Starting phenix.real_space_refine on Wed Jun 25 11:15:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5xb1_6714/06_2025/5xb1_6714.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xb1_6714/06_2025/5xb1_6714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5xb1_6714/06_2025/5xb1_6714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xb1_6714/06_2025/5xb1_6714.map" model { file = "/net/cci-nas-00/data/ceres_data/5xb1_6714/06_2025/5xb1_6714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xb1_6714/06_2025/5xb1_6714.cif" } resolution = 3.0 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= 0.017 sd= 0.165 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 168 5.16 5 C 19248 2.51 5 N 5472 2.21 5 O 5959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30847 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "B" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "C" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "D" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "E" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "F" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "G" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "H" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "I" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "J" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "K" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "L" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "M" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "N" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "O" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "P" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "Q" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "R" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "S" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "T" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "U" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "V" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "W" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "X" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 17.76, per 1000 atoms: 0.58 Number of scatterers: 30847 At special positions: 0 Unit cell: (132.744, 132.744, 132.744, 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 168 16.00 O 5959 8.00 N 5472 7.00 C 19248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 9.51 Conformation dependent library (CDL) restraints added in 4.4 seconds 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7200 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 0 sheets defined 76.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 37 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 77 removed outlier: 3.737A pdb=" N HIS A 58 " --> pdb=" O LYS A 54 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 65 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 125 removed outlier: 3.508A pdb=" N ALA A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 158 removed outlier: 4.249A pdb=" N LEU A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 37 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 77 removed outlier: 3.705A pdb=" N HIS B 58 " --> pdb=" O LYS B 54 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU B 65 " --> pdb=" O HIS B 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 125 removed outlier: 3.515A pdb=" N ALA B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 158 removed outlier: 4.249A pdb=" N LEU B 139 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU B 141 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 31 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 37 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 77 removed outlier: 3.730A pdb=" N HIS C 58 " --> pdb=" O LYS C 54 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU C 65 " --> pdb=" O HIS C 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 125 removed outlier: 3.515A pdb=" N ALA C 100 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 159 removed outlier: 4.250A pdb=" N LEU C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN C 140 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU C 141 " --> pdb=" O HIS C 137 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C 151 " --> pdb=" O LYS C 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET C 159 " --> pdb=" O ASN C 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 31 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER D 37 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 77 removed outlier: 3.731A pdb=" N HIS D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 65 " --> pdb=" O HIS D 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 67 " --> pdb=" O GLU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 125 removed outlier: 3.511A pdb=" N ALA D 100 " --> pdb=" O SER D 96 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 158 removed outlier: 4.249A pdb=" N LEU D 139 " --> pdb=" O GLU D 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN D 140 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU D 141 " --> pdb=" O HIS D 137 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP D 151 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA E 31 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 36 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER E 37 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 77 removed outlier: 3.739A pdb=" N HIS E 58 " --> pdb=" O LYS E 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU E 65 " --> pdb=" O HIS E 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 125 removed outlier: 3.506A pdb=" N ALA E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 159 removed outlier: 4.249A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN E 140 " --> pdb=" O THR E 136 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU E 141 " --> pdb=" O HIS E 137 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP E 151 " --> pdb=" O LYS E 147 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR E 154 " --> pdb=" O GLY E 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN E 155 " --> pdb=" O ASP E 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 31 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR F 33 " --> pdb=" O LEU F 29 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 36 " --> pdb=" O SER F 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER F 37 " --> pdb=" O TYR F 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.694A pdb=" N HIS F 58 " --> pdb=" O LYS F 54 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG F 64 " --> pdb=" O SER F 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU F 65 " --> pdb=" O HIS F 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 125 removed outlier: 3.518A pdb=" N ALA F 100 " --> pdb=" O SER F 96 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 159 removed outlier: 4.249A pdb=" N LEU F 139 " --> pdb=" O GLU F 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN F 140 " --> pdb=" O THR F 136 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU F 141 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP