk 537 optimal weight: 6.9990 chunk 432 optimal weight: 10.0000 chunk 540 optimal weight: 0.4980 chunk 153 optimal weight: 9.9990 overall best weight: 6.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 77 ASN B 348 HIS ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN I 170 HIS I 218 ASN I 224 GLN J 53 GLN J 73 HIS J 340 GLN K 77 ASN K 212 ASN L 30 ASN O 197 HIS S 30 ASN E 3 HIS ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 ASN ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 32 GLN V 235 GLN V 264 ASN W 116 HIS W 152 HIS W 252 ASN X 7 ASN X 120 ASN X 131 HIS X 304 GLN X 348 HIS Y 73 HIS Y 348 HIS Z 62 HIS ** Z 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 331 ASN ** Z 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.166271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.108647 restraints weight = 88725.572| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.90 r_work: 0.3023 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.161 69494 Z= 0.505 Angle : 0.771 17.218 94641 Z= 0.395 Chirality : 0.051 0.470 10722 Planarity : 0.006 0.072 12159 Dihedral : 7.233 57.741 10857 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.30 % Favored : 92.47 % Rotamer: Outliers : 4.23 % Allowed : 11.99 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.09), residues: 8607 helix: 2.26 (0.16), residues: 1022 sheet: -0.89 (0.10), residues: 2488 loop : -1.62 (0.08), residues: 5097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP f 195 HIS 0.016 0.002 HIS H 230 PHE 0.030 0.002 PHE K 50 TYR 0.028 0.002 TYR H 137 ARG 0.010 0.001 ARG T 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1274 residues out of total 7348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 311 poor density : 963 time to evaluate : 5.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8910 (pttm) REVERT: A 130 LYS cc_start: 0.8633 (ttmt) cc_final: 0.7985 (tmtt) REVERT: A 136 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8541 (ptm) REVERT: A 269 MET cc_start: 0.8998 (ttm) cc_final: 0.8679 (mtm) REVERT: A 319 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8695 (t) REVERT: B 56 ILE cc_start: 0.8552 (mp) cc_final: 0.8309 (mt) REVERT: B 77 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.8059 (p0) REVERT: B 261 ASP cc_start: 0.8226 (t0) cc_final: 0.8005 (t0) REVERT: B 305 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.6715 (m-80) REVERT: D 177 MET cc_start: 0.8443 (mpp) cc_final: 0.8019 (mpp) REVERT: D 183 LYS cc_start: 0.7733 (pptt) cc_final: 0.7127 (ptmm) REVERT: F 211 ASN cc_start: 0.8555 (p0) cc_final: 0.8312 (t0) REVERT: G 315 VAL cc_start: 0.9055 (t) cc_final: 0.8699 (p) REVERT: H 139 ASN cc_start: 0.9361 (t0) cc_final: 0.9137 (t0) REVERT: H 151 ASP cc_start: 0.8918 (p0) cc_final: 0.8560 (p0) REVERT: H 174 ASP cc_start: 0.8890 (m-30) cc_final: 0.8525 (m-30) REVERT: H 211 ASN cc_start: 0.8803 (t0) cc_final: 0.8481 (m-40) REVERT: H 295 THR cc_start: 0.8847 (m) cc_final: 0.8473 (p) REVERT: H 377 SER cc_start: 0.8951 (t) cc_final: 0.8725 (p) REVERT: I 50 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8173 (m-10) REVERT: I 298 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.8796 (p) REVERT: I 344 GLU cc_start: 0.8945 (pm20) cc_final: 0.8658 (pm20) REVERT: J 50 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7771 (m-10) REVERT: J 256 ILE cc_start: 0.8423 (pt) cc_final: 0.8222 (pt) REVERT: J 344 GLU cc_start: 0.8967 (pm20) cc_final: 0.8703 (pm20) REVERT: J 394 LYS cc_start: 0.6897 (ttmm) cc_final: 0.6495 (ttmt) REVERT: K 77 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7532 (p0) REVERT: K 169 MET cc_start: 0.8278 (mmt) cc_final: 0.7486 (mmt) REVERT: K 250 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7434 (mtp-110) REVERT: K 269 MET cc_start: 0.8560 (mmm) cc_final: 0.8337 (mtm) REVERT: L 40 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7196 (mt-10) REVERT: O 162 LYS cc_start: 0.8755 (tmtt) cc_final: 0.8403 (ttpt) REVERT: O 183 LYS cc_start: 0.8069 (ptpt) cc_final: 0.7726 (tptt) REVERT: O 252 ASN cc_start: 0.8238 (t0) cc_final: 0.7807 (m-40) REVERT: P 147 LYS cc_start: 0.8178 (pptt) cc_final: 0.7733 (pptt) REVERT: Q 177 MET cc_start: 0.7565 (mmm) cc_final: 0.7306 (mmm) REVERT: E 19 ILE cc_start: 0.8977 (mt) cc_final: 0.8764 (mt) REVERT: E 146 VAL cc_start: 0.9341 (t) cc_final: 0.9125 (m) REVERT: E 245 LYS cc_start: 0.9331 (ptpt) cc_final: 0.8954 (pttt) REVERT: R 182 SER cc_start: 0.7542 (m) cc_final: 0.7219 (p) REVERT: R 199 TYR cc_start: 0.7613 (p90) cc_final: 0.7121 (p90) REVERT: R 213 SER cc_start: 0.7920 (t) cc_final: 0.7520 (m) REVERT: R 215 MET cc_start: 0.7088 (mmm) cc_final: 0.6846 (mmm) REVERT: R 224 GLN cc_start: 0.6490 (mt0) cc_final: 0.5706 (mt0) REVERT: R 346 LYS cc_start: 0.8089 (tttm) cc_final: 0.7770 (ttmm) REVERT: T 183 LYS cc_start: 0.7291 (ttpp) cc_final: 0.7058 (ttpp) REVERT: T 252 ASN cc_start: 0.7606 (m-40) cc_final: 0.7201 (t0) REVERT: U 67 GLU cc_start: 0.8067 (tp30) cc_final: 0.7627 (pm20) REVERT: U 182 ASP cc_start: 0.8771 (p0) cc_final: 0.8550 (p0) REVERT: U 246 GLU cc_start: 0.6106 (pt0) cc_final: 0.5638 (pt0) REVERT: U 364 SER cc_start: 0.9469 (t) cc_final: 0.8857 (m) REVERT: V 99 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6669 (mp0) REVERT: V 188 ASP cc_start: 0.8938 (t0) cc_final: 0.8687 (t0) REVERT: V 281 ASN cc_start: 0.8931 (t0) cc_final: 0.8425 (t0) REVERT: V 402 MET cc_start: 0.6992 (mmt) cc_final: 0.6785 (mmt) REVERT: W 31 MET cc_start: 0.9123 (mtm) cc_final: 0.8920 (mtm) REVERT: W 182 ASP cc_start: 0.8655 (p0) cc_final: 0.8021 (t0) REVERT: W 242 TYR cc_start: 0.5415 (m-10) cc_final: 0.5076 (m-10) REVERT: X 10 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8506 (mtmt) REVERT: X 40 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8525 (pt0) REVERT: X 50 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.7849 (m-10) REVERT: X 199 TYR cc_start: 0.7527 (p90) cc_final: 0.7031 (p90) REVERT: X 224 GLN cc_start: 0.6788 (mt0) cc_final: 0.6375 (mt0) REVERT: X 325 MET cc_start: 0.8995 (ppp) cc_final: 0.8718 (ptm) REVERT: Y 165 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: Y 215 MET cc_start: 0.7679 (mtm) cc_final: 0.7397 (mtt) REVERT: Y 392 ARG cc_start: 0.7315 (tmm-80) cc_final: 0.6962 (tmt170) REVERT: Y 393 SER cc_start: 0.7955 (t) cc_final: 0.7506 (p) REVERT: Z 40 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8760 (pt0) REVERT: Z 50 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8633 (m-10) REVERT: Z 61 ASN cc_start: 0.8086 (t0) cc_final: 0.7877 (t0) REVERT: Z 168 ASP cc_start: 0.8699 (m-30) cc_final: 0.8324 (m-30) REVERT: Z 169 MET cc_start: 0.8388 (mmt) cc_final: 0.7830 (mmt) REVERT: Z 250 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7934 (mtp-110) REVERT: Z 251 LYS cc_start: 0.8622 (ptmm) cc_final: 0.8154 (mtpp) REVERT: Z 253 LYS cc_start: 0.9008 (mttm) cc_final: 0.8701 (mttt) REVERT: Z 378 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7151 (mp) REVERT: d 157 LYS cc_start: 0.8896 (pttt) cc_final: 0.8570 (pttp) REVERT: d 252 ASN cc_start: 0.8293 (t0) cc_final: 0.7791 (t0) REVERT: e 139 LYS cc_start: 0.7651 (mttp) cc_final: 0.7357 (mttm) REVERT: e 141 MET cc_start: 0.8639 (mtt) cc_final: 0.8340 (mtp) REVERT: e 179 SER cc_start: 0.7520 (t) cc_final: 0.7198 (p) REVERT: e 252 ASN cc_start: 0.7288 (t0) cc_final: 0.6247 (m-40) REVERT: e 253 LYS cc_start: 0.6534 (mtpp) cc_final: 0.6019 (mtpt) REVERT: e 255 MET cc_start: 0.7194 (mmp) cc_final: 0.6957 (mmm) REVERT: f 162 LYS cc_start: 0.8371 (mmmt) cc_final: 0.7982 (mmmm) outliers start: 311 outliers final: 188 residues processed: 1201 average time/residue: 0.6038 time to fit residues: 1257.6976 Evaluate side-chains 1038 residues out of total 7348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 833 time to evaluate : 5.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain F residue 62 CYS Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 142 GLN Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 395 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 397 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 298 THR Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 263 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 388 LEU Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 250 ARG Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 362 TYR Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain O residue 147 LYS Chi-restraints excluded: chain O residue 251 TRP Chi-restraints excluded: chain O residue 265 GLU Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 230 VAL Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 265 CYS Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 317 THR Chi-restraints excluded: chain R residue 379 ILE Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain U residue 62 CYS Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 84 VAL Chi-restraints excluded: chain U residue 299 LEU Chi-restraints excluded: chain U residue 305 THR Chi-restraints excluded: chain U residue 343 THR Chi-restraints excluded: chain U residue 366 VAL Chi-restraints excluded: chain U residue 385 ASP Chi-restraints excluded: chain U residue 395 SER Chi-restraints excluded: chain U residue 410 VAL Chi-restraints excluded: chain U residue 427 VAL Chi-restraints excluded: chain U residue 432 THR Chi-restraints excluded: chain V residue 96 CYS Chi-restraints excluded: chain V residue 98 SER Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain V residue 329 SER Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain W residue 2 GLU Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 120 SER Chi-restraints excluded: chain W residue 144 VAL Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 205 SER Chi-restraints excluded: chain W residue 236 THR Chi-restraints excluded: chain W residue 295 THR Chi-restraints excluded: chain W residue 322 THR Chi-restraints excluded: chain W residue 329 SER Chi-restraints excluded: chain W residue 334 SER Chi-restraints excluded: chain W residue 338 THR Chi-restraints excluded: chain W residue 397 VAL Chi-restraints excluded: chain W residue 434 ILE Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 40 GLU Chi-restraints excluded: chain X residue 50 PHE Chi-restraints excluded: chain X residue 101 ILE Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 175 THR Chi-restraints excluded: chain X residue 197 VAL Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 305 TYR Chi-restraints excluded: chain X residue 389 VAL Chi-restraints excluded: chain X residue 397 THR Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 165 GLU Chi-restraints excluded: chain Y residue 167 ILE Chi-restraints excluded: chain Y residue 242 VAL Chi-restraints excluded: chain Y residue 250 ARG Chi-restraints excluded: chain Y residue 256 ILE Chi-restraints excluded: chain Y residue 260 LEU Chi-restraints excluded: chain Y residue 263 ILE Chi-restraints excluded: chain Y residue 299 LEU Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 367 VAL Chi-restraints excluded: chain Y residue 388 LEU Chi-restraints excluded: chain Z residue 32 VAL Chi-restraints excluded: chain Z residue 40 GLU Chi-restraints excluded: chain Z residue 50 PHE Chi-restraints excluded: chain Z residue 53 GLN Chi-restraints excluded: chain Z residue 62 HIS Chi-restraints excluded: chain Z residue 136 VAL Chi-restraints excluded: chain Z residue 154 THR Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain Z residue 250 ARG Chi-restraints excluded: chain Z residue 261 ASP Chi-restraints excluded: chain Z residue 295 SER Chi-restraints excluded: chain Z residue 299 LEU Chi-restraints excluded: chain Z residue 305 TYR Chi-restraints excluded: chain Z residue 344 GLU Chi-restraints excluded: chain Z residue 362 TYR Chi-restraints excluded: chain Z residue 374 SER Chi-restraints excluded: chain Z residue 378 LEU Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain b residue 43 VAL Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 200 VAL Chi-restraints excluded: chain e residue 113 MET Chi-restraints excluded: chain e residue 149 VAL Chi-restraints excluded: chain e residue 194 ASN Chi-restraints excluded: chain e residue 208 THR Chi-restraints excluded: chain f residue 111 MET Chi-restraints excluded: chain f residue 200 VAL Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain f residue 255 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 818 optimal weight: 6.9990 chunk 391 optimal weight: 5.9990 chunk 757 optimal weight: 3.9990 chunk 352 optimal weight: 1.9990 chunk 836 optimal weight: 20.0000 chunk 361 optimal weight: 10.0000 chunk 448 optimal weight: 4.9990 chunk 533 optimal weight: 5.9990 chunk 652 optimal weight: 6.9990 chunk 330 optimal weight: 5.9990 chunk 528 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 62 HIS B 77 ASN B 170 HIS B 340 GLN B 348 HIS ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 HIS ** H 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 HIS J 184 GLN J 224 GLN J 348 HIS K 255 HIS Q 196 HIS ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 ASN ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 340 GLN U 32 GLN ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 142 GLN X 120 ASN Y 170 HIS Y 348 HIS Z 62 HIS ** Z 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.166454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121787 restraints weight = 88532.286| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.53 r_work: 0.3013 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 69494 Z= 0.332 Angle : 0.645 11.319 94641 Z= 0.327 Chirality : 0.047 0.520 10722 Planarity : 0.005 0.062 12159 Dihedral : 6.391 59.687 10854 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.09 % Favored : 93.70 % Rotamer: Outliers : 3.84 % Allowed : 14.43 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.09), residues: 8607 helix: 2.42 (0.16), residues: 1038 sheet: -0.90 (0.10), residues: 2576 loop : -1.59 (0.08), residues: 4993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 329 HIS 0.022 0.001 HIS Z 62 PHE 0.024 0.002 PHE K 50 TYR 0.023 0.002 TYR H 137 ARG 0.006 0.000 ARG Z 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1144 residues out of total 7348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 282 poor density : 862 time to evaluate : 5.