F 151 " --> pdb=" O LYS F 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR F 154 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN F 155 " --> pdb=" O ASP F 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET F 159 " --> pdb=" O ASN F 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN G 22 " --> pdb=" O GLU G 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA G 31 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER G 37 " --> pdb=" O TYR G 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 77 removed outlier: 3.730A pdb=" N HIS G 58 " --> pdb=" O LYS G 54 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG G 64 " --> pdb=" O SER G 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU G 65 " --> pdb=" O HIS G 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA G 67 " --> pdb=" O GLU G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 125 removed outlier: 3.519A pdb=" N ALA G 100 " --> pdb=" O SER G 96 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU G 117 " --> pdb=" O GLN G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 158 removed outlier: 4.250A pdb=" N LEU G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ASN G 140 " --> pdb=" O THR G 136 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU G 141 " --> pdb=" O HIS G 137 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL G 143 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP G 151 " --> pdb=" O LYS G 147 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR G 154 " --> pdb=" O GLY G 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN G 155 " --> pdb=" O ASP G 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN H 22 " --> pdb=" O GLU H 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA H 31 " --> pdb=" O LEU H 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR H 33 " --> pdb=" O LEU H 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU H 36 " --> pdb=" O SER H 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER H 37 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR H 40 " --> pdb=" O LEU H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 77 removed outlier: 3.751A pdb=" N HIS H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG H 64 " --> pdb=" O SER H 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU H 65 " --> pdb=" O HIS H 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA H 67 " --> pdb=" O GLU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 125 removed outlier: 3.505A pdb=" N ALA H 100 " --> pdb=" O SER H 96 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU H 117 " --> pdb=" O GLN H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 159 removed outlier: 4.250A pdb=" N LEU H 139 " --> pdb=" O GLU H 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN H 140 " --> pdb=" O THR H 136 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU H 141 " --> pdb=" O HIS H 137 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL H 143 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP H 151 " --> pdb=" O LYS H 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR H 154 " --> pdb=" O GLY H 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN H 155 " --> pdb=" O ASP H 151 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET H 159 " --> pdb=" O ASN H 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN I 22 " --> pdb=" O GLU I 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA I 31 " --> pdb=" O LEU I 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR I 33 " --> pdb=" O LEU I 29 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU I 36 " --> pdb=" O SER I 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER I 37 " --> pdb=" O TYR I 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR I 40 " --> pdb=" O LEU I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 77 removed outlier: 3.675A pdb=" N HIS I 58 " --> pdb=" O LYS I 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG I 64 " --> pdb=" O SER I 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU I 65 " --> pdb=" O HIS I 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA I 67 " --> pdb=" O GLU I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 125 removed outlier: 3.519A pdb=" N ALA I 100 " --> pdb=" O SER I 96 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU I 117 " --> pdb=" O GLN I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 159 removed outlier: 4.250A pdb=" N LEU I 139 " --> pdb=" O GLU I 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN I 140 " --> pdb=" O THR I 136 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU I 141 " --> pdb=" O HIS I 137 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL I 143 " --> pdb=" O LEU I 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP I 151 " --> pdb=" O LYS I 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR I 154 " --> pdb=" O GLY I 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN I 155 " --> pdb=" O ASP I 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET I 159 " --> pdb=" O ASN I 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN J 22 " --> pdb=" O GLU J 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA J 31 " --> pdb=" O LEU J 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR J 33 " --> pdb=" O LEU J 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU J 36 " --> pdb=" O SER J 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER J 37 " --> pdb=" O TYR J 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 77 removed outlier: 3.736A pdb=" N HIS J 58 " --> pdb=" O LYS J 54 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU J 65 " --> pdb=" O HIS J 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA J 67 " --> pdb=" O GLU J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 125 removed outlier: 3.516A pdb=" N ALA J 100 " --> pdb=" O SER J 96 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU J 117 " --> pdb=" O GLN J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 159 removed outlier: 4.249A pdb=" N LEU J 139 " --> pdb=" O GLU J 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN J 140 " --> pdb=" O THR J 136 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU J 141 " --> pdb=" O HIS J 137 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP J 151 " --> pdb=" O LYS J 147 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR J 154 " --> pdb=" O GLY J 150 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN J 155 " --> pdb=" O ASP J 151 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET J 159 " --> pdb=" O ASN J 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN K 22 " --> pdb=" O GLU K 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA K 31 " --> pdb=" O LEU K 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU K 36 " --> pdb=" O SER K 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER K 37 " --> pdb=" O TYR K 33 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR K 40 " --> pdb=" O LEU K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 77 removed outlier: 3.716A pdb=" N HIS K 58 " --> pdb=" O LYS K 54 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU K 65 " --> pdb=" O HIS K 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA K 67 " --> pdb=" O GLU K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 125 removed outlier: 3.519A pdb=" N ALA K 100 " --> pdb=" O SER K 96 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU K 117 " --> pdb=" O GLN K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 158 removed outlier: 4.249A pdb=" N LEU K 139 " --> pdb=" O GLU K 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN K 140 " --> pdb=" O THR K 136 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU K 141 " --> pdb=" O HIS K 137 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL K 143 " --> pdb=" O LEU K 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP K 151 " --> pdb=" O LYS K 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR K 154 " --> pdb=" O GLY K 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN K 155 " --> pdb=" O ASP K 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN L 22 " --> pdb=" O GLU L 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA L 31 " --> pdb=" O LEU L 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU L 36 " --> pdb=" O SER L 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER L 37 " --> pdb=" O TYR L 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 77 removed outlier: 3.686A pdb=" N HIS L 58 " --> pdb=" O LYS L 54 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG L 64 " --> pdb=" O SER L 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU L 65 " --> pdb=" O HIS L 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA L 67 " --> pdb=" O GLU L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 125 removed outlier: 3.513A pdb=" N ALA L 100 " --> pdb=" O SER L 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU L 117 " --> pdb=" O GLN L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 159 removed outlier: 4.250A pdb=" N LEU L 139 " --> pdb=" O GLU L 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN L 140 " --> pdb=" O THR L 136 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU L 141 " --> pdb=" O HIS L 137 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL L 143 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP L 151 " --> pdb=" O LYS L 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR L 154 " --> pdb=" O GLY L 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN L 155 " --> pdb=" O ASP L 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET L 159 " --> pdb=" O ASN L 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 40 removed outlier: 3.502A pdb=" N ASN M 22 " --> pdb=" O GLU M 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA M 31 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR M 33 " --> pdb=" O LEU M 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU M 36 " --> pdb=" O SER M 32 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER M 37 " --> pdb=" O TYR M 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 77 removed outlier: 3.715A pdb=" N HIS M 58 " --> pdb=" O LYS M 54 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG M 64 " --> pdb=" O SER M 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU M 65 " --> pdb=" O HIS M 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA M 67 " --> pdb=" O GLU M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 125 removed outlier: 3.522A pdb=" N ALA M 100 " --> pdb=" O SER M 96 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU M 117 " --> pdb=" O GLN M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 158 removed outlier: 4.249A pdb=" N LEU M 139 " --> pdb=" O GLU M 135 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ASN M 140 " --> pdb=" O THR M 136 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU M 141 " --> pdb=" O HIS M 137 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL M 143 " --> pdb=" O LEU M 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP M 151 " --> pdb=" O LYS M 147 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR M 154 " --> pdb=" O GLY M 150 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN M 155 " --> pdb=" O ASP M 151 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN N 22 " --> pdb=" O GLU N 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA N 31 " --> pdb=" O LEU N 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR N 33 " --> pdb=" O LEU N 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU N 36 " --> pdb=" O SER N 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER N 37 " --> pdb=" O TYR N 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR N 40 " --> pdb=" O LEU N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 77 removed outlier: 3.726A pdb=" N HIS N 58 " --> pdb=" O LYS N 54 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG N 64 " --> pdb=" O SER N 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU N 65 " --> pdb=" O HIS N 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA N 67 " --> pdb=" O GLU N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 125 removed outlier: 3.513A pdb=" N ALA N 100 " --> pdb=" O SER N 96 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU N 117 " --> pdb=" O GLN N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 127 through 159 removed outlier: 4.249A pdb=" N LEU N 139 " --> pdb=" O GLU N 135 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ASN N 140 " --> pdb=" O THR N 136 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU N 141 " --> pdb=" O HIS N 137 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL N 143 " --> pdb=" O LEU N 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP N 151 " --> pdb=" O LYS N 147 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR N 154 " --> pdb=" O GLY N 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN N 155 " --> pdb=" O ASP N 151 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET N 159 " --> pdb=" O ASN N 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN O 22 " --> pdb=" O GLU O 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA O 31 " --> pdb=" O LEU O 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR O 33 " --> pdb=" O LEU O 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU O 36 " --> pdb=" O SER O 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER O 37 " --> pdb=" O TYR O 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR O 40 " --> pdb=" O LEU O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 77 removed outlier: 3.615A pdb=" N HIS O 58 " --> pdb=" O LYS O 54 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG O 64 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU O 65 " --> pdb=" O HIS O 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA O 67 " --> pdb=" O GLU O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 125 removed outlier: 3.518A pdb=" N ALA O 100 " --> pdb=" O SER O 96 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU O 117 " --> pdb=" O GLN O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 158 removed outlier: 4.249A pdb=" N LEU O 139 " --> pdb=" O GLU O 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN O 140 " --> pdb=" O THR O 136 