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.8639 (ttmt) cc_final: 0.8423 (mtpp) REVERT: A 136 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8615 (ptm) REVERT: A 188 ASP cc_start: 0.8721 (t0) cc_final: 0.8498 (t0) REVERT: B 50 PHE cc_start: 0.8913 (m-10) cc_final: 0.8344 (m-10) REVERT: B 77 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.7775 (p0) REVERT: B 132 ASP cc_start: 0.9170 (t0) cc_final: 0.8920 (t70) REVERT: B 174 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.7499 (p0) REVERT: D 177 MET cc_start: 0.8536 (mpp) cc_final: 0.8099 (mpp) REVERT: D 183 LYS cc_start: 0.7710 (pptt) cc_final: 0.7465 (pttp) REVERT: G 72 GLU cc_start: 0.8092 (pm20) cc_final: 0.7858 (pm20) REVERT: H 139 ASN cc_start: 0.9355 (t0) cc_final: 0.9096 (t0) REVERT: H 151 ASP cc_start: 0.8685 (p0) cc_final: 0.8446 (p0) REVERT: H 174 ASP cc_start: 0.8985 (m-30) cc_final: 0.8678 (m-30) REVERT: H 295 THR cc_start: 0.8892 (m) cc_final: 0.8505 (p) REVERT: I 50 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7793 (m-10) REVERT: I 215 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.6989 (tmm) REVERT: J 50 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7740 (m-10) REVERT: J 65 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8264 (t) REVERT: J 196 LYS cc_start: 0.7444 (ptmt) cc_final: 0.7002 (ptpp) REVERT: J 261 ASP cc_start: 0.8637 (t0) cc_final: 0.8181 (m-30) REVERT: J 394 LYS cc_start: 0.7126 (ttmm) cc_final: 0.6704 (ttmt) REVERT: K 97 MET cc_start: 0.8589 (tpt) cc_final: 0.7816 (ttt) REVERT: K 269 MET cc_start: 0.8611 (mmm) cc_final: 0.8406 (mtm) REVERT: L 37 ARG cc_start: 0.7088 (mmt180) cc_final: 0.6887 (mmt180) REVERT: L 40 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6701 (mt-10) REVERT: M 8 MET cc_start: 0.4181 (OUTLIER) cc_final: 0.3971 (mtp) REVERT: N 40 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.5452 (mt-10) REVERT: O 113 MET cc_start: 0.5560 (OUTLIER) cc_final: 0.5171 (mpt) REVERT: O 162 LYS cc_start: 0.8764 (tmtt) cc_final: 0.8423 (ttpt) REVERT: O 183 LYS cc_start: 0.8108 (ptpt) cc_final: 0.7872 (tptt) REVERT: O 252 ASN cc_start: 0.8426 (t0) cc_final: 0.8036 (m-40) REVERT: P 147 LYS cc_start: 0.8270 (pptt) cc_final: 0.7864 (pptt) REVERT: Q 167 ASP cc_start: 0.7892 (t0) cc_final: 0.7658 (t0) REVERT: Q 177 MET cc_start: 0.7794 (mmm) cc_final: 0.7478 (mmm) REVERT: E 19 ILE cc_start: 0.9056 (mt) cc_final: 0.8835 (mt) REVERT: E 194 SER cc_start: 0.9427 (m) cc_final: 0.9218 (t) REVERT: E 245 LYS cc_start: 0.9240 (ptpt) cc_final: 0.8931 (pttt) REVERT: E 341 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8104 (pm20) REVERT: R 169 MET cc_start: 0.8615 (mmm) cc_final: 0.8123 (mmm) REVERT: R 182 SER cc_start: 0.7606 (m) cc_final: 0.7264 (p) REVERT: R 199 TYR cc_start: 0.7715 (p90) cc_final: 0.7273 (p90) REVERT: R 213 SER cc_start: 0.7930 (t) cc_final: 0.7546 (m) REVERT: R 215 MET cc_start: 0.7012 (mmm) cc_final: 0.6716 (mmm) REVERT: R 224 GLN cc_start: 0.6488 (mt0) cc_final: 0.6130 (mt0) REVERT: R 346 LYS cc_start: 0.8184 (tttm) cc_final: 0.7911 (ttmm) REVERT: T 252 ASN cc_start: 0.7823 (m-40) cc_final: 0.7545 (t0) REVERT: U 67 GLU cc_start: 0.8104 (tp30) cc_final: 0.7731 (pm20) REVERT: U 182 ASP cc_start: 0.8707 (p0) cc_final: 0.8467 (p0) REVERT: U 269 MET cc_start: 0.8575 (mtm) cc_final: 0.8352 (mtp) REVERT: V 99 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7162 (mp0) REVERT: V 281 ASN cc_start: 0.8964 (t0) cc_final: 0.8443 (t0) REVERT: V 402 MET cc_start: 0.7211 (mmt) cc_final: 0.6987 (mmt) REVERT: W 182 ASP cc_start: 0.8606 (p0) cc_final: 0.7906 (t0) REVERT: W 242 TYR cc_start: 0.5445 (m-10) cc_final: 0.5209 (m-10) REVERT: X 50 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7887 (m-10) REVERT: X 199 TYR cc_start: 0.7477 (p90) cc_final: 0.7177 (p90) REVERT: X 325 MET cc_start: 0.8993 (ppp) cc_final: 0.8340 (ptt) REVERT: X 326 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8502 (pt0) REVERT: Y 165 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: Y 393 SER cc_start: 0.8269 (t) cc_final: 0.7788 (p) REVERT: Z 7 ASN cc_start: 0.8729 (t0) cc_final: 0.8347 (t0) REVERT: Z 50 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8611 (m-10) REVERT: Z 168 ASP cc_start: 0.8737 (m-30) cc_final: 0.8416 (m-30) REVERT: Z 169 MET cc_start: 0.8544 (mmt) cc_final: 0.8062 (mmt) REVERT: Z 253 LYS cc_start: 0.8982 (mttm) cc_final: 0.8724 (mttt) REVERT: d 157 LYS cc_start: 0.8973 (pttt) cc_final: 0.8665 (pttp) REVERT: d 221 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8170 (mmt-90) REVERT: d 252 ASN cc_start: 0.8279 (t0) cc_final: 0.7832 (t0) REVERT: e 162 LYS cc_start: 0.8739 (tttm) cc_final: 0.8420 (ttmt) REVERT: e 252 ASN cc_start: 0.7199 (t0) cc_final: 0.6307 (m-40) REVERT: e 253 LYS cc_start: 0.6622 (mtpp) cc_final: 0.6238 (mtpt) REVERT: f 162 LYS cc_start: 0.8382 (mmmt) cc_final: 0.7941 (mmmm) REVERT: f 167 ASP cc_start: 0.8508 (t0) cc_final: 0.8263 (t0) REVERT: f 252 ASN cc_start: 0.7968 (t0) cc_final: 0.7668 (t0) outliers start: 282 outliers final: 202 residues processed: 1074 average time/residue: 0.5934 time to fit residues: 1112.3832 Evaluate side-chains 1011 residues out of total 7348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 793 time to evaluate : 5.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 362 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain F residue 62 CYS Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 142 GLN Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 395 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 230 HIS Chi-restraints excluded: chain H residue 238 SER Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 338 THR Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 397 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 263 ILE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 362 TYR Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain M residue 8 MET Chi-restraints excluded: chain N residue 8 MET Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 251 TRP Chi-restraints excluded: chain O residue 265 GLU Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 208 THR Chi-restraints excluded: chain Q residue 230 VAL Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 370 CYS Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain E residue 396 ASN Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 305 TYR Chi-restraints excluded: chain R residue 379 ILE Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 62 CYS Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 84 VAL Chi-restraints excluded: chain U residue 142 GLN Chi-restraints excluded: chain U residue 299 LEU Chi-restraints excluded: chain U residue 305 THR Chi-restraints excluded: chain U residue 343 THR Chi-restraints excluded: chain U residue 366 VAL Chi-restraints excluded: chain U residue 395 SER Chi-restraints excluded: chain U residue 410 VAL Chi-restraints excluded: chain V residue 62 CYS Chi-restraints excluded: chain V residue 96 CYS Chi-restraints excluded: chain V residue 98 SER Chi-restraints excluded: chain V residue 145 ASP Chi-restraints excluded: chain V residue 160 GLN Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain V residue 329 SER Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain W residue 2 GLU Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain W residue 101 THR Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 205 SER Chi-restraints excluded: chain W residue 295 THR Chi-restraints excluded: chain W residue 305 THR Chi-restraints excluded: chain W residue 329 SER Chi-restraints excluded: chain W residue 334 SER Chi-restraints excluded: chain W residue 338 THR Chi-restraints excluded: chain W residue 353 THR Chi-restraints excluded: chain W residue 366 VAL Chi-restraints excluded: chain W residue 397 VAL Chi-restraints excluded: chain W residue 432 THR Chi-restraints excluded: chain W residue 434 ILE Chi-restraints excluded: chain X residue 50 PHE Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 79 VAL Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 101 ILE Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 143 ILE Chi-restraints excluded: chain X residue 175 THR Chi-restraints excluded: chain X residue 197 VAL Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 305 TYR Chi-restraints excluded: chain X residue 326 GLU Chi-restraints excluded: chain X residue 397 THR Chi-restraints excluded: chain Y residue 53 GLN Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 142 THR Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 165 GLU Chi-restraints excluded: chain Y residue 167 ILE Chi-restraints excluded: chain Y residue 242 VAL Chi-restraints excluded: chain Y residue 250 ARG Chi-restraints excluded: chain Y residue 256 ILE Chi-restraints excluded: chain Y residue 260 LEU Chi-restraints excluded: chain Y residue 263 ILE Chi-restraints excluded: chain Y residue 299 LEU Chi-restraints excluded: chain Y residue 305 TYR Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 367 VAL Chi-restraints excluded: chain Y residue 388 LEU Chi-restraints excluded: chain Z residue 40 GLU Chi-restraints excluded: chain Z residue 50 PHE Chi-restraints excluded: chain Z residue 62 HIS Chi-restraints excluded: chain Z residue 136 VAL Chi-restraints excluded: chain Z residue 154 THR Chi-restraints excluded: chain Z residue 215 MET Chi-restraints excluded: chain Z residue 295 SER Chi-restraints excluded: chain Z residue 299 LEU Chi-restraints excluded: chain Z residue 322 VAL Chi-restraints excluded: chain Z residue 362 TYR Chi-restraints excluded: chain Z residue 374 SER Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain b residue 43 VAL Chi-restraints excluded: chain c residue 8 MET Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 200 VAL Chi-restraints excluded: chain d residue 221 ARG Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain e residue 113 MET Chi-restraints excluded: chain e residue 149 VAL Chi-restraints excluded: chain e residue 208 THR Chi-restraints excluded: chain f residue 111 MET Chi-restraints excluded: chain f residue 255 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 280 optimal weight: 0.1980 chunk 60 optimal weight: 20.0000 chunk 355 optimal weight: 9.9990 chunk 378 optimal weight: 10.0000 chunk 170 optimal weight: 50.0000 chunk 381 optimal weight: 8.9990 chunk 506 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 354 optimal weight: 0.9980 chunk 303 optimal weight: 30.0000 chunk 89 optimal weight: 50.0000 overall best weight: 4.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 HIS B 77 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 304 GLN J 53 GLN J 224 GLN ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 120 ASN Y 62 HIS Y 170 HIS Y 340 GLN Z 26 HIS ** Z 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 348 HIS f 196 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.165471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.120864 restraints weight = 88174.886| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.59 r_work: 0.3010 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 69494 Z= 0.319 Angle : 0.628 9.915 94641 Z= 0.318 Chirality : 0.046 0.420 10722 Planarity : 0.005 0.067 12159 Dihedral : 6.119 59.024 10854 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.94 % Favored : 92.83 % Rotamer: Outliers : 4.42 % Allowed : 15.11 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.09), residues: 8607 helix: 2.54 (0.16), residues: 1038 sheet: -0.94 (0.10), residues: 2464 loop : -1.59 (0.08), residues: 5105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 329 HIS 0.011 0.001 HIS Z 62 PHE 0.021 0.001 PHE V 95 TYR 0.022 0.002 TYR H 93 ARG 0.006 0.000 ARG H 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 7348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 325 poor density : 835 time to evaluate : 6.