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU O 141 " --> pdb=" O HIS O 137 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL O 143 " --> pdb=" O LEU O 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP O 151 " --> pdb=" O LYS O 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR O 154 " --> pdb=" O GLY O 150 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN O 155 " --> pdb=" O ASP O 151 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 40 removed outlier: 3.502A pdb=" N ASN P 22 " --> pdb=" O GLU P 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA P 31 " --> pdb=" O LEU P 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR P 33 " --> pdb=" O LEU P 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU P 36 " --> pdb=" O SER P 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER P 37 " --> pdb=" O TYR P 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR P 40 " --> pdb=" O LEU P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 77 removed outlier: 3.738A pdb=" N HIS P 58 " --> pdb=" O LYS P 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG P 64 " --> pdb=" O SER P 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU P 65 " --> pdb=" O HIS P 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA P 67 " --> pdb=" O GLU P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 125 removed outlier: 3.514A pdb=" N ALA P 100 " --> pdb=" O SER P 96 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU P 117 " --> pdb=" O GLN P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 159 removed outlier: 4.250A pdb=" N LEU P 139 " --> pdb=" O GLU P 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN P 140 " --> pdb=" O THR P 136 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU P 141 " --> pdb=" O HIS P 137 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL P 143 " --> pdb=" O LEU P 139 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP P 151 " --> pdb=" O LYS P 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR P 154 " --> pdb=" O GLY P 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN P 155 " --> pdb=" O ASP P 151 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET P 159 " --> pdb=" O ASN P 155 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN Q 22 " --> pdb=" O GLU Q 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA Q 31 " --> pdb=" O LEU Q 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR Q 33 " --> pdb=" O LEU Q 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU Q 36 " --> pdb=" O SER Q 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER Q 37 " --> pdb=" O TYR Q 33 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR Q 40 " --> pdb=" O LEU Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 77 removed outlier: 3.685A pdb=" N HIS Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG Q 64 " --> pdb=" O SER Q 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU Q 65 " --> pdb=" O HIS Q 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA Q 67 " --> pdb=" O GLU Q 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 96 through 125 removed outlier: 3.512A pdb=" N ALA Q 100 " --> pdb=" O SER Q 96 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU Q 117 " --> pdb=" O GLN Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 159 removed outlier: 4.250A pdb=" N LEU Q 139 " --> pdb=" O GLU Q 135 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ASN Q 140 " --> pdb=" O THR Q 136 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU Q 141 " --> pdb=" O HIS Q 137 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL Q 143 " --> pdb=" O LEU Q 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP Q 151 " --> pdb=" O LYS Q 147 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR Q 154 " --> pdb=" O GLY Q 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN Q 155 " --> pdb=" O ASP Q 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET Q 159 " --> pdb=" O ASN Q 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 40 removed outlier: 3.504A pdb=" N ASN R 22 " --> pdb=" O GLU R 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA R 31 " --> pdb=" O LEU R 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU R 36 " --> pdb=" O SER R 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER R 37 " --> pdb=" O TYR R 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR R 40 " --> pdb=" O LEU R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 77 removed outlier: 3.693A pdb=" N HIS R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG R 64 " --> pdb=" O SER R 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU R 65 " --> pdb=" O HIS R 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA R 67 " --> pdb=" O GLU R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 125 removed outlier: 3.519A pdb=" N ALA R 100 " --> pdb=" O SER R 96 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU R 117 " --> pdb=" O GLN R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 158 removed outlier: 4.249A pdb=" N LEU R 139 " --> pdb=" O GLU R 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN R 140 " --> pdb=" O THR R 136 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU R 141 " --> pdb=" O HIS R 137 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL R 143 " --> pdb=" O LEU R 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR R 154 " --> pdb=" O GLY R 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN R 155 " --> pdb=" O ASP R 151 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN S 22 " --> pdb=" O GLU S 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA S 31 " --> pdb=" O LEU S 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR S 33 " --> pdb=" O LEU S 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU S 36 " --> pdb=" O SER S 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER S 37 " --> pdb=" O TYR S 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 77 removed outlier: 3.690A pdb=" N HIS S 58 " --> pdb=" O LYS S 54 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG S 64 " --> pdb=" O SER S 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU S 65 " --> pdb=" O HIS S 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA S 67 " --> pdb=" O GLU S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 125 removed outlier: 3.515A pdb=" N ALA S 100 " --> pdb=" O SER S 96 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU S 117 " --> pdb=" O GLN S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 159 removed outlier: 4.249A pdb=" N LEU S 139 " --> pdb=" O GLU S 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN S 140 " --> pdb=" O THR S 136 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU S 141 " --> pdb=" O HIS S 137 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL S 143 " --> pdb=" O LEU S 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP S 151 " --> pdb=" O LYS S 147 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN S 155 " --> pdb=" O ASP S 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET S 159 " --> pdb=" O ASN S 155 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN T 22 " --> pdb=" O GLU T 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA T 31 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR T 33 " --> pdb=" O LEU T 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU T 36 " --> pdb=" O SER T 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER T 37 " --> pdb=" O TYR T 33 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR T 40 " --> pdb=" O LEU T 36 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 77 removed outlier: 3.738A pdb=" N HIS T 58 " --> pdb=" O LYS T 54 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG T 64 " --> pdb=" O SER T 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU T 65 " --> pdb=" O HIS T 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA T 67 " --> pdb=" O GLU T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 125 removed outlier: 3.514A pdb=" N ALA T 100 " --> pdb=" O SER T 96 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU T 117 " --> pdb=" O GLN T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 158 removed outlier: 4.250A pdb=" N LEU T 139 " --> pdb=" O GLU T 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN T 140 " --> pdb=" O THR T 136 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU T 141 " --> pdb=" O HIS T 137 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL T 143 " --> pdb=" O LEU T 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP T 151 " --> pdb=" O LYS T 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR T 154 " --> pdb=" O GLY T 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN T 155 " --> pdb=" O ASP T 151 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 40 removed outlier: 3.504A pdb=" N ASN U 22 " --> pdb=" O GLU U 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA U 31 " --> pdb=" O LEU U 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR U 33 " --> pdb=" O LEU U 29 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU U 36 " --> pdb=" O SER U 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER U 37 " --> pdb=" O TYR U 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR U 40 " --> pdb=" O LEU U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 77 removed outlier: 3.722A pdb=" N HIS U 58 " --> pdb=" O LYS U 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG U 64 " --> pdb=" O SER U 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA U 67 " --> pdb=" O GLU U 63 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 125 removed outlier: 3.508A pdb=" N ALA U 100 " --> pdb=" O SER U 96 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU U 117 " --> pdb=" O GLN U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 159 removed outlier: 4.249A pdb=" N LEU U 139 " --> pdb=" O GLU U 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN U 140 " --> pdb=" O THR U 136 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU U 141 " --> pdb=" O HIS U 137 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL U 143 " --> pdb=" O LEU U 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP U 151 " --> pdb=" O LYS U 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR U 154 " --> pdb=" O GLY U 150 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN U 155 " --> pdb=" O ASP U 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET U 159 " --> pdb=" O ASN U 155 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN V 22 " --> pdb=" O GLU V 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA V 31 " --> pdb=" O LEU V 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR V 33 " --> pdb=" O LEU V 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU V 36 " --> pdb=" O SER V 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER V 37 " --> pdb=" O TYR V 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR V 40 " --> pdb=" O LEU V 36 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 77 removed outlier: 3.690A pdb=" N HIS V 58 " --> pdb=" O LYS V 54 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG V 64 " --> pdb=" O SER V 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA V 67 " --> pdb=" O GLU V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 96 through 125 removed outlier: 3.504A pdb=" N ALA V 100 " --> pdb=" O SER V 96 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU V 117 " --> pdb=" O GLN V 113 " (cutoff:3.500A) Processing helix chain 'V' and resid 127 through 159 removed outlier: 4.249A pdb=" N LEU V 139 " --> pdb=" O GLU V 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN V 140 " --> pdb=" O THR V 136 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU V 141 " --> pdb=" O HIS V 137 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL V 143 " --> pdb=" O LEU V 139 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP V 151 " --> pdb=" O LYS V 147 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR V 154 " --> pdb=" O GLY V 150 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN V 155 " --> pdb=" O ASP V 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET V 159 " --> pdb=" O ASN V 155 " (cutoff:3.500A) Processing helix chain 'W' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN W 22 " --> pdb=" O GLU W 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA W 31 " --> pdb=" O LEU W 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR W 33 " --> pdb=" O LEU W 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU W 36 " --> pdb=" O SER W 32 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER W 37 " --> pdb=" O TYR W 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR W 40 " --> pdb=" O LEU W 36 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 77 removed outlier: 3.721A pdb=" N HIS W 58 " --> pdb=" O LYS W 54 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG W 64 " --> pdb=" O SER W 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU W 65 " --> pdb=" O HIS W 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA W 67 " --> pdb=" O GLU W 63 " (cutoff:3.500A) Processing helix chain 'W' and resid 96 through 125 removed outlier: 3.508A pdb=" N ALA W 100 " --> pdb=" O SER W 96 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU W 117 " --> pdb=" O GLN W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 159 removed outlier: 4.250A pdb=" N LEU W 139 " --> pdb=" O GLU W 135 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ASN W 140 " --> pdb=" O THR W 136 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU W 141 " --> pdb=" O HIS W 137 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL W 143 " --> pdb=" O LEU W 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP W 151 " --> pdb=" O LYS W 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR W 154 " --> pdb=" O GLY W 150 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN W 155 " --> pdb=" O ASP W 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET W 159 " --> pdb=" O ASN W 155 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 40 removed outlier: 3.502A pdb=" N ASN X 22 " --> pdb=" O GLU X 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA X 31 " --> pdb=" O LEU X 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR X 33 " --> pdb=" O LEU X 29 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU X 