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.8668 (ttmt) cc_final: 0.7977 (tmtt) REVERT: A 142 GLN cc_start: 0.8702 (mt0) cc_final: 0.8422 (mt0) REVERT: A 151 ASP cc_start: 0.8616 (p0) cc_final: 0.8396 (p0) REVERT: A 188 ASP cc_start: 0.8706 (t0) cc_final: 0.8503 (t0) REVERT: B 50 PHE cc_start: 0.8918 (m-10) cc_final: 0.8508 (m-10) REVERT: B 77 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7802 (p0) REVERT: B 119 ARG cc_start: 0.8666 (mpp80) cc_final: 0.7926 (mtt90) REVERT: B 132 ASP cc_start: 0.9194 (t0) cc_final: 0.8880 (t70) REVERT: B 215 MET cc_start: 0.6909 (mtt) cc_final: 0.6687 (mtt) REVERT: B 305 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.7440 (m-80) REVERT: D 162 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8794 (tttp) REVERT: D 177 MET cc_start: 0.8506 (mpp) cc_final: 0.8114 (mpt) REVERT: D 183 LYS cc_start: 0.7718 (pptt) cc_final: 0.7467 (pttp) REVERT: G 59 TYR cc_start: 0.8971 (t80) cc_final: 0.8743 (t80) REVERT: H 139 ASN cc_start: 0.9360 (t0) cc_final: 0.9109 (t0) REVERT: H 151 ASP cc_start: 0.8685 (p0) cc_final: 0.8463 (p0) REVERT: H 174 ASP cc_start: 0.8998 (m-30) cc_final: 0.8689 (m-30) REVERT: H 295 THR cc_start: 0.8897 (m) cc_final: 0.8446 (p) REVERT: I 50 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7927 (m-10) REVERT: I 153 CYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8402 (p) REVERT: I 215 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7112 (tmm) REVERT: J 50 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7817 (m-10) REVERT: J 65 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8240 (t) REVERT: J 196 LYS cc_start: 0.7482 (ptmt) cc_final: 0.7210 (ptpp) REVERT: J 212 ASN cc_start: 0.8162 (m-40) cc_final: 0.7701 (t0) REVERT: J 261 ASP cc_start: 0.8621 (t0) cc_final: 0.8214 (m-30) REVERT: J 325 MET cc_start: 0.9130 (ppp) cc_final: 0.7921 (ptt) REVERT: J 394 LYS cc_start: 0.7262 (ttmm) cc_final: 0.7006 (ttpp) REVERT: K 250 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7052 (mtp-110) REVERT: K 269 MET cc_start: 0.8594 (mmm) cc_final: 0.8376 (mtm) REVERT: L 40 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6661 (mt-10) REVERT: M 8 MET cc_start: 0.4245 (OUTLIER) cc_final: 0.4032 (mtp) REVERT: N 40 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.4491 (mt-10) REVERT: O 113 MET cc_start: 0.5644 (OUTLIER) cc_final: 0.5251 (mpt) REVERT: O 162 LYS cc_start: 0.8732 (tmtt) cc_final: 0.8438 (ttpt) REVERT: O 207 PHE cc_start: 0.9018 (m-10) cc_final: 0.8723 (m-10) REVERT: O 252 ASN cc_start: 0.8411 (t0) cc_final: 0.8038 (m-40) REVERT: P 147 LYS cc_start: 0.8270 (pptt) cc_final: 0.7849 (pptt) REVERT: Q 167 ASP cc_start: 0.8038 (t0) cc_final: 0.7782 (t0) REVERT: Q 177 MET cc_start: 0.7703 (mmm) cc_final: 0.7385 (mmm) REVERT: E 19 ILE cc_start: 0.9109 (mt) cc_final: 0.8907 (mt) REVERT: E 95 PHE cc_start: 0.7631 (t80) cc_final: 0.7403 (t80) REVERT: E 245 LYS cc_start: 0.9275 (ptpt) cc_final: 0.8951 (pttt) REVERT: E 341 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8235 (pm20) REVERT: R 169 MET cc_start: 0.8585 (mmm) cc_final: 0.8225 (mmm) REVERT: R 182 SER cc_start: 0.7599 (m) cc_final: 0.7339 (p) REVERT: R 199 TYR cc_start: 0.7842 (p90) cc_final: 0.7351 (p90) REVERT: R 213 SER cc_start: 0.7960 (t) cc_final: 0.7556 (m) REVERT: R 215 MET cc_start: 0.7064 (mmm) cc_final: 0.6766 (mmm) REVERT: R 224 GLN cc_start: 0.6514 (mt0) cc_final: 0.6133 (mt0) REVERT: R 346 LYS cc_start: 0.8104 (tttm) cc_final: 0.7890 (ttmm) REVERT: T 252 ASN cc_start: 0.7819 (m-40) cc_final: 0.7547 (t0) REVERT: U 67 GLU cc_start: 0.8204 (tp30) cc_final: 0.7931 (pm20) REVERT: U 182 ASP cc_start: 0.8682 (p0) cc_final: 0.8454 (p0) REVERT: U 246 GLU cc_start: 0.6485 (pt0) cc_final: 0.6109 (pt0) REVERT: V 36 THR cc_start: 0.9056 (p) cc_final: 0.8835 (p) REVERT: V 99 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7049 (mp0) REVERT: V 281 ASN cc_start: 0.9038 (t0) cc_final: 0.8533 (t0) REVERT: V 299 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8927 (tt) REVERT: V 402 MET cc_start: 0.7333 (mmt) cc_final: 0.7118 (mmt) REVERT: W 182 ASP cc_start: 0.8638 (p0) cc_final: 0.7944 (t0) REVERT: W 242 TYR cc_start: 0.5418 (m-10) cc_final: 0.5198 (m-10) REVERT: X 199 TYR cc_start: 0.7628 (p90) cc_final: 0.7377 (p90) REVERT: Y 165 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: Y 393 SER cc_start: 0.8358 (t) cc_final: 0.7893 (p) REVERT: Z 7 ASN cc_start: 0.8881 (t0) cc_final: 0.8475 (t0) REVERT: Z 50 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8676 (m-10) REVERT: Z 53 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8274 (pm20) REVERT: Z 169 MET cc_start: 0.8537 (mmt) cc_final: 0.8037 (mmt) REVERT: b 8 MET cc_start: 0.6487 (mpp) cc_final: 0.6038 (mtm) REVERT: c 50 ASP cc_start: 0.8501 (m-30) cc_final: 0.8220 (m-30) REVERT: d 141 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7476 (mtm) REVERT: d 157 LYS cc_start: 0.9049 (pttt) cc_final: 0.8745 (pttp) REVERT: d 221 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8178 (mmt-90) REVERT: d 252 ASN cc_start: 0.8442 (t0) cc_final: 0.8022 (t0) REVERT: e 162 LYS cc_start: 0.8682 (tttm) cc_final: 0.8381 (ttmt) REVERT: e 252 ASN cc_start: 0.7254 (t0) cc_final: 0.6370 (m-40) REVERT: e 253 LYS cc_start: 0.6704 (mtpp) cc_final: 0.6208 (mtpt) REVERT: f 162 LYS cc_start: 0.8411 (mmmt) cc_final: 0.7965 (mmmm) REVERT: f 167 ASP cc_start: 0.8500 (t0) cc_final: 0.8297 (t0) REVERT: f 177 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8361 (mtt) REVERT: f 252 ASN cc_start: 0.8013 (t0) cc_final: 0.7789 (t0) outliers start: 325 outliers final: 242 residues processed: 1078 average time/residue: 0.5958 time to fit residues: 1120.1380 Evaluate side-chains 1055 residues out of total 7348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 262 poor density : 793 time to evaluate : 5.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 362 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain D residue 162 LYS Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain F residue 62 CYS Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 142 GLN Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 395 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 230 HIS Chi-restraints excluded: chain H residue 238 SER Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 16 ILE Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 153 CYS Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain J residue 224 GLN Chi-restraints excluded: chain J residue 263 ILE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 362 TYR Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain J residue 388 LEU Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 250 ARG Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 362 TYR Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain M residue 8 MET Chi-restraints excluded: chain N residue 8 MET Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 251 TRP Chi-restraints excluded: chain O residue 265 GLU Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 208 THR Chi-restraints excluded: chain Q residue 230 VAL Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 370 CYS Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 254 VAL Chi-restraints excluded: chain R residue 265 CYS Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 305 TYR Chi-restraints excluded: chain R residue 318 ILE Chi-restraints excluded: chain R residue 379 ILE Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 62 CYS Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 84 VAL Chi-restraints excluded: chain U residue 142 GLN Chi-restraints excluded: chain U residue 280 MET Chi-restraints excluded: chain U residue 299 LEU Chi-restraints excluded: chain U residue 305 THR Chi-restraints excluded: chain U residue 317 THR Chi-restraints excluded: chain U residue 343 THR Chi-restraints excluded: chain U residue 366 VAL Chi-restraints excluded: chain U residue 395 SER Chi-restraints excluded: chain U residue 410 VAL Chi-restraints excluded: chain U residue 422 ILE Chi-restraints excluded: chain V residue 62 CYS Chi-restraints excluded: chain V residue 96 CYS Chi-restraints excluded: chain V residue 98 SER Chi-restraints excluded: chain V residue 145 ASP Chi-restraints excluded: chain V residue 160 GLN Chi-restraints excluded: chain V residue 234 THR Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain V residue 305 THR Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain V residue 329 SER Chi-restraints excluded: chain V residue 370 CYS Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain W residue 2 GLU Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 205 SER Chi-restraints excluded: chain W residue 271 CYS Chi-restraints excluded: chain W residue 273 VAL Chi-restraints excluded: chain W residue 295 THR Chi-restraints excluded: chain W residue 329 SER Chi-restraints excluded: chain W residue 334 SER Chi-restraints excluded: chain W residue 338 THR Chi-restraints excluded: chain W residue 366 VAL Chi-restraints excluded: chain W residue 377 SER Chi-restraints excluded: chain W residue 397 VAL Chi-restraints excluded: chain W residue 432 THR Chi-restraints excluded: chain W residue 434 ILE Chi-restraints excluded: chain X residue 50 PHE Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 79 VAL Chi-restraints excluded: chain X residue 88 SER Chi-restraints excluded: chain X residue 101 ILE Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 122 VAL Chi-restraints excluded: chain X residue 143 ILE Chi-restraints excluded: chain X residue 175 THR Chi-restraints excluded: chain X residue 197 VAL Chi-restraints excluded: chain X residue 202 THR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 305 TYR Chi-restraints excluded: chain X residue 361 LEU Chi-restraints excluded: chain Y residue 50 PHE Chi-restraints excluded: chain Y residue 53 GLN Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 142 THR Chi-restraints excluded: chain Y residue 165 GLU Chi-restraints excluded: chain Y residue 167 ILE Chi-restraints excluded: chain Y residue 242 VAL Chi-restraints excluded: chain Y residue 250 ARG Chi-restraints excluded: chain Y residue 256 ILE Chi-restraints excluded: chain Y residue 260 LEU Chi-restraints excluded: chain Y residue 263 ILE Chi-restraints excluded: chain Y residue 290 HIS Chi-restraints excluded: chain Y residue 299 LEU Chi-restraints excluded: chain Y residue 305 TYR Chi-restraints excluded: chain Y residue 367 VAL Chi-restraints excluded: chain Y residue 389 VAL Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Z residue 40 GLU Chi-restraints excluded: chain Z residue 50 PHE Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 53 GLN Chi-restraints excluded: chain Z residue 64 TYR Chi-restraints excluded: chain Z residue 136 VAL Chi-restraints excluded: chain Z residue 154 THR Chi-restraints excluded: chain Z residue 250 ARG Chi-restraints excluded: chain Z residue 260 LEU Chi-restraints excluded: chain Z residue 261 ASP Chi-restraints excluded: chain Z residue 295 SER Chi-restraints excluded: chain Z residue 299 LEU Chi-restraints excluded: chain Z residue 322 VAL Chi-restraints excluded: chain Z residue 362 TYR Chi-restraints excluded: chain Z residue 374 SER Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain b residue 43 VAL Chi-restraints excluded: chain c residue 8 MET Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 141 MET Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 200 VAL Chi-restraints excluded: chain d residue 221 ARG Chi-restraints excluded: chain e residue 113 MET Chi-restraints excluded: chain e residue 149 VAL Chi-restraints excluded: chain e residue 208 THR Chi-restraints excluded: chain f residue 111 MET Chi-restraints excluded: chain f residue 173 ILE Chi-restraints excluded: chain f residue 177 MET Chi-restraints excluded: chain f residue 255 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 765 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 251 optimal weight: 1.9990 chunk 655 optimal weight: 5.9990 chunk 667 optimal weight: 3.9990 chunk 566 optimal weight: 20.0000 chunk 496 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 618 optimal weight: 10.0000 chunk 651 optimal weight: 2.9990 chunk 832 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN B 226 HIS ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS ** H 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 GLN J 224 GLN K 212 ASN ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 120 ASN Z 62 HIS ** Z 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.166675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.122044 restraints weight = 87915.794| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.55 r_work: 0.3026 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 69494 Z= 0.230 Angle : 0.588 9.737 94641 Z= 0.297 Chirality : 0.045 0.476 10722 Planarity : 0.005 0.076 12159 Dihedral : 5.835 59.345 10854 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.95 % Favored : 93.82 % Rotamer: Outliers : 4.22 % Allowed : 15.96 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.09), residues: 8607 helix: 2.67 (0.16), residues: 1038 sheet: -0.82 (0.10), residues: 2544 loop : -1.51 (0.08), residues: 5025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Y 329 HIS 0.007 0.001 HIS R 5 PHE 0.023 0.001 PHE V 95 TYR 0.023 0.001 TYR H 93 ARG 0.007 0.000 ARG H 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1155 residues out of total 7348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 310 poor density : 845 time to evaluate : 5.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.8638 (ttmt) cc_final: 0.8407 (mtpp) REVERT: A 151 ASP cc_start: 0.8602 (p0) cc_final: 0.8317 (p0) REVERT: A 351 LYS cc_start: 0.8689 (ttmm) cc_final: 0.8335 (ttmm) REVERT: B 50 PHE cc_start: 0.8904 (m-10) cc_final: 0.8543 (m-10) REVERT: B 119 ARG cc_start: 0.8677 (mpp80) cc_final: 0.8028 (mtt90) REVERT: B 132 ASP cc_start: 0.9193 (t0) cc_final: 0.8852 (t70) REVERT: B 167 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8456 (mm) REVERT: B 215 MET cc_start: 0.7031 (mtt) cc_final: 0.6790 (mtt) REVERT: B 251 LYS cc_start: 0.8795 (mmmm) cc_final: 0.8513 (mmmt) REVERT: B 305 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.7485 (m-80) REVERT: C 208 ILE cc_start: 0.3710 (OUTLIER) cc_final: 0.3421 (mm) REVERT: D 162 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8803 (tttp) REVERT: D 177 MET cc_start: 0.8483 (mpp) cc_final: 0.8091 (mpt) REVERT: D 183 LYS cc_start: 0.7748 (pptt) cc_final: 0.7507 (pttp) REVERT: F 95 PHE cc_start: 0.7857 (t80) cc_final: 0.7594 (t80) REVERT: F 182 ASP cc_start: 0.8761 (t70) cc_final: 0.8528 (t0) REVERT: G 59 TYR cc_start: 0.8982 (t80) cc_final: 0.8748 (t80) REVERT: H 7 MET cc_start: 0.9052 (ttp) cc_final: 0.8814 (ptm) REVERT: H 139 ASN cc_start: 0.9347 (t0) cc_final: 0.9133 (t0) REVERT: H 174 ASP cc_start: 0.8994 (m-30) cc_final: 0.8692 (m-30) REVERT: I 50 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.8099 (m-10) REVERT: I 153 CYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8367 (p) REVERT: I 215 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7101 (tmm) REVERT: I 301 GLU cc_start: 0.8925 (tp30) cc_final: 0.8143 (tt0) REVERT: J 50 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7704 (m-10) REVERT: J 196 LYS cc_start: 0.7429 (ptmt) cc_final: 0.7152 (ptpp) REVERT: J 212 ASN cc_start: 0.8123 (m-40) cc_final: 0.7626 (t0) REVERT: J 224 GLN cc_start: 0.6123 (OUTLIER) cc_final: 0.5636 (tp40) REVERT: J 261 ASP cc_start: 0.8576 (t0) cc_final: 0.8195 (m-30) REVERT: J 267 VAL cc_start: 0.9620 (OUTLIER) cc_final: 0.9309 (m) REVERT: J 394 LYS cc_start: 0.7301 (ttmm) cc_final: 0.6821 (ttmt) REVERT: K 139 GLU cc_start: 0.8807 (tt0) cc_final: 0.8527 (tt0) REVERT: K 169 MET cc_start: 0.8542 (mmt) cc_final: 0.7890 (mmt) REVERT: K 196 LYS cc_start: 0.7809 (ptpp) cc_final: 0.7534 (ptmm) REVERT: K 250 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7712 (mtp-110) REVERT: K 269 MET cc_start: 0.8549 (mmm) cc_final: 0.8342 (mtm) REVERT: O 113 MET cc_start: 0.5650 (OUTLIER) cc_final: 0.5256 (mpt) REVERT: O 162 LYS cc_start: 0.8710 (tmtt) cc_final: 0.8432 (ttpt) REVERT: O 207 PHE cc_start: 0.9001 (m-10) cc_final: 0.8581 (m-10) REVERT: O 240 GLU cc_start: 0.3527 (tm-30) cc_final: 0.3224 (tm-30) REVERT: O 252 ASN cc_start: 0.8423 (t0) cc_final: 0.8047 (m-40) REVERT: P 147 LYS cc_start: 0.8271 (pptt) cc_final: 0.7850 (pptt) REVERT: P 162 LYS cc_start: 0.8576 (tttm) cc_final: 0.8105 (tmtt) REVERT: P 194 ASN cc_start: 0.7686 (m110) cc_final: 0.7434 (m110) REVERT: Q 167 ASP cc_start: 0.8024 (t0) cc_final: 0.7750 (t0) REVERT: Q 177 MET cc_start: 0.7704 (mmm) cc_final: 0.7376 (mmm) REVERT: E 19 ILE cc_start: 0.9115 (mt) cc_final: 0.8904 (mt) REVERT: E 117 ASP cc_start: 0.8883 (t70) cc_final: 0.8504 (m-30) REVERT: E 245 LYS cc_start: 0.9244 (ptpt) cc_final: 0.8925 (pttt) REVERT: E 364 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.7857 (p) REVERT: R 199 TYR cc_start: 0.7740 (p90) cc_final: 0.7210 (p90) REVERT: R 213 SER cc_start: 0.7868 (t) cc_final: 0.7451 (m) REVERT: R 215 MET cc_start: 0.7061 (mmm) cc_final: 0.6742 (mmm) REVERT: R 224 GLN cc_start: 0.6566 (mt0) cc_final: 0.6270 (mt0) REVERT: R 246 ASP cc_start: 0.7744 (m-30) cc_final: 0.7048 (t0) REVERT: R 346 LYS cc_start: 0.8095 (tttm) cc_final: 0.7892 (ttmm) REVERT: T 252 ASN cc_start: 0.7779 (m-40) cc_final: 0.7527 (t0) REVERT: U 67 GLU cc_start: 0.8147 (tp30) cc_final: 0.7894 (pm20) REVERT: U 182 ASP cc_start: 0.8659 (p0) cc_final: 0.8440 (p0) REVERT: U 246 GLU cc_start: 0.6473 (pt0) cc_final: 0.6105 (pt0) REVERT: V 99 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7133 (mp0) REVERT: V 160 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: V 281 ASN cc_start: 0.9046 (t0) cc_final: 0.8496 (t0) REVERT: V 402 MET cc_start: 0.7330 (mmt) cc_final: 0.7129 (mmt) REVERT: W 182 ASP cc_start: 0.8610 (p0) cc_final: 0.7920 (t0) REVERT: Y 165 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: Z 7 ASN cc_start: 0.8861 (t0) cc_final: 0.8523 (t0) REVERT: Z 50 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8640 (m-10) REVERT: Z 169 MET cc_start: 0.8548 (mmt) cc_final: 0.8090 (mmt) REVERT: Z 196 LYS cc_start: 0.7454 (ptpp) cc_final: 0.7022 (pttp) REVERT: Z 251 LYS cc_start: 0.8777 (ptmm) cc_final: 0.8171 (mtpp) REVERT: b 8 MET cc_start: 0.6209 (mpp) cc_final: 0.5851 (mtm) REVERT: c 50 ASP cc_start: 0.8561 (m-30) cc_final: 0.8285 (m-30) REVERT: d 141 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7638 (mtp) REVERT: d 157 LYS cc_start: 0.9039 (pttt) cc_final: 0.8747 (pttp) REVERT: d 188 LYS cc_start: 0.8111 (mtmm) cc_final: 0.7716 (mttp) REVERT: d 221 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8205 (mmt-90) REVERT: d 252 ASN cc_start: 0.8442 (t0) cc_final: 0.8022 (t0) REVERT: e 162 LYS cc_start: 0.8647 (tttm) cc_final: 0.8367 (ttmt) REVERT: e 187 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7751 (mp0) REVERT: e 252 ASN cc_start: 0.7248 (t0) cc_final: 0.6414 (m-40) REVERT: e 253 LYS cc_start: 0.6710 (mtpp) cc_final: 0.6265 (mtpt) REVERT: f 167 ASP cc_start: 0.8659 (t0) cc_final: 0.8289 (t0) REVERT: f 252 ASN cc_start: 0.8009 (t0) cc_final: 0.7780 (t0) outliers start: 310 outliers final: 223 residues processed: 1080 average time/residue: 0.6096 time to fit residues: 1143.8738 Evaluate side-chains 1040 residues out of total 7348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 799 time to evaluate : 5.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 362 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 162 LYS Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain F residue 62 CYS Chi-restraints excluded: chain F residue 142 GLN Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 395 SER Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 230 HIS Chi-restraints excluded: chain H residue 238 SER Chi-restraints excluded: chain H residue 264 ASN Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 338 THR Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 16 ILE Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 153 CYS Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 265 CYS Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 53 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain J residue 224 GLN Chi-restraints excluded: chain J residue 263 ILE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 362 TYR Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain J residue 388 LEU Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 250 ARG Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 362 TYR Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain N residue 8 MET Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 251 TRP Chi-restraints excluded: chain O residue 265 GLU Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 208 THR Chi-restraints excluded: chain Q residue 230 VAL Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 370 CYS Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 254 VAL Chi-restraints excluded: chain R residue 265 CYS Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 305 TYR Chi-restraints excluded: chain R residue 318 ILE Chi-restraints excluded: chain R residue 379 ILE Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain U residue 62 CYS Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 84 VAL Chi-restraints excluded: chain U residue 142 GLN Chi-restraints excluded: chain U residue 299 LEU Chi-restraints excluded: chain U residue 305 THR Chi-restraints excluded: chain U residue 352 VAL Chi-restraints excluded: chain U residue 366 VAL Chi-restraints excluded: chain U residue 395 SER Chi-restraints excluded: chain U residue 410 VAL Chi-restraints excluded: chain U residue 432 THR Chi-restraints excluded: chain V residue 10 VAL Chi-restraints excluded: chain V residue 62 CYS Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 96 CYS Chi-restraints excluded: chain V residue 98 SER Chi-restraints excluded: chain V residue 145 ASP Chi-restraints excluded: chain V residue 160 GLN Chi-restraints excluded: chain V residue 234 THR Chi-restraints excluded: chain V residue 271 CYS Chi-restraints excluded: chain V residue 305 THR Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain V residue 370 CYS Chi-restraints excluded: chain W residue 2 GLU Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 273 VAL Chi-restraints excluded: chain W residue 295 THR Chi-restraints excluded: chain W residue 329 SER Chi-restraints excluded: chain W residue 334 SER Chi-restraints excluded: chain W residue 353 THR Chi-restraints excluded: chain W residue 366 VAL Chi-restraints excluded: chain W residue 377 SER Chi-restraints excluded: chain W residue 397 VAL Chi-restraints excluded: chain X residue 50 PHE Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 79 VAL Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 101 ILE Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 143 ILE Chi-restraints excluded: chain X residue 175 THR Chi-restraints excluded: chain X residue 197 VAL Chi-restraints excluded: chain X residue 202 THR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 305 TYR Chi-restraints excluded: chain X residue 361 LEU Chi-restraints excluded: chain X residue 397 THR Chi-restraints excluded: chain Y residue 50 PHE Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 142 THR Chi-restraints excluded: chain Y residue 165 GLU Chi-restraints excluded: chain Y residue 167 ILE Chi-restraints excluded: chain Y residue 242 VAL Chi-restraints excluded: chain Y residue 250 ARG Chi-restraints excluded: chain Y residue 256 ILE Chi-restraints excluded: chain Y residue 260 LEU Chi-restraints excluded: chain Y residue 263 ILE Chi-restraints excluded: chain Y residue 290 HIS Chi-restraints excluded: chain Y residue 299 LEU Chi-restraints excluded: chain Y residue 305 TYR Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 367 VAL Chi-restraints excluded: chain Y residue 388 LEU Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Z residue 40 GLU Chi-restraints excluded: chain Z residue 50 PHE Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 62 HIS Chi-restraints excluded: chain Z residue 64 TYR Chi-restraints excluded: chain Z residue 136 VAL Chi-restraints excluded: chain Z residue 142 THR Chi-restraints excluded: chain Z residue 154 THR Chi-restraints excluded: chain Z residue 256 ILE Chi-restraints excluded: chain Z residue 260 LEU Chi-restraints excluded: chain Z residue 261 ASP Chi-restraints excluded: chain Z residue 295 SER Chi-restraints excluded: chain Z residue 299 LEU Chi-restraints excluded: chain Z residue 322 VAL Chi-restraints excluded: chain Z residue 362 TYR Chi-restraints excluded: chain Z residue 374 SER Chi-restraints excluded: chain Z residue 415 CYS Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 141 MET Chi-restraints excluded: chain d residue 200 VAL Chi-restraints excluded: chain d residue 221 ARG Chi-restraints excluded: chain e residue 113 MET Chi-restraints excluded: chain e residue 149 VAL Chi-restraints excluded: chain e residue 208 THR Chi-restraints excluded: chain f residue 111 MET Chi-restraints excluded: chain f residue 173 ILE Chi-restraints excluded: chain f residue 187 GLU Chi-restraints excluded: chain f residue 255 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 850 optimal weight: 10.0000 chunk 284 optimal weight: 8.9990 chunk 373 optimal weight: 40.0000 chunk 694 optimal weight: 6.9990 chunk 635 optimal weight: 3.9990 chunk 591 optimal weight: 8.9990 chunk 589 optimal weight: 9.9990 chunk 446 optimal weight: 7.9990 chunk 217 optimal weight: 7.9990 chunk 571 optimal weight: 10.0000 chunk 406 optimal weight: 40.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN C 170 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** H 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 GLN K 94 HIS K 212 ASN ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 170 HIS R 340 GLN T 196 HIS U 32 GLN ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 62 HIS Y 340 GLN Z 26 HIS ** Z 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN d 196 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.161422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117248 restraints weight = 88373.446| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.63 r_work: 0.2946 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 69494 Z= 0.496 Angle : 0.718 12.041 94641 Z= 0.366 Chirality : 0.050 0.343 10722 Planarity : 0.005 0.068 12159 Dihedral : 6.213 57.788 10854 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.95 % Favored : 91.84 % Rotamer: Outliers : 4.90 % Allowed : 16.21 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.09), residues: 8607 helix: 2.10 (0.16), residues: 1086 sheet: -1.03 (0.10), residues: 2504 loop : -1.69 (0.08), residues: 5017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 235 HIS 0.048 0.002 HIS Z 62 PHE 0.033 0.002 PHE K 50 TYR 0.028 0.002 TYR H 93 ARG 0.007 0.001 ARG H 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1177 residues out of total 7348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 360 poor density : 817 time to evaluate : 5.