36 " --> pdb=" O SER X 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER X 37 " --> pdb=" O TYR X 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR X 40 " --> pdb=" O LEU X 36 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 77 removed outlier: 3.693A pdb=" N HIS X 58 " --> pdb=" O LYS X 54 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG X 64 " --> pdb=" O SER X 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU X 65 " --> pdb=" O HIS X 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA X 67 " --> pdb=" O GLU X 63 " (cutoff:3.500A) Processing helix chain 'X' and resid 96 through 125 removed outlier: 3.515A pdb=" N ALA X 100 " --> pdb=" O SER X 96 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU X 117 " --> pdb=" O GLN X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 127 through 159 removed outlier: 4.250A pdb=" N LEU X 139 " --> pdb=" O GLU X 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN X 140 " --> pdb=" O THR X 136 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU X 141 " --> pdb=" O HIS X 137 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL X 143 " --> pdb=" O LEU X 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP X 151 " --> pdb=" O LYS X 147 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR X 154 " --> pdb=" O GLY X 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN X 155 " --> pdb=" O ASP X 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET X 159 " --> pdb=" O ASN X 155 " (cutoff:3.500A) 1992 hydrogen bonds defined for protein. 5976 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: 11.54 Time building geometry restraints manager: 9.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10532 1.34 - 1.45: 4301 1.45 - 1.57: 16295 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 31392 Sorted by residual: bond pdb=" CB ARG B 64 " pdb=" CG ARG B 64 " ideal model delta sigma weight residual 1.520 1.429 0.091 3.00e-02 1.11e+03 9.14e+00 bond pdb=" CG ARG J 64 " pdb=" CD ARG J 64 " ideal model delta sigma weight residual 1.520 1.438 0.082 3.00e-02 1.11e+03 7.49e+00 bond pdb=" CG ARG G 64 " pdb=" CD ARG G 64 " ideal model delta sigma weight residual 1.520 1.443 0.077 3.00e-02 1.11e+03 6.66e+00 bond pdb=" CG ARG B 64 " pdb=" CD ARG B 64 " ideal model delta sigma weight residual 1.520 1.456 0.064 3.00e-02 1.11e+03 4.48e+00 bond pdb=" CG ARG N 64 " pdb=" CD ARG N 64 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.13e+00 ... (remaining 31387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 41075 1.82 - 3.64: 985 3.64 - 5.46: 119 5.46 - 7.29: 56 7.29 - 9.11: 5 Bond angle restraints: 42240 Sorted by residual: angle pdb=" NE ARG J 64 " pdb=" CZ ARG J 64 " pdb=" NH1 ARG J 64 " ideal model delta sigma weight residual 121.50 115.95 5.55 1.00e+00 1.00e+00 3.08e+01 angle pdb=" NE ARG G 64 " pdb=" CZ ARG G 64 " pdb=" NH1 ARG G 64 " ideal model delta sigma weight residual 121.50 116.03 5.47 1.00e+00 1.00e+00 2.99e+01 angle pdb=" NE ARG N 64 " pdb=" CZ ARG N 64 " pdb=" NH1 ARG N 64 " ideal model delta sigma weight residual 121.50 116.96 4.54 1.00e+00 1.00e+00 2.06e+01 angle pdb=" C GLU B 63 " pdb=" N ARG B 64 " pdb=" CA ARG B 64 " ideal model delta sigma weight residual 122.06 113.99 8.07 1.86e+00 2.89e-01 1.88e+01 angle pdb=" CG ARG B 64 " pdb=" CD ARG B 64 " pdb=" NE ARG B 64 " ideal model delta sigma weight residual 112.00 102.89 9.11 2.20e+00 2.07e-01 1.71e+01 ... (remaining 42235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 18514 16.16 - 32.32: 291 32.32 - 48.48: 178 48.48 - 64.64: 49 64.64 - 80.80: 48 Dihedral angle restraints: 19080 sinusoidal: 7992 harmonic: 11088 Sorted by residual: dihedral pdb=" CA ASP P 151 " pdb=" C ASP P 151 " pdb=" N HIS P 152 " pdb=" CA HIS P 152 " ideal model delta harmonic sigma weight residual 180.00 157.48 22.52 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ASP A 151 " pdb=" C ASP A 151 " pdb=" N HIS A 152 " pdb=" CA HIS A 152 " ideal model delta harmonic sigma weight residual 180.00 157.49 22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ASP R 151 " pdb=" C ASP R 151 " pdb=" N HIS R 152 " pdb=" CA HIS R 152 " ideal model delta harmonic sigma weight residual 180.00 157.49 22.51 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 19077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2808 0.042 - 0.084: 1359 0.084 - 0.126: 221 0.126 - 0.167: 50 0.167 - 0.209: 2 Chirality restraints: 4440 Sorted by residual: chirality pdb=" CA ASN I 140 " pdb=" N ASN I 140 " pdb=" C ASN I 140 " pdb=" CB ASN I 140 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ASN H 140 " pdb=" N ASN H 140 " pdb=" C ASN H 140 " pdb=" CB ASN H 140 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA GLU I 141 " pdb=" N GLU I 141 " pdb=" C GLU I 141 " pdb=" CB GLU I 141 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.68e-01 ... (remaining 4437 not shown) Planarity restraints: 5568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR U 33 " -0.026 2.00e-02 2.50e+03 1.92e-02 7.40e+00 pdb=" CG TYR U 33 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR U 33 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR U 33 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR U 33 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR U 33 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR U 33 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR U 33 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR T 33 " -0.026 2.00e-02 2.50e+03 1.92e-02 7.38e+00 pdb=" CG TYR T 33 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR T 33 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR T 33 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR T 33 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR T 33 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR T 33 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR T 33 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR V 33 " 0.026 2.00e-02 2.50e+03 1.92e-02 7.38e+00 pdb=" CG TYR V 33 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR V 33 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR V 33 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR V 33 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR V 33 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR V 33 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR V 33 " 0.005 2.00e-02 2.50e+03 ... (remaining 5565 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1257 2.72 - 3.26: 30137 3.26 - 3.81: 44501 3.81 - 4.35: 64149 4.35 - 4.90: 105510 Nonbonded interactions: 245554 Sorted by model distance: nonbonded pdb=" OG SER B 7 " pdb=" OD2 ASP N 45 " model vdw 2.173 3.040 nonbonded pdb=" OG SER H 7 " pdb=" OD2 ASP T 45 " model vdw 2.173 3.040 nonbonded pdb=" OD2 ASP E 45 " pdb=" OG SER Q 7 " model vdw 2.177 3.040 nonbonded pdb=" OE1 GLU B 28 " pdb=" O HOH B 201 " model vdw 2.178 3.040 nonbonded pdb=" OE1 GLU D 28 " pdb=" O HOH D 201 " model vdw 2.187 3.040 ... (remaining 245549 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.150 Check model and map are aligned: 0.210 Set scattering table: 0.290 Process input model: 66.890 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.330 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:70.