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8439 (mtpp) REVERT: A 151 ASP cc_start: 0.8829 (p0) cc_final: 0.8536 (p0) REVERT: B 50 PHE cc_start: 0.9029 (m-10) cc_final: 0.8646 (m-10) REVERT: B 119 ARG cc_start: 0.8686 (mpp80) cc_final: 0.8104 (mtt90) REVERT: B 132 ASP cc_start: 0.9210 (t0) cc_final: 0.8883 (t70) REVERT: B 158 GLN cc_start: 0.8094 (mp10) cc_final: 0.7595 (mp10) REVERT: B 174 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.7558 (p0) REVERT: B 215 MET cc_start: 0.6868 (mtt) cc_final: 0.6592 (mtt) REVERT: C 208 ILE cc_start: 0.4223 (OUTLIER) cc_final: 0.3940 (mm) REVERT: D 138 ASP cc_start: 0.8709 (p0) cc_final: 0.8476 (p0) REVERT: D 183 LYS cc_start: 0.7851 (pptt) cc_final: 0.7551 (ptmm) REVERT: D 266 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8669 (mt-10) REVERT: F 93 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.6172 (p90) REVERT: G 59 TYR cc_start: 0.8952 (t80) cc_final: 0.8660 (t80) REVERT: H 139 ASN cc_start: 0.9310 (t0) cc_final: 0.9088 (t0) REVERT: H 321 LYS cc_start: 0.8919 (mtmm) cc_final: 0.8325 (mttp) REVERT: H 323 ASP cc_start: 0.9317 (OUTLIER) cc_final: 0.9076 (p0) REVERT: H 395 SER cc_start: 0.9187 (m) cc_final: 0.8961 (m) REVERT: I 50 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.8076 (m-10) REVERT: I 153 CYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8391 (p) REVERT: I 168 ASP cc_start: 0.8556 (m-30) cc_final: 0.8183 (m-30) REVERT: I 298 THR cc_start: 0.9252 (OUTLIER) cc_final: 0.8779 (p) REVERT: J 50 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.7916 (m-10) REVERT: J 196 LYS cc_start: 0.7506 (ptmt) cc_final: 0.7216 (ptpp) REVERT: J 212 ASN cc_start: 0.8080 (m-40) cc_final: 0.7509 (t0) REVERT: J 261 ASP cc_start: 0.8706 (t0) cc_final: 0.8237 (m-30) REVERT: J 325 MET cc_start: 0.9135 (ppp) cc_final: 0.8227 (ptt) REVERT: J 415 CYS cc_start: 0.8244 (t) cc_final: 0.7629 (p) REVERT: K 169 MET cc_start: 0.8603 (mmt) cc_final: 0.7867 (mmt) REVERT: K 196 LYS cc_start: 0.7937 (ptpp) cc_final: 0.7539 (ptmm) REVERT: K 250 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7681 (mtp-110) REVERT: K 269 MET cc_start: 0.8578 (mmm) cc_final: 0.8368 (mtm) REVERT: O 113 MET cc_start: 0.5715 (OUTLIER) cc_final: 0.5292 (mpt) REVERT: O 162 LYS cc_start: 0.8766 (tmtt) cc_final: 0.8454 (ttpt) REVERT: O 252 ASN cc_start: 0.8486 (t0) cc_final: 0.8070 (m-40) REVERT: O 253 LYS cc_start: 0.8371 (tptp) cc_final: 0.7915 (tptp) REVERT: P 147 LYS cc_start: 0.8318 (pptt) cc_final: 0.7889 (pptt) REVERT: P 162 LYS cc_start: 0.8683 (tttm) cc_final: 0.8253 (tmtt) REVERT: P 194 ASN cc_start: 0.7777 (m110) cc_final: 0.7436 (m110) REVERT: Q 167 ASP cc_start: 0.8072 (t0) cc_final: 0.7782 (t0) REVERT: E 19 ILE cc_start: 0.9134 (mt) cc_final: 0.8912 (mt) REVERT: E 72 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8338 (mm-30) REVERT: E 245 LYS cc_start: 0.9286 (ptpt) cc_final: 0.8912 (pttt) REVERT: R 168 ASP cc_start: 0.8303 (m-30) cc_final: 0.8095 (m-30) REVERT: R 169 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8067 (mmt) REVERT: R 199 TYR cc_start: 0.7866 (p90) cc_final: 0.7255 (p90) REVERT: R 213 SER cc_start: 0.8065 (t) cc_final: 0.7863 (m) REVERT: R 215 MET cc_start: 0.7149 (mmm) cc_final: 0.6847 (mmm) REVERT: R 218 ASN cc_start: 0.7719 (m-40) cc_final: 0.7156 (p0) REVERT: R 224 GLN cc_start: 0.7100 (mt0) cc_final: 0.6827 (mt0) REVERT: R 246 ASP cc_start: 0.7705 (m-30) cc_final: 0.6833 (p0) REVERT: T 183 LYS cc_start: 0.7471 (ttpp) cc_final: 0.7206 (tptt) REVERT: U 182 ASP cc_start: 0.8714 (p0) cc_final: 0.8457 (p0) REVERT: U 246 GLU cc_start: 0.6130 (pt0) cc_final: 0.5685 (pt0) REVERT: V 99 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7049 (mp0) REVERT: V 281 ASN cc_start: 0.9098 (t0) cc_final: 0.8636 (t0) REVERT: V 299 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8719 (tt) REVERT: W 110 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8259 (ttm110) REVERT: W 182 ASP cc_start: 0.8766 (p0) cc_final: 0.8139 (t0) REVERT: Y 165 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: Y 169 MET cc_start: 0.8035 (mmt) cc_final: 0.7770 (mmt) REVERT: Z 7 ASN cc_start: 0.8962 (t0) cc_final: 0.8577 (t0) REVERT: Z 50 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8823 (m-10) REVERT: Z 53 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8516 (pm20) REVERT: Z 61 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7871 (m-40) REVERT: Z 169 MET cc_start: 0.8592 (mmt) cc_final: 0.8144 (mmt) REVERT: Z 196 LYS cc_start: 0.7495 (ptpp) cc_final: 0.7002 (pttp) REVERT: Z 251 LYS cc_start: 0.8739 (ptmm) cc_final: 0.8086 (mtpp) REVERT: Z 253 LYS cc_start: 0.9131 (mttm) cc_final: 0.8864 (mttt) REVERT: Z 382 PHE cc_start: 0.6725 (m-10) cc_final: 0.6371 (t80) REVERT: c 50 ASP cc_start: 0.8733 (m-30) cc_final: 0.8515 (m-30) REVERT: d 141 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7556 (mtm) REVERT: d 157 LYS cc_start: 0.9064 (pttt) cc_final: 0.8738 (pttp) REVERT: d 188 LYS cc_start: 0.8163 (mtmm) cc_final: 0.7791 (mttp) REVERT: d 221 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8231 (mmt-90) REVERT: d 234 VAL cc_start: 0.9226 (t) cc_final: 0.8880 (m) REVERT: d 252 ASN cc_start: 0.8540 (t0) cc_final: 0.8067 (t0) REVERT: e 132 TYR cc_start: 0.9084 (m-80) cc_final: 0.8628 (m-80) REVERT: e 162 LYS cc_start: 0.8745 (tttm) cc_final: 0.8446 (ttmt) REVERT: e 252 ASN cc_start: 0.7357 (t0) cc_final: 0.6459 (m-40) REVERT: e 253 LYS cc_start: 0.6984 (mtpp) cc_final: 0.6482 (mtpt) REVERT: e 264 SER cc_start: 0.9373 (p) cc_final: 0.8877 (m) REVERT: f 145 HIS cc_start: 0.9269 (p-80) cc_final: 0.9060 (p-80) REVERT: f 162 LYS cc_start: 0.8325 (mmmt) cc_final: 0.7862 (tppp) REVERT: f 167 ASP cc_start: 0.8659 (t0) cc_final: 0.8375 (t0) outliers start: 360 outliers final: 272 residues processed: 1100 average time/residue: 0.5817 time to fit residues: 1121.5214 Evaluate side-chains 1071 residues out of total 7348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 291 poor density : 780 time to evaluate : 5.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 362 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain F residue 62 CYS Chi-restraints excluded: chain F residue 93 TYR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 142 GLN Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 395 SER Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 259 CYS Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 230 HIS Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 323 ASP Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 330 VAL Chi-restraints excluded: chain H residue 338 THR Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain I residue 16 ILE Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 153 CYS Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 298 THR Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 263 ILE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain J residue 388 LEU Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 73 HIS Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 250 ARG Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 362 TYR Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 379 ILE Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain N residue 8 MET Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 251 TRP Chi-restraints excluded: chain O residue 265 GLU Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 208 THR Chi-restraints excluded: chain Q residue 230 VAL Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 370 CYS Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 169 MET Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 254 VAL Chi-restraints excluded: chain R residue 265 CYS Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 305 TYR Chi-restraints excluded: chain R residue 379 ILE Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 62 CYS Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 84 VAL Chi-restraints excluded: chain U residue 142 GLN Chi-restraints excluded: chain U residue 280 MET Chi-restraints excluded: chain U residue 299 LEU Chi-restraints excluded: chain U residue 305 THR Chi-restraints excluded: chain U residue 343 THR Chi-restraints excluded: chain U residue 352 VAL Chi-restraints excluded: chain U residue 366 VAL Chi-restraints excluded: chain U residue 385 ASP Chi-restraints excluded: chain U residue 395 SER Chi-restraints excluded: chain U residue 410 VAL Chi-restraints excluded: chain U residue 432 THR Chi-restraints excluded: chain U residue 434 ILE Chi-restraints excluded: chain V residue 62 CYS Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 96 CYS Chi-restraints excluded: chain V residue 98 SER Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 145 ASP Chi-restraints excluded: chain V residue 160 GLN Chi-restraints excluded: chain V residue 174 ASP Chi-restraints excluded: chain V residue 234 THR Chi-restraints excluded: chain V residue 271 CYS Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain V residue 305 THR Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain V residue 329 SER Chi-restraints excluded: chain V residue 358 THR Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain W residue 2 GLU Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 68 CYS Chi-restraints excluded: chain W residue 110 ARG Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 236 THR Chi-restraints excluded: chain W residue 271 CYS Chi-restraints excluded: chain W residue 273 VAL Chi-restraints excluded: chain W residue 295 THR Chi-restraints excluded: chain W residue 305 THR Chi-restraints excluded: chain W residue 329 SER Chi-restraints excluded: chain W residue 334 SER Chi-restraints excluded: chain W residue 338 THR Chi-restraints excluded: chain W residue 366 VAL Chi-restraints excluded: chain W residue 377 SER Chi-restraints excluded: chain W residue 397 VAL Chi-restraints excluded: chain W residue 427 VAL Chi-restraints excluded: chain W residue 434 ILE Chi-restraints excluded: chain X residue 50 PHE Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 79 VAL Chi-restraints excluded: chain X residue 88 SER Chi-restraints excluded: chain X residue 101 ILE Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 122 VAL Chi-restraints excluded: chain X residue 143 ILE Chi-restraints excluded: chain X residue 175 THR Chi-restraints excluded: chain X residue 197 VAL Chi-restraints excluded: chain X residue 202 THR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 305 TYR Chi-restraints excluded: chain X residue 389 VAL Chi-restraints excluded: chain X residue 397 THR Chi-restraints excluded: chain Y residue 45 MET Chi-restraints excluded: chain Y residue 50 PHE Chi-restraints excluded: chain Y residue 53 GLN Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 142 THR Chi-restraints excluded: chain Y residue 165 GLU Chi-restraints excluded: chain Y residue 167 ILE Chi-restraints excluded: chain Y residue 242 VAL Chi-restraints excluded: chain Y residue 250 ARG Chi-restraints excluded: chain Y residue 256 ILE Chi-restraints excluded: chain Y residue 260 LEU Chi-restraints excluded: chain Y residue 263 ILE Chi-restraints excluded: chain Y residue 286 LEU Chi-restraints excluded: chain Y residue 299 LEU Chi-restraints excluded: chain Y residue 305 TYR Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 367 VAL Chi-restraints excluded: chain Y residue 388 LEU Chi-restraints excluded: chain Y residue 389 VAL Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Z residue 40 GLU Chi-restraints excluded: chain Z residue 50 PHE Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 53 GLN Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 111 LEU Chi-restraints excluded: chain Z residue 136 VAL Chi-restraints excluded: chain Z residue 142 THR Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain Z residue 260 LEU Chi-restraints excluded: chain Z residue 295 SER Chi-restraints excluded: chain Z residue 299 LEU Chi-restraints excluded: chain Z residue 322 VAL Chi-restraints excluded: chain Z residue 362 TYR Chi-restraints excluded: chain Z residue 374 SER Chi-restraints excluded: chain Z residue 415 CYS Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 141 MET Chi-restraints excluded: chain d residue 179 SER Chi-restraints excluded: chain d residue 200 VAL Chi-restraints excluded: chain d residue 221 ARG Chi-restraints excluded: chain e residue 113 MET Chi-restraints excluded: chain e residue 149 VAL Chi-restraints excluded: chain e residue 208 THR Chi-restraints excluded: chain f residue 173 ILE Chi-restraints excluded: chain f residue 187 GLU Chi-restraints excluded: chain f residue 255 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 381 optimal weight: 20.0000 chunk 610 optimal weight: 0.9990 chunk 753 optimal weight: 0.5980 chunk 437 optimal weight: 1.9990 chunk 847 optimal weight: 20.0000 chunk 633 optimal weight: 5.9990 chunk 742 optimal weight: 6.9990 chunk 526 optimal weight: 0.5980 chunk 35 optimal weight: 8.9990 chunk 698 optimal weight: 5.9990 chunk 84 optimal weight: 30.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 218 ASN J 53 GLN J 340 GLN K 212 ASN P 252 ASN ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 184 GLN R 340 GLN T 252 ASN U 32 GLN U 43 ASN ** U 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 62 HIS Y 340 GLN ** Z 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 192 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.165026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.119538 restraints weight = 87496.352| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.40 r_work: 0.2998 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 69494 Z= 0.198 Angle : 0.595 9.812 94641 Z= 0.301 Chirality : 0.045 0.417 10722 Planarity : 0.004 0.068 12159 Dihedral : 5.799 58.787 10854 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.72 % Favored : 94.09 % Rotamer: Outliers : 3.32 % Allowed : 18.32 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.09), residues: 8607 helix: 2.35 (0.16), residues: 1086 sheet: -0.83 (0.10), residues: 2592 loop : -1.58 (0.08), residues: 4929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Y 329 HIS 0.006 0.001 HIS e 125 PHE 0.033 0.001 PHE V 95 TYR 0.030 0.001 TYR E 93 ARG 0.008 0.000 ARG H 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 7348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 818 time to evaluate : 5.