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 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 0.091 31392 Z= 0.315 Angle : 0.712 9.107 42240 Z= 0.390 Chirality : 0.045 0.209 4440 Planarity : 0.004 0.037 5568 Dihedral : 10.819 80.801 11880 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -6.31 (0.08), residues: 3672 helix: -4.34 (0.04), residues: 2904 sheet: None (None), residues: 0 loop : -2.03 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.005 TRP Q 94 HIS 0.011 0.002 HIS N 152 PHE 0.017 0.003 PHE J 56 TYR 0.046 0.005 TYR U 33 ARG 0.013 0.002 ARG A 64 Details of bonding type rmsd hydrogen bonds : bond 0.40184 ( 1992) hydrogen bonds : angle 9.54652 ( 5976) covalent geometry : bond 0.00725 (31392) covalent geometry : angle 0.71164 (42240) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1192 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1192 time to evaluate : 3.708 Fit side-chains REVERT: A 23 ARG cc_start: 0.8922 (mtm-85) cc_final: 0.8552 (mtt90) REVERT: A 64 ARG cc_start: 0.7770 (ttp-170) cc_final: 0.7555 (ttt180) REVERT: A 103 CYS cc_start: 0.8315 (t) cc_final: 0.7874 (m) REVERT: B 23 ARG cc_start: 0.8932 (mtm-85) cc_final: 0.8559 (mtt90) REVERT: B 44 ARG cc_start: 0.8703 (mtp180) cc_final: 0.8459 (mtm180) REVERT: B 103 CYS cc_start: 0.8382 (t) cc_final: 0.7912 (m) REVERT: C 23 ARG cc_start: 0.8906 (mtm-85) cc_final: 0.8555 (mtt90) REVERT: C 44 ARG cc_start: 0.8793 (mtp180) cc_final: 0.8590 (mtm180) REVERT: C 64 ARG cc_start: 0.8180 (mtm110) cc_final: 0.7828 (mmm160) REVERT: C 101 MET cc_start: 0.9110 (mmt) cc_final: 0.8870 (mmt) REVERT: D 23 ARG cc_start: 0.8896 (mtm-85) cc_final: 0.8552 (mtt90) REVERT: D 64 ARG cc_start: 0.8305 (ttt90) cc_final: 0.8098 (ttt180) REVERT: D 101 MET cc_start: 0.9119 (mmt) cc_final: 0.8910 (mmt) REVERT: D 103 CYS cc_start: 0.8386 (t) cc_final: 0.7972 (m) REVERT: D 117 GLU cc_start: 0.8943 (mp0) cc_final: 0.8440 (mm-30) REVERT: E 23 ARG cc_start: 0.8976 (mtm-85) cc_final: 0.8607 (mtt90) REVERT: E 103 CYS cc_start: 0.8333 (t) cc_final: 0.7870 (m) REVERT: F 23 ARG cc_start: 0.8902 (mtm-85) cc_final: 0.8557 (mtt90) REVERT: F 44 ARG cc_start: 0.8757 (mtp180) cc_final: 0.8531 (mtm180) REVERT: F 54 LYS cc_start: 0.9352 (ttpp) cc_final: 0.9152 (ttpm) REVERT: F 103 CYS cc_start: 0.8326 (t) cc_final: 0.7841 (m) REVERT: G 23 ARG cc_start: 0.8929 (mtm-85) cc_final: 0.8579 (mtt90) REVERT: G 44 ARG cc_start: 0.8831 (mtp180) cc_final: 0.8563 (mtm180) REVERT: G 101 MET cc_start: 0.9101 (mmt) cc_final: 0.8901 (mmt) REVERT: H 23 ARG cc_start: 0.8934 (mtm-85) cc_final: 0.8702 (mtp180) REVERT: H 103 CYS cc_start: 0.8162 (t) cc_final: 0.7709 (m) REVERT: I 23 ARG cc_start: 0.8843 (mtm-85) cc_final: 0.8510 (mtt90) REVERT: I 44 ARG cc_start: 0.8788 (mtp180) cc_final: 0.8510 (mtm180) REVERT: I 54 LYS cc_start: 0.9420 (ttpt) cc_final: 0.9070 (ttpm) REVERT: I 64 ARG cc_start: 0.8617 (ttp-110) cc_final: 0.8330 (ttt180) REVERT: I 101 MET cc_start: 0.9128 (mmt) cc_final: 0.8860 (mmt) REVERT: J 23 ARG cc_start: 0.8868 (mtm-85) cc_final: 0.8532 (mtt90) REVERT: J 103 CYS cc_start: 0.8301 (t) cc_final: 0.7844 (m) REVERT: J 117 GLU cc_start: 0.8900 (mp0) cc_final: 0.8375 (mm-30) REVERT: K 23 ARG cc_start: 0.8845 (mtm-85) cc_final: 0.8500 (mtt90) REVERT: K 44 ARG cc_start: 0.8755 (mtp180) cc_final: 0.8484 (mtm180) REVERT: K 101 MET cc_start: 0.9116 (mmt) cc_final: 0.8903 (mmt) REVERT: K 117 GLU cc_start: 0.8887 (mp0) cc_final: 0.8381 (mm-30) REVERT: L 23 ARG cc_start: 0.8923 (mtm-85) cc_final: 0.8559 (mtt90) REVERT: L 54 LYS cc_start: 0.9347 (ttpt) cc_final: 0.8989 (ttpm) REVERT: L 103 CYS cc_start: 0.8375 (t) cc_final: 0.7905 (m) REVERT: M 18 GLU cc_start: 0.8880 (tt0) cc_final: 0.8667 (tt0) REVERT: M 30 TYR cc_start: 0.9072 (t80) cc_final: 0.8848 (t80) REVERT: M 44 ARG cc_start: 0.8757 (mtp180) cc_final: 0.8473 (mtm180) REVERT: M 64 ARG cc_start: 0.7728 (ttp-170) cc_final: 0.7455 (ttt180) REVERT: M 101 MET cc_start: 0.9134 (mmt) cc_final: 0.8912 (mmt) REVERT: M 114 SER cc_start: 0.8859 (t) cc_final: 0.8647 (m) REVERT: M 117 GLU cc_start: 0.8895 (mp0) cc_final: 0.8352 (mm-30) REVERT: N 44 ARG cc_start: 0.8824 (mtp180) cc_final: 0.8560 (mtm180) REVERT: N 64 ARG cc_start: 0.8456 (ttp-170) cc_final: 0.8147 (ptt180) REVERT: N 101 MET cc_start: 0.9143 (mmt) cc_final: 0.8937 (mmt) REVERT: N 114 SER cc_start: 0.8910 (t) cc_final: 0.8673 (m) REVERT: N 117 GLU cc_start: 0.8918 (mp0) cc_final: 0.8429 (mm-30) REVERT: O 23 ARG cc_start: 0.8917 (mtm-85) cc_final: 0.8553 (mtt90) REVERT: O 44 ARG cc_start: 0.8825 (mtp180) cc_final: 0.8594 (mtm180) REVERT: O 64 ARG cc_start: 0.8593 (ttp-110) cc_final: 0.7546 (ttt180) REVERT: O 103 CYS cc_start: 0.8428 (t) cc_final: 0.7930 (m) REVERT: O 141 GLU cc_start: 0.8651 (mp0) cc_final: 0.8238 (mt-10) REVERT: P 23 ARG cc_start: 0.8906 (mtm-85) cc_final: 0.8562 (mtt90) REVERT: P 38 MET cc_start: 0.9077 (mtt) cc_final: 0.8845 (mtm) REVERT: P 103 CYS cc_start: 0.8345 (t) cc_final: 0.7865 (m) REVERT: Q 23 ARG cc_start: 0.8867 (mtm-85) cc_final: 0.8531 (mtt90) REVERT: Q 44 ARG cc_start: 0.8797 (mtp180) cc_final: 0.8556 (mtm180) REVERT: R 23 ARG cc_start: 0.8904 (mtm-85) cc_final: 0.8561 (mtt90) REVERT: R 44 ARG cc_start: 0.8795 (mtp180) cc_final: 0.8524 (mtm180) REVERT: S 23 ARG cc_start: 0.8896 (mtm-85) cc_final: 0.8555 (mtt90) REVERT: S 44 ARG cc_start: 0.8771 (mtp180) cc_final: 0.8515 (mtm180) REVERT: S 54 LYS cc_start: 0.9424 (ttpt) cc_final: 0.9066 (ttpm) REVERT: S 64 ARG cc_start: 0.8258 (ttp-110) cc_final: 0.7963 (ttt180) REVERT: S 103 CYS cc_start: 0.8456 (t) cc_final: 0.8023 (m) REVERT: S 117 GLU cc_start: 0.8893 (mp0) cc_final: 0.8389 (mm-30) REVERT: S 120 LYS cc_start: 0.8778 (tttt) cc_final: 0.8575 (ttpm) REVERT: T 18 GLU cc_start: 0.8871 (tt0) cc_final: 0.8659 (tt0) REVERT: T 23 ARG cc_start: 0.8931 (mtm-85) cc_final: 0.8594 (mtt90) REVERT: T 64 ARG cc_start: 0.7899 (ttp-170) cc_final: 0.7572 (ttt180) REVERT: T 101 MET cc_start: 0.9119 (mmt) cc_final: 0.8894 (mmt) REVERT: U 23 ARG cc_start: 0.8930 (mtm-85) cc_final: 0.8574 (mtt90) REVERT: U 44 ARG cc_start: 0.8804 (mtp180) cc_final: 0.8589 (mtm180) REVERT: U 64 ARG cc_start: 0.8634 (ttp-110) cc_final: 0.8250 (ptt180) REVERT: U 101 MET cc_start: 0.9171 (mmt) cc_final: 0.8946 (mmt) REVERT: U 103 CYS cc_start: 0.8500 (t) cc_final: 0.8073 (m) REVERT: V 23 ARG cc_start: 0.8938 (mtm-85) cc_final: 0.8569 (mtt90) REVERT: V 54 LYS cc_start: 0.9440 (ttpt) cc_final: 0.9109 (ttpm) REVERT: V 64 ARG cc_start: 0.8264 (ttp-110) cc_final: 0.7935 (ttt180) REVERT: V 103 CYS cc_start: 0.8376 (t) cc_final: 0.7899 (m) REVERT: W 23 ARG cc_start: 0.8919 (mtm-85) cc_final: 0.8558 (mtt90) REVERT: W 101 MET cc_start: 0.9151 (mmt) cc_final: 0.8933 (mmt) REVERT: W 103 CYS cc_start: 0.8360 (t) cc_final: 0.7886 (m) REVERT: X 23 ARG cc_start: 0.8882 (mtm-85) cc_final: 0.8537 (mtt90) REVERT: X 44 ARG cc_start: 0.8804 (mtp180) cc_final: 0.8579 (mtm180) REVERT: X 64 ARG cc_start: 0.8444 (ttp-170) cc_final: 0.8039 (ttp-170) REVERT: X 101 MET cc_start: 0.9092 (mmt) cc_final: 0.8836 (mmt) REVERT: X 103 CYS cc_start: 0.8335 (t) cc_final: 0.7863 (m) outliers start: 0 outliers final: 0 residues processed: 1192 average time/residue: 2.1193 time to fit residues: 2861.7902 Evaluate side-chains 796 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 796 time to evaluate : 3.