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.8624 (ttmt) cc_final: 0.8384 (mtpp) REVERT: A 151 ASP cc_start: 0.8605 (p0) cc_final: 0.8314 (p0) REVERT: B 119 ARG cc_start: 0.8674 (mpp80) cc_final: 0.8051 (mtt90) REVERT: B 132 ASP cc_start: 0.9177 (t0) cc_final: 0.8828 (t70) REVERT: B 158 GLN cc_start: 0.8129 (mp10) cc_final: 0.7699 (mp10) REVERT: B 215 MET cc_start: 0.7011 (mtt) cc_final: 0.6716 (mtt) REVERT: B 251 LYS cc_start: 0.8830 (mmmm) cc_final: 0.8606 (mmmt) REVERT: C 208 ILE cc_start: 0.4107 (OUTLIER) cc_final: 0.3799 (mm) REVERT: D 266 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8627 (mt-10) REVERT: F 95 PHE cc_start: 0.7646 (t80) cc_final: 0.7394 (t80) REVERT: G 59 TYR cc_start: 0.8971 (t80) cc_final: 0.8693 (t80) REVERT: H 7 MET cc_start: 0.9053 (ttp) cc_final: 0.8836 (ptm) REVERT: H 321 LYS cc_start: 0.8904 (mtmm) cc_final: 0.8540 (mttp) REVERT: I 50 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7781 (m-10) REVERT: I 153 CYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8269 (p) REVERT: I 168 ASP cc_start: 0.8460 (m-30) cc_final: 0.7996 (m-30) REVERT: I 215 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7269 (tmm) REVERT: I 301 GLU cc_start: 0.8893 (tp30) cc_final: 0.8146 (tt0) REVERT: J 50 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7823 (m-10) REVERT: J 196 LYS cc_start: 0.7496 (ptmt) cc_final: 0.7195 (ptpp) REVERT: J 212 ASN cc_start: 0.8100 (m-40) cc_final: 0.7577 (t0) REVERT: J 261 ASP cc_start: 0.8527 (t0) cc_final: 0.8122 (m-30) REVERT: J 267 VAL cc_start: 0.9606 (OUTLIER) cc_final: 0.9305 (m) REVERT: J 415 CYS cc_start: 0.8205 (t) cc_final: 0.7496 (p) REVERT: K 169 MET cc_start: 0.8435 (mmt) cc_final: 0.7898 (mmt) REVERT: K 196 LYS cc_start: 0.7968 (ptpp) cc_final: 0.7560 (ptmm) REVERT: K 250 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8037 (mtp180) REVERT: O 113 MET cc_start: 0.5726 (OUTLIER) cc_final: 0.5317 (mpt) REVERT: O 162 LYS cc_start: 0.8673 (tmtt) cc_final: 0.8381 (ttpt) REVERT: O 207 PHE cc_start: 0.8951 (m-10) cc_final: 0.8667 (m-10) REVERT: O 252 ASN cc_start: 0.8445 (t0) cc_final: 0.8040 (m-40) REVERT: O 253 LYS cc_start: 0.8375 (tptp) cc_final: 0.7914 (tptp) REVERT: P 147 LYS cc_start: 0.8295 (pptt) cc_final: 0.7872 (pptt) REVERT: P 162 LYS cc_start: 0.8554 (tttm) cc_final: 0.8082 (tmtt) REVERT: E 2 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8157 (tp30) REVERT: E 19 ILE cc_start: 0.9079 (mt) cc_final: 0.8855 (mt) REVERT: E 72 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8312 (mm-30) REVERT: E 95 PHE cc_start: 0.7602 (t80) cc_final: 0.7285 (t80) REVERT: E 117 ASP cc_start: 0.8875 (t70) cc_final: 0.8545 (m-30) REVERT: E 245 LYS cc_start: 0.9259 (ptpt) cc_final: 0.8937 (pttt) REVERT: E 364 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.7846 (p) REVERT: R 169 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8062 (mtp) REVERT: R 199 TYR cc_start: 0.7759 (p90) cc_final: 0.7191 (p90) REVERT: R 213 SER cc_start: 0.7885 (t) cc_final: 0.7545 (m) REVERT: R 215 MET cc_start: 0.7192 (mmm) cc_final: 0.6828 (mmm) REVERT: R 224 GLN cc_start: 0.6819 (mt0) cc_final: 0.6346 (mt0) REVERT: R 246 ASP cc_start: 0.7587 (m-30) cc_final: 0.6773 (p0) REVERT: U 67 GLU cc_start: 0.7449 (pm20) cc_final: 0.7211 (pm20) REVERT: U 182 ASP cc_start: 0.8672 (p0) cc_final: 0.8461 (p0) REVERT: U 246 GLU cc_start: 0.6396 (pt0) cc_final: 0.5944 (pt0) REVERT: V 99 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7212 (mp0) REVERT: V 160 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: V 281 ASN cc_start: 0.9061 (t0) cc_final: 0.8570 (t0) REVERT: V 299 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8758 (tt) REVERT: W 110 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8256 (ttm110) REVERT: W 182 ASP cc_start: 0.8664 (p0) cc_final: 0.8055 (t0) REVERT: Y 134 GLN cc_start: 0.8253 (mm-40) cc_final: 0.8026 (mm-40) REVERT: Y 165 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: Y 169 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7631 (mmt) REVERT: Z 7 ASN cc_start: 0.8934 (t0) cc_final: 0.8479 (t0) REVERT: Z 50 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8668 (m-10) REVERT: Z 53 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8350 (pm20) REVERT: Z 169 MET cc_start: 0.8535 (mmt) cc_final: 0.8103 (mmt) REVERT: Z 196 LYS cc_start: 0.7412 (ptpp) cc_final: 0.6937 (pttp) REVERT: Z 251 LYS cc_start: 0.8704 (ptmm) cc_final: 0.8130 (mtpp) REVERT: Z 253 LYS cc_start: 0.8992 (mttm) cc_final: 0.8745 (mttt) REVERT: Z 382 PHE cc_start: 0.6711 (m-10) cc_final: 0.6350 (t80) REVERT: c 50 ASP cc_start: 0.8697 (m-30) cc_final: 0.8496 (m-30) REVERT: d 141 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7541 (mtp) REVERT: d 157 LYS cc_start: 0.9082 (pttt) cc_final: 0.8812 (pttp) REVERT: d 188 LYS cc_start: 0.8128 (mtmm) cc_final: 0.7869 (mtmt) REVERT: d 221 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8227 (mmt-90) REVERT: d 234 VAL cc_start: 0.9226 (t) cc_final: 0.8897 (m) REVERT: d 252 ASN cc_start: 0.8524 (t0) cc_final: 0.8056 (t0) REVERT: e 132 TYR cc_start: 0.9041 (m-80) cc_final: 0.8554 (m-80) REVERT: e 162 LYS cc_start: 0.8625 (tttm) cc_final: 0.8325 (ttmt) REVERT: e 221 ARG cc_start: 0.9215 (ttt180) cc_final: 0.8982 (mtt180) REVERT: e 252 ASN cc_start: 0.7246 (t0) cc_final: 0.6423 (m110) REVERT: e 253 LYS cc_start: 0.6876 (mtpp) cc_final: 0.6372 (mtpt) REVERT: f 162 LYS cc_start: 0.8254 (mmmt) cc_final: 0.7790 (tppp) REVERT: f 167 ASP cc_start: 0.8609 (t0) cc_final: 0.8276 (t0) REVERT: f 253 LYS cc_start: 0.8265 (tptp) cc_final: 0.7879 (mtpt) outliers start: 244 outliers final: 197 residues processed: 1002 average time/residue: 0.6001 time to fit residues: 1047.5793 Evaluate side-chains 1013 residues out of total 7348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 796 time to evaluate : 5.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 362 TYR Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain F residue 62 CYS Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 142 GLN Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 395 SER Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 323 ASP Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 338 THR Chi-restraints excluded: chain H residue 371 SER Chi-restraints excluded: chain I residue 16 ILE Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 153 CYS Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 53 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 263 ILE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain J residue 388 LEU Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 250 ARG Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 362 TYR Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain N residue 8 MET Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 251 TRP Chi-restraints excluded: chain O residue 265 GLU Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 130 THR Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 230 VAL Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 370 CYS Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 169 MET Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 265 CYS Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 305 TYR Chi-restraints excluded: chain R residue 379 ILE Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain U residue 62 CYS Chi-restraints excluded: chain U residue 142 GLN Chi-restraints excluded: chain U residue 259 CYS Chi-restraints excluded: chain U residue 299 LEU Chi-restraints excluded: chain U residue 352 VAL Chi-restraints excluded: chain U residue 366 VAL Chi-restraints excluded: chain U residue 395 SER Chi-restraints excluded: chain V residue 62 CYS Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 96 CYS Chi-restraints excluded: chain V residue 98 SER Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 145 ASP Chi-restraints excluded: chain V residue 160 GLN Chi-restraints excluded: chain V residue 236 THR Chi-restraints excluded: chain V residue 271 CYS Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain V residue 305 THR Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain V residue 329 SER Chi-restraints excluded: chain W residue 2 GLU Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 68 CYS Chi-restraints excluded: chain W residue 110 ARG Chi-restraints excluded: chain W residue 273 VAL Chi-restraints excluded: chain W residue 295 THR Chi-restraints excluded: chain W residue 329 SER Chi-restraints excluded: chain W residue 334 SER Chi-restraints excluded: chain W residue 366 VAL Chi-restraints excluded: chain W residue 377 SER Chi-restraints excluded: chain W residue 434 ILE Chi-restraints excluded: chain X residue 50 PHE Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 101 ILE Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 122 VAL Chi-restraints excluded: chain X residue 143 ILE Chi-restraints excluded: chain X residue 175 THR Chi-restraints excluded: chain X residue 197 VAL Chi-restraints excluded: chain X residue 202 THR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 305 TYR Chi-restraints excluded: chain X residue 397 THR Chi-restraints excluded: chain Y residue 53 GLN Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 142 THR Chi-restraints excluded: chain Y residue 165 GLU Chi-restraints excluded: chain Y residue 167 ILE Chi-restraints excluded: chain Y residue 169 MET Chi-restraints excluded: chain Y residue 250 ARG Chi-restraints excluded: chain Y residue 256 ILE Chi-restraints excluded: chain Y residue 260 LEU Chi-restraints excluded: chain Y residue 263 ILE Chi-restraints excluded: chain Y residue 290 HIS Chi-restraints excluded: chain Y residue 299 LEU Chi-restraints excluded: chain Y residue 305 TYR Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 388 LEU Chi-restraints excluded: chain Z residue 50 PHE Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 53 GLN Chi-restraints excluded: chain Z residue 111 LEU Chi-restraints excluded: chain Z residue 136 VAL Chi-restraints excluded: chain Z residue 260 LEU Chi-restraints excluded: chain Z residue 295 SER Chi-restraints excluded: chain Z residue 299 LEU Chi-restraints excluded: chain Z residue 322 VAL Chi-restraints excluded: chain Z residue 326 GLU Chi-restraints excluded: chain Z residue 361 LEU Chi-restraints excluded: chain Z residue 362 TYR Chi-restraints excluded: chain Z residue 415 CYS Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 141 MET Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 200 VAL Chi-restraints excluded: chain d residue 221 ARG Chi-restraints excluded: chain e residue 113 MET Chi-restraints excluded: chain e residue 208 THR Chi-restraints excluded: chain f residue 111 MET Chi-restraints excluded: chain f residue 173 ILE Chi-restraints excluded: chain f residue 187 GLU Chi-restraints excluded: chain f residue 255 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 435 optimal weight: 0.3980 chunk 332 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 521 optimal weight: 20.0000 chunk 214 optimal weight: 9.9990 chunk 224 optimal weight: 4.9990 chunk 231 optimal weight: 7.9990 chunk 269 optimal weight: 0.9990 chunk 251 optimal weight: 0.0770 chunk 53 optimal weight: 4.9990 chunk 648 optimal weight: 9.9990 overall best weight: 2.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** H 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 218 ASN J 340 GLN ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 252 ASN ** U 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 62 HIS ** Z 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 192 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.163506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.107989 restraints weight = 88237.277| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.96 r_work: 0.2993 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.6128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 69494 Z= 0.209 Angle : 0.592 10.366 94641 Z= 0.299 Chirality : 0.045 0.323 10722 Planarity : 0.004 0.066 12159 Dihedral : 5.626 58.086 10854 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.29 % Favored : 93.52 % Rotamer: Outliers : 3.43 % Allowed : 18.37 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.09), residues: 8607 helix: 2.37 (0.16), residues: 1094 sheet: -0.76 (0.10), residues: 2592 loop : -1.51 (0.09), residues: 4921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Y 329 HIS 0.008 0.001 HIS f 145 PHE 0.035 0.001 PHE V 95 TYR 0.027 0.001 TYR E 93 ARG 0.009 0.000 ARG H 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 7348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 252 poor density : 806 time to evaluate : 5.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8808 (ttp-110) cc_final: 0.8439 (mtm110) REVERT: A 130 LYS cc_start: 0.8604 (ttmt) cc_final: 0.8379 (mtpp) REVERT: A 151 ASP cc_start: 0.8631 (p0) cc_final: 0.8361 (p0) REVERT: A 228 MET cc_start: 0.8878 (mtp) cc_final: 0.8525 (ttm) REVERT: B 119 ARG cc_start: 0.8664 (mpp80) cc_final: 0.8054 (mtt90) REVERT: B 132 ASP cc_start: 0.9177 (t0) cc_final: 0.8812 (t70) REVERT: B 158 GLN cc_start: 0.8133 (mp10) cc_final: 0.7700 (mp10) REVERT: B 215 MET cc_start: 0.7087 (mtt) cc_final: 0.6776 (mtt) REVERT: C 208 ILE cc_start: 0.4247 (OUTLIER) cc_final: 0.3907 (mm) REVERT: D 266 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8640 (mt-10) REVERT: F 93 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.6114 (p90) REVERT: F 95 PHE cc_start: 0.7638 (t80) cc_final: 0.7304 (t80) REVERT: G 59 TYR cc_start: 0.8949 (t80) cc_final: 0.8664 (t80) REVERT: H 321 LYS cc_start: 0.8902 (mtmm) cc_final: 0.8518 (mttp) REVERT: I 50 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.8033 (m-10) REVERT: I 153 CYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8279 (p) REVERT: I 168 ASP cc_start: 0.8445 (m-30) cc_final: 0.7973 (m-30) REVERT: I 215 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7282 (tmm) REVERT: I 301 GLU cc_start: 0.8897 (tp30) cc_final: 0.8150 (tt0) REVERT: J 50 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7661 (m-10) REVERT: J 196 LYS cc_start: 0.7470 (ptmt) cc_final: 0.7189 (ptpp) REVERT: J 212 ASN cc_start: 0.8062 (m-40) cc_final: 0.7511 (t0) REVERT: J 261 ASP cc_start: 0.8518 (t0) cc_final: 0.8087 (m-30) REVERT: J 267 VAL cc_start: 0.9594 (OUTLIER) cc_final: 0.9280 (m) REVERT: J 415 CYS cc_start: 0.8189 (t) cc_final: 0.7514 (p) REVERT: K 169 MET cc_start: 0.8415 (mmt) cc_final: 0.7903 (mmt) REVERT: K 196 LYS cc_start: 0.7927 (ptpp) cc_final: 0.7529 (ptmm) REVERT: K 250 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7649 (mtp-110) REVERT: O 113 MET cc_start: 0.5726 (OUTLIER) cc_final: 0.5334 (mpt) REVERT: O 162 LYS cc_start: 0.8680 (tmtt) cc_final: 0.8392 (ttpt) REVERT: O 207 PHE cc_start: 0.8917 (m-10) cc_final: 0.8665 (m-10) REVERT: O 221 ARG cc_start: 0.8734 (mmt90) cc_final: 0.8506 (mmt90) REVERT: O 252 ASN cc_start: 0.8447 (t0) cc_final: 0.8033 (m-40) REVERT: O 253 LYS cc_start: 0.8343 (tptp) cc_final: 0.7860 (tptp) REVERT: P 147 LYS cc_start: 0.8300 (pptt) cc_final: 0.7825 (pptt) REVERT: P 162 LYS cc_start: 0.8520 (tttm) cc_final: 0.8017 (tmtt) REVERT: Q 252 ASN cc_start: 0.8241 (m-40) cc_final: 0.7870 (t0) REVERT: E 2 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8108 (tp30) REVERT: E 19 ILE cc_start: 0.9094 (mt) cc_final: 0.8866 (mt) REVERT: E 72 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8307 (mm-30) REVERT: E 95 PHE cc_start: 0.7604 (t80) cc_final: 0.7281 (t80) REVERT: E 117 ASP cc_start: 0.8844 (t70) cc_final: 0.8529 (m-30) REVERT: E 245 LYS cc_start: 0.9237 (ptpt) cc_final: 0.8898 (pttt) REVERT: E 364 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.7830 (p) REVERT: R 169 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7967 (mtp) REVERT: R 199 TYR cc_start: 0.7716 (p90) cc_final: 0.7141 (p90) REVERT: R 213 SER cc_start: 0.7845 (t) cc_final: 0.7515 (m) REVERT: R 215 MET cc_start: 0.7167 (mmm) cc_final: 0.6825 (mmm) REVERT: R 224 GLN cc_start: 0.6785 (mt0) cc_final: 0.6302 (mt0) REVERT: R 246 ASP cc_start: 0.7520 (m-30) cc_final: 0.6737 (p0) REVERT: U 67 GLU cc_start: 0.7537 (pm20) cc_final: 0.7303 (pm20) REVERT: U 246 GLU cc_start: 0.6512 (pt0) cc_final: 0.6154 (pt0) REVERT: V 99 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7180 (mp0) REVERT: V 113 VAL cc_start: 0.8970 (OUTLIER) cc_final: 0.8760 (t) REVERT: V 160 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: V 281 ASN cc_start: 0.9055 (t0) cc_final: 0.8587 (t0) REVERT: V 299 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8732 (tt) REVERT: W 110 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8229 (ttm110) REVERT: W 182 ASP cc_start: 0.8618 (p0) cc_final: 0.8012 (t0) REVERT: Y 165 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: Y 169 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7690 (mmt) REVERT: Z 7 ASN cc_start: 0.8919 (t0) cc_final: 0.8474 (t0) REVERT: Z 50 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8674 (m-10) REVERT: Z 53 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: Z 196 LYS cc_start: 0.7470 (ptpp) cc_final: 0.7060 (pttp) REVERT: Z 251 LYS cc_start: 0.8670 (ptmm) cc_final: 0.7973 (mtpp) REVERT: Z 253 LYS cc_start: 0.8985 (mttm) cc_final: 0.8718 (mttt) REVERT: Z 382 PHE cc_start: 0.6696 (m-10) cc_final: 0.6314 (t80) REVERT: Z 415 CYS cc_start: 0.7314 (m) cc_final: 0.7044 (p) REVERT: c 50 ASP cc_start: 0.8708 (m-30) cc_final: 0.8499 (m-30) REVERT: d 141 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7605 (mtp) REVERT: d 157 LYS cc_start: 0.9097 (pttt) cc_final: 0.8834 (pttp) REVERT: d 188 LYS cc_start: 0.8145 (mtmm) cc_final: 0.7879 (mtmt) REVERT: d 221 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8359 (mmt-90) REVERT: d 234 VAL cc_start: 0.9232 (t) cc_final: 0.8913 (m) REVERT: d 252 ASN cc_start: 0.8502 (t0) cc_final: 0.8055 (t0) REVERT: e 132 TYR cc_start: 0.9033 (m-80) cc_final: 0.8567 (m-80) REVERT: e 162 LYS cc_start: 0.8590 (tttm) cc_final: 0.8307 (ttmt) REVERT: e 187 GLU cc_start: 0.8547 (mt-10) cc_final: 0.7820 (mp0) REVERT: e 221 ARG cc_start: 0.9191 (ttt180) cc_final: 0.8973 (mtt180) REVERT: e 252 ASN cc_start: 0.7259 (t0) cc_final: 0.6463 (m-40) REVERT: e 253 LYS cc_start: 0.6866 (mtpp) cc_final: 0.6380 (mtpt) REVERT: f 162 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7735 (tppp) REVERT: f 167 ASP cc_start: 0.8638 (t0) cc_final: 0.8248 (t0) REVERT: f 253 LYS cc_start: 0.8141 (tptp) cc_final: 0.7728 (mtmt) outliers start: 252 outliers final: 214 residues processed: 995 average time/residue: 0.5947 time to fit residues: 1030.8901 Evaluate side-chains 1012 residues out of total 7348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 776 time to evaluate : 5.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 362 TYR Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain F residue 62 CYS Chi-restraints excluded: chain F residue 93 TYR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 142 GLN Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 395 SER Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 94 CYS Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 323 ASP Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 338 THR Chi-restraints excluded: chain H residue 371 SER Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 153 CYS Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 265 CYS Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 263 ILE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 362 TYR Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain J residue 388 LEU Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 250 ARG Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 362 TYR Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain N residue 8 MET Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 251 TRP Chi-restraints excluded: chain O residue 265 GLU Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 130 THR Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 208 THR Chi-restraints excluded: chain Q residue 230 VAL Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 370 CYS Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 169 MET Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 265 CYS Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 305 TYR Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain U residue 62 CYS Chi-restraints excluded: chain U residue 142 GLN Chi-restraints excluded: chain U residue 299 LEU Chi-restraints excluded: chain U residue 317 THR Chi-restraints excluded: chain U residue 352 VAL Chi-restraints excluded: chain U residue 366 VAL Chi-restraints excluded: chain U residue 395 SER Chi-restraints excluded: chain V residue 62 CYS Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 96 CYS Chi-restraints excluded: chain V residue 98 SER Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 145 ASP Chi-restraints excluded: chain V residue 160 GLN Chi-restraints excluded: chain V residue 236 THR Chi-restraints excluded: chain V residue 271 CYS Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain V residue 305 THR Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain W residue 2 GLU Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 68 CYS Chi-restraints excluded: chain W residue 110 ARG Chi-restraints excluded: chain W residue 273 VAL Chi-restraints excluded: chain W residue 295 THR Chi-restraints excluded: chain W residue 329 SER Chi-restraints excluded: chain W residue 338 THR Chi-restraints excluded: chain W residue 366 VAL Chi-restraints excluded: chain W residue 377 SER Chi-restraints excluded: chain W residue 434 ILE Chi-restraints excluded: chain X residue 50 PHE Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 101 ILE Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 122 VAL Chi-restraints excluded: chain X residue 143 ILE Chi-restraints excluded: chain X residue 175 THR Chi-restraints excluded: chain X residue 202 THR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 305 TYR Chi-restraints excluded: chain X residue 397 THR Chi-restraints excluded: chain Y residue 45 MET Chi-restraints excluded: chain Y residue 50 PHE Chi-restraints excluded: chain Y residue 53 GLN Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 142 THR Chi-restraints excluded: chain Y residue 165 GLU Chi-restraints excluded: chain Y residue 167 ILE Chi-restraints excluded: chain Y residue 169 MET Chi-restraints excluded: chain Y residue 242 VAL Chi-restraints excluded: chain Y residue 250 ARG Chi-restraints excluded: chain Y residue 256 ILE Chi-restraints excluded: chain Y residue 260 LEU Chi-restraints excluded: chain Y residue 263 ILE Chi-restraints excluded: chain Y residue 290 HIS Chi-restraints excluded: chain Y residue 299 LEU Chi-restraints excluded: chain Y residue 305 TYR Chi-restraints excluded: chain Y residue 326 GLU Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 388 LEU Chi-restraints excluded: chain Y residue 389 VAL Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Z residue 50 PHE Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 53 GLN Chi-restraints excluded: chain Z residue 111 LEU Chi-restraints excluded: chain Z residue 136 VAL Chi-restraints excluded: chain Z residue 142 THR Chi-restraints excluded: chain Z residue 250 ARG Chi-restraints excluded: chain Z residue 256 ILE Chi-restraints excluded: chain Z residue 260 LEU Chi-restraints excluded: chain Z residue 295 SER Chi-restraints excluded: chain Z residue 299 LEU Chi-restraints excluded: chain Z residue 322 VAL Chi-restraints excluded: chain Z residue 326 GLU Chi-restraints excluded: chain Z residue 361 LEU Chi-restraints excluded: chain Z residue 362 TYR Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 141 MET Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 200 VAL Chi-restraints excluded: chain d residue 221 ARG Chi-restraints excluded: chain e residue 113 MET Chi-restraints excluded: chain e residue 208 THR Chi-restraints excluded: chain f residue 111 MET Chi-restraints excluded: chain f residue 172 GLN Chi-restraints excluded: chain f residue 173 ILE Chi-restraints excluded: chain f residue 187 GLU Chi-restraints excluded: chain f residue 255 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 227 optimal weight: 7.9990 chunk 462 optimal weight: 4.9990 chunk 840 optimal weight: 7.9990 chunk 72 optimal weight: 0.0770 chunk 61 optimal weight: 10.0000 chunk 435 optimal weight: 3.9990 chunk 327 optimal weight: 4.9990 chunk 388 optimal weight: 20.0000 chunk 678 optimal weight: 0.0980 chunk 168 optimal weight: 30.0000 chunk 672 optimal weight: 2.9990 overall best weight: 2.4344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 218 ASN J 340 GLN ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 252 ASN ** U 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 62 HIS Y 170 HIS ** Z 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.163716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.107964 restraints weight = 87978.489| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.88 r_work: 0.3000 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.6219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 69494 Z= 0.213 Angle : 0.589 9.937 94641 Z= 0.297 Chirality : 0.045 0.340 10722 Planarity : 0.005 0.072 12159 Dihedral : 5.531 58.166 10854 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.04 % Favored : 93.78 % Rotamer: Outliers : 3.39 % Allowed : 18.56 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.17 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.09), residues: 8607 helix: 2.42 (0.16), residues: 1094 sheet: -0.74 (0.10), residues: 2608 loop : -1.48 (0.09), residues: 4905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 338 HIS 0.009 0.001 HIS f 145 PHE 0.036 0.001 PHE V 95 TYR 0.028 0.001 TYR E 93 ARG 0.009 0.000 ARG H 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17214 Ramachandran restraints generated. 8607 Oldfield, 0 Emsley, 8607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 7348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 797 time to evaluate : 5.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8769 (ttp-110) cc_final: 0.8444 (mtm110) REVERT: A 130 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8379 (mtpp) REVERT: A 151 ASP cc_start: 0.8569 (p0) cc_final: 0.8290 (p0) REVERT: A 228 MET cc_start: 0.8860 (mtp) cc_final: 0.8475 (ttm) REVERT: B 119 ARG cc_start: 0.8648 (mpp80) cc_final: 0.8063 (mtt90) REVERT: B 132 ASP cc_start: 0.9144 (t0) cc_final: 0.8786 (t70) REVERT: B 158 GLN cc_start: 0.8260 (mp10) cc_final: 0.7810 (mp10) REVERT: B 171 MET cc_start: 0.8782 (mmt) cc_final: 0.8427 (mmt) REVERT: B 215 MET cc_start: 0.7043 (mtt) cc_final: 0.6744 (mtt) REVERT: B 251 LYS cc_start: 0.8775 (mmmm) cc_final: 0.8516 (mmmt) REVERT: C 208 ILE cc_start: 0.4298 (OUTLIER) cc_final: 0.3963 (mm) REVERT: D 183 LYS cc_start: 0.7780 (pttp) cc_final: 0.7116 (ptpp) REVERT: D 266 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8649 (mt-10) REVERT: F 93 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.6271 (p90) REVERT: F 95 PHE cc_start: 0.7623 (t80) cc_final: 0.7305 (t80) REVERT: G 59 TYR cc_start: 0.8943 (t80) cc_final: 0.8662 (t80) REVERT: H 321 LYS cc_start: 0.8907 (mtmm) cc_final: 0.8518 (mttp) REVERT: I 50 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.7986 (m-80) REVERT: I 153 CYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8296 (p) REVERT: I 169 MET cc_start: 0.8392 (mmt) cc_final: 0.8165 (mtp) REVERT: I 215 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7410 (tmm) REVERT: I 301 GLU cc_start: 0.8906 (tp30) cc_final: 0.8143 (tt0) REVERT: J 50 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7609 (m-10) REVERT: J 196 LYS cc_start: 0.7411 (ptmt) cc_final: 0.7139 (ptpp) REVERT: J 212 ASN cc_start: 0.8093 (m-40) cc_final: 0.7503 (t0) REVERT: J 261 ASP cc_start: 0.8505 (t0) cc_final: 0.8081 (m-30) REVERT: J 267 VAL cc_start: 0.9589 (OUTLIER) cc_final: 0.9274 (m) REVERT: J 415 CYS cc_start: 0.8238 (t) cc_final: 0.7585 (p) REVERT: K 139 GLU cc_start: 0.8836 (tt0) cc_final: 0.8573 (tt0) REVERT: K 169 MET cc_start: 0.8409 (mmt) cc_final: 0.7878 (mmt) REVERT: K 196 LYS cc_start: 0.7921 (ptpp) cc_final: 0.7513 (ptmm) REVERT: K 250 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7652 (mtp-110) REVERT: O 113 MET cc_start: 0.5793 (OUTLIER) cc_final: 0.5390 (mpt) REVERT: O 162 LYS cc_start: 0.8651 (tmtt) cc_final: 0.8361 (ttpt) REVERT: O 207 PHE cc_start: 0.8905 (m-10) cc_final: 0.8646 (m-10) REVERT: O 221 ARG cc_start: 0.8724 (mmt90) cc_final: 0.8507 (mmt90) REVERT: O 252 ASN cc_start: 0.8468 (t0) cc_final: 0.8058 (m-40) REVERT: O 253 LYS cc_start: 0.8340 (tptp) cc_final: 0.7865 (tptp) REVERT: P 147 LYS cc_start: 0.8216 (pptt) cc_final: 0.7798 (pptt) REVERT: P 162 LYS cc_start: 0.8510 (tttm) cc_final: 0.8005 (tmtt) REVERT: Q 124 LYS cc_start: 0.8484 (tppt) cc_final: 0.8109 (tppt) REVERT: Q 252 ASN cc_start: 0.8249 (m-40) cc_final: 0.7935 (t0) REVERT: E 2 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8127 (tp30) REVERT: E 19 ILE cc_start: 0.9115 (mt) cc_final: 0.8870 (mt) REVERT: E 72 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8304 (mm-30) REVERT: E 95 PHE cc_start: 0.7620 (t80) cc_final: 0.7365 (t80) REVERT: E 117 ASP cc_start: 0.8837 (t70) cc_final: 0.8523 (m-30) REVERT: E 245 LYS cc_start: 0.9260 (ptpt) cc_final: 0.8935 (pttt) REVERT: E 364 SER cc_start: 0.8530 (OUTLIER) cc_final: 0.7833 (p) REVERT: R 169 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7758 (mtp) REVERT: R 199 TYR cc_start: 0.7727 (p90) cc_final: 0.7135 (p90) REVERT: R 213 SER cc_start: 0.7776 (t) cc_final: 0.7478 (m) REVERT: R 215 MET cc_start: 0.7169 (mmm) cc_final: 0.6830 (mmm) REVERT: R 224 GLN cc_start: 0.6732 (mt0) cc_final: 0.6276 (mt0) REVERT: R 246 ASP cc_start: 0.7526 (m-30) cc_final: 0.6753 (p0) REVERT: U 67 GLU cc_start: 0.7639 (pm20) cc_final: 0.7426 (pm20) REVERT: U 246 GLU cc_start: 0.6541 (pt0) cc_final: 0.6185 (pt0) REVERT: V 99 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7191 (mp0) REVERT: V 113 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8746 (t) REVERT: V 160 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: V 281 ASN cc_start: 0.9048 (t0) cc_final: 0.8572 (t0) REVERT: V 299 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8716 (tt) REVERT: W 110 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8200 (ttm110) REVERT: W 182 ASP cc_start: 0.8627 (p0) cc_final: 0.8033 (t0) REVERT: Y 165 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: Y 169 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7670 (mmt) REVERT: Z 7 ASN cc_start: 0.8907 (t0) cc_final: 0.8451 (t0) REVERT: Z 50 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8637 (m-10) REVERT: Z 53 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8403 (pm20) REVERT: Z 196 LYS cc_start: 0.7452 (ptpp) cc_final: 0.7013 (pttp) REVERT: Z 251 LYS cc_start: 0.8584 (ptmm) cc_final: 0.8032 (mtpp) REVERT: Z 253 LYS cc_start: 0.9005 (mttm) cc_final: 0.8751 (mttt) REVERT: Z 382 PHE cc_start: 0.6745 (m-10) cc_final: 0.6346 (t80) REVERT: Z 415 CYS cc_start: 0.7320 (m) cc_final: 0.7057 (p) REVERT: c 50 ASP cc_start: 0.8711 (m-30) cc_final: 0.8495 (m-30) REVERT: d 141 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7622 (mtp) REVERT: d 157 LYS cc_start: 0.9102 (pttt) cc_final: 0.8840 (pttp) REVERT: d 188 LYS cc_start: 0.8134 (mtmm) cc_final: 0.7868 (mtmt) REVERT: d 221 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8382 (mmt-90) REVERT: d 234 VAL cc_start: 0.9211 (t) cc_final: 0.8892 (m) REVERT: d 252 ASN cc_start: 0.8526 (t0) cc_final: 0.8087 (t0) REVERT: e 132 TYR cc_start: 0.9065 (m-80) cc_final: 0.8616 (m-80) REVERT: e 162 LYS cc_start: 0.8565 (tttm) cc_final: 0.8304 (ttmt) REVERT: e 187 GLU cc_start: 0.8572 (mt-10) cc_final: 0.7835 (mp0) REVERT: e 221 ARG cc_start: 0.9200 (ttt180) cc_final: 0.8994 (mtt180) REVERT: e 252 ASN cc_start: 0.7282 (t0) cc_final: 0.6490 (m-40) REVERT: e 253 LYS cc_start: 0.6834 (mtpp) cc_final: 0.6342 (mtpt) REVERT: f 143 PRO cc_start: 0.8812 (Cg_exo) cc_final: 0.8480 (Cg_endo) REVERT: f 162 LYS cc_start: 0.8168 (mmmt) cc_final: 0.7761 (tppp) REVERT: f 167 ASP cc_start: 0.8589 (t0) cc_final: 0.8230 (t0) REVERT: f 253 LYS cc_start: 0.8123 (tptp) cc_final: 0.7737 (mtmt) outliers start: 249 outliers final: 210 residues processed: 984 average time/residue: 0.6012 time to fit residues: 1028.5441 Evaluate side-chains 1003 residues out of total 7348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 771 time to evaluate : 5.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 362 TYR Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain F residue 62 CYS Chi-restraints excluded: chain F residue 93 TYR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 142 GLN Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 395 SER Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 259 CYS Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 94 CYS Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 323 ASP Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 330 VAL Chi-restraints excluded: chain H residue 338 THR Chi-restraints excluded: chain H residue 371 SER Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 153 CYS Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 263 ILE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 362 TYR Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain J residue 388 LEU Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 250 ARG Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 362 TYR Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain N residue 8 MET Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 251 TRP Chi-restraints excluded: chain O residue 265 GLU Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 130 THR Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 208 THR Chi-restraints excluded: chain Q residue 230 VAL Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 370 CYS Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 169 MET Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 265 CYS Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 305 TYR Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain U residue 62 CYS Chi-restraints excluded: chain U residue 299 LEU Chi-restraints excluded: chain U residue 343 THR Chi-restraints excluded: chain U residue 352 VAL Chi-restraints excluded: chain U residue 366 VAL Chi-restraints excluded: chain U residue 395 SER Chi-restraints excluded: chain V residue 62 CYS Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 96 CYS Chi-restraints excluded: chain V residue 98 SER Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 145 ASP Chi-restraints excluded: chain V residue 160 GLN Chi-restraints excluded: chain V residue 236 THR Chi-restraints excluded: chain V residue 271 CYS Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain V residue 305 THR Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 68 CYS Chi-restraints excluded: chain W residue 110 ARG Chi-restraints excluded: chain W residue 236 THR Chi-restraints excluded: chain W residue 273 VAL Chi-restraints excluded: chain W residue 295 THR Chi-restraints excluded: chain W residue 329 SER Chi-restraints excluded: chain W residue 334 SER Chi-restraints excluded: chain W residue 338 THR Chi-restraints excluded: chain W residue 366 VAL Chi-restraints excluded: chain W residue 377 SER Chi-restraints excluded: chain W residue 434 ILE Chi-restraints excluded: chain X residue 50 PHE Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 88 SER Chi-restraints excluded: chain X residue 101 ILE Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 143 ILE Chi-restraints excluded: chain X residue 175 THR Chi-restraints excluded: chain X residue 197 VAL Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 305 TYR Chi-restraints excluded: chain X residue 397 THR Chi-restraints excluded: chain Y residue 45 MET Chi-restraints excluded: chain Y residue 50 PHE Chi-restraints excluded: chain Y residue 53 GLN Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 142 THR Chi-restraints excluded: chain Y residue 165 GLU Chi-restraints excluded: chain Y residue 167 ILE Chi-restraints excluded: chain Y residue 169 MET Chi-restraints excluded: chain Y residue 242 VAL Chi-restraints excluded: chain Y residue 250 ARG Chi-restraints excluded: chain Y residue 256 ILE Chi-restraints excluded: chain Y residue 260 LEU Chi-restraints excluded: chain Y residue 263 ILE Chi-restraints excluded: chain Y residue 290 HIS Chi-restraints excluded: chain Y residue 299 LEU Chi-restraints excluded: chain Y residue 305 TYR Chi-restraints excluded: chain Y residue 326 GLU Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 388 LEU Chi-restraints excluded: chain Y residue 389 VAL Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Z residue 40 GLU Chi-restraints excluded: chain Z residue 50 PHE Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 53 GLN Chi-restraints excluded: chain Z residue 111 LEU Chi-restraints excluded: chain Z residue 136 VAL Chi-restraints excluded: chain Z residue 142 THR Chi-restraints excluded: chain Z residue 256 ILE Chi-restraints excluded: chain Z residue 260 LEU Chi-restraints excluded: chain Z residue 295 SER Chi-restraints excluded: chain Z residue 299 LEU Chi-restraints excluded: chain Z residue 322 VAL Chi-restraints excluded: chain Z residue 326 GLU Chi-restraints excluded: chain Z residue 361 LEU Chi-restraints excluded: chain Z residue 362 TYR Chi-restraints excluded: chain a residue 8 MET Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 141 MET Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 200 VAL Chi-restraints excluded: chain d residue 221 ARG Chi-restraints excluded: chain e residue 113 MET Chi-restraints excluded: chain e residue 208 THR Chi-restraints excluded: chain f residue 172 GLN Chi-restraints excluded: chain f residue 173 ILE Chi-restraints excluded: chain f residue 187 GLU Chi-restraints excluded: chain f residue 255 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 26 optimal weight: 5.9990 chunk 523 optimal weight: 30.0000 chunk 134 optimal weight: 3.9990 chunk 319 optimal weight: 20.0000 chunk 500 optimal weight: 0.8980 chunk 724 optimal weight: 20.0000 chunk 606 optimal weight: 9.9990 chunk 710 optimal weight: 4.9990 chunk 776 optimal weight: 2.9990 chunk 745 optimal weight: 5.9990 chunk 402 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** H 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 GLN ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 GLN T 252 ASN U 142 GLN ** U 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 62 HIS ** Z 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 170 HIS ** Z 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 145 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.162409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117409 restraints weight = 88012.428| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.49 r_work: 0.2963 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.6334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 69494 Z= 0.283 Angle : 0.617 10.488 94641 Z= 0.312 Chirality : 0.046 0.353 10722 Planarity : 0.005 0.065 12159 Dihedral : 5.601 58.216 10854 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.88 % Favored : 92.94 % Rotamer: Outliers : 3.52 % Allowed : 18.49 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.09), residues: 8607 helix: 2.38 (0.16), residues: 1094 sheet: -0.77 (0.10), residues: 2592 loop : -1.51 (0.09), residues: 4921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 329 HIS 0.010 0.001 HIS f 145 PHE 0.034 0.001 PHE V 95 TYR 0.030 0.001 TYR E 93 ARG 0.010 0.000 ARG U 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41787.64 seconds wall clock time: 715 minutes 21.90 seconds (42921.90 seconds total)