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.9980 chunk 272 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 282 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 210 optimal weight: 10.0000 chunk 326 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN A 84 GLN B 74 GLN B 84 GLN C 74 GLN C 84 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN D 76 GLN D 84 GLN E 74 GLN ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN F 84 GLN G 74 GLN H 74 GLN H 84 GLN I 74 GLN I 84 GLN J 11 GLN J 74 GLN J 84 GLN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 GLN K 76 GLN K 84 GLN L 74 GLN L 84 GLN M 74 GLN M 84 GLN ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 GLN N 84 GLN O 74 GLN O 84 GLN ** P 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 GLN P 84 GLN ** Q 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 74 GLN Q 84 GLN R 74 GLN R 84 GLN S 11 GLN S 74 GLN S 84 GLN ** T 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 GLN T 84 GLN ** U 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 GLN U 84 GLN ** V 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 74 GLN V 84 GLN ** W 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 74 GLN W 76 GLN W 84 GLN X 74 GLN X 84 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.149878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.140761 restraints weight = 30874.055| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 0.67 r_work: 0.3384 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 31392 Z= 0.174 Angle : 0.557 5.064 42240 Z= 0.314 Chirality : 0.037 0.122 4440 Planarity : 0.005 0.050 5568 Dihedral : 4.837 20.990 4056 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.88 % Allowed : 11.28 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.71 (0.11), residues: 3672 helix: -0.87 (0.08), residues: 2904 sheet: None (None), residues: 0 loop : -1.51 (0.19), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP O 94 HIS 0.005 0.002 HIS A 129 PHE 0.009 0.002 PHE I 56 TYR 0.027 0.003 TYR V 33 ARG 0.011 0.001 ARG G 64 Details of bonding type rmsd hydrogen bonds : bond 0.09692 ( 1992) hydrogen bonds : angle 3.75751 ( 5976) covalent geometry : bond 0.00350 (31392) covalent geometry : angle 0.55696 (42240) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 766 time to evaluate : 5.552 Fit side-chains REVERT: A 30 TYR cc_start: 0.8937 (t80) cc_final: 0.8675 (t80) REVERT: A 38 MET cc_start: 0.8846 (mtt) cc_final: 0.8645 (ttm) REVERT: B 30 TYR cc_start: 0.8912 (t80) cc_final: 0.8654 (t80) REVERT: B 44 ARG cc_start: 0.8761 (mtp180) cc_final: 0.8557 (mtm180) REVERT: B 64 ARG cc_start: 0.8288 (ptm160) cc_final: 0.7550 (ttm170) REVERT: C 30 TYR cc_start: 0.8866 (t80) cc_final: 0.8593 (t80) REVERT: C 44 ARG cc_start: 0.8759 (mtp180) cc_final: 0.8550 (mtm180) REVERT: C 101 MET cc_start: 0.8456 (mmt) cc_final: 0.8239 (mmt) REVERT: C 103 CYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7510 (m) REVERT: D 30 TYR cc_start: 0.8925 (t80) cc_final: 0.8654 (t80) REVERT: D 38 MET cc_start: 0.8887 (mtt) cc_final: 0.8674 (ttm) REVERT: D 101 MET cc_start: 0.8449 (mmt) cc_final: 0.8230 (mmt) REVERT: E 30 TYR cc_start: 0.8908 (t80) cc_final: 0.8644 (t80) REVERT: F 30 TYR cc_start: 0.8852 (t80) cc_final: 0.8562 (t80) REVERT: G 30 TYR cc_start: 0.8861 (t80) cc_final: 0.8582 (t80) REVERT: G 44 ARG cc_start: 0.8766 (mtp180) cc_final: 0.8563 (mtm180) REVERT: G 101 MET cc_start: 0.8432 (mmt) cc_final: 0.8204 (mmt) REVERT: G 103 CYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7459 (m) REVERT: H 143 VAL cc_start: 0.8931 (t) cc_final: 0.8712 (m) REVERT: I 30 TYR cc_start: 0.8834 (t80) cc_final: 0.8547 (t80) REVERT: I 38 MET cc_start: 0.8869 (mtt) cc_final: 0.8666 (ttm) REVERT: I 64 ARG cc_start: 0.8397 (ttp-110) cc_final: 0.7985 (ttt180) REVERT: I 101 MET cc_start: 0.8460 (mmt) cc_final: 0.8238 (mmt) REVERT: I 103 CYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7466 (m) REVERT: J 30 TYR cc_start: 0.8860 (t80) cc_final: 0.8574 (t80) REVERT: K 30 TYR cc_start: 0.8855 (t80) cc_final: 0.8555 (t80) REVERT: K 38 MET cc_start: 0.8857 (mtt) cc_final: 0.8651 (ttm) REVERT: K 76 GLN cc_start: 0.8345 (tt0) cc_final: 0.8128 (tt0) REVERT: K 101 MET cc_start: 0.8491 (mmt) cc_final: 0.8289 (mmt) REVERT: K 103 CYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7505 (m) REVERT: L 30 TYR cc_start: 0.8888 (t80) cc_final: 0.8623 (t80) REVERT: L 54 LYS cc_start: 0.9072 (ttpt) cc_final: 0.8692 (tttm) REVERT: M 23 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.7999 (mtp180) REVERT: M 30 TYR cc_start: 0.8831 (t80) cc_final: 0.8527 (t80) REVERT: M 38 MET cc_start: 0.8885 (mtt) cc_final: 0.8668 (ttm) REVERT: M 43 ASP cc_start: 0.8509 (t70) cc_final: 0.8295 (t70) REVERT: M 101 MET cc_start: 0.8447 (mmt) cc_final: 0.8227 (mmt) REVERT: M 103 CYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7490 (m) REVERT: M 114 SER cc_start: 0.8795 (t) cc_final: 0.8515 (m) REVERT: N 23 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.7982 (mtp180) REVERT: N 30 TYR cc_start: 0.8877 (t80) cc_final: 0.8592 (t80) REVERT: N 101 MET cc_start: 0.8452 (mmt) cc_final: 0.8242 (mmt) REVERT: N 103 CYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7523 (m) REVERT: N 110 ASN cc_start: 0.8372 (m-40) cc_final: 0.8129 (m-40) REVERT: N 114 SER cc_start: 0.8800 (t) cc_final: 0.8513 (m) REVERT: N 143 VAL cc_start: 0.8905 (t) cc_final: 0.8662 (m) REVERT: O 30 TYR cc_start: 0.8891 (t80) cc_final: 0.8605 (t80) REVERT: O 64 ARG cc_start: 0.8366 (ttp-110) cc_final: 0.7916 (ptt180) REVERT: P 30 TYR cc_start: 0.8854 (t80) cc_final: 0.8567 (t80) REVERT: Q 30 TYR cc_start: 0.8864 (t80) cc_final: 0.8576 (t80) REVERT: Q 103 CYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7463 (m) REVERT: R 30 TYR cc_start: 0.8834 (t80) cc_final: 0.8536 (t80) REVERT: R 38 MET cc_start: 0.8885 (mtm) cc_final: 0.8647 (ttm) REVERT: R 103 CYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7477 (m) REVERT: S 30 TYR cc_start: 0.8874 (t80) cc_final: 0.8581 (t80) REVERT: S 159 MET cc_start: 0.7658 (mtm) cc_final: 0.7097 (mtt) REVERT: T 30 TYR cc_start: 0.8872 (t80) cc_final: 0.8585 (t80) REVERT: T 101 MET cc_start: 0.8429 (mmt) cc_final: 0.8206 (mmt) REVERT: T 103 CYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7483 (m) REVERT: U 30 TYR cc_start: 0.8907 (t80) cc_final: 0.8638 (t80) REVERT: U 44 ARG cc_start: 0.8750 (mtp180) cc_final: 0.8549 (mtm180) REVERT: U 64 ARG cc_start: 0.8396 (ttp-110) cc_final: 0.7939 (ptt180) REVERT: U 101 MET cc_start: 0.8491 (mmt) cc_final: 0.8288 (mmt) REVERT: V 30 TYR cc_start: 0.8906 (t80) cc_final: 0.8633 (t80) REVERT: W 30 TYR cc_start: 0.8904 (t80) cc_final: 0.8634 (t80) REVERT: W 101 MET cc_start: 0.8475 (mmt) cc_final: 0.8263 (mmt) REVERT: X 30 TYR cc_start: 0.8874 (t80) cc_final: 0.8586 (t80) REVERT: X 64 ARG cc_start: 0.7994 (ttp-170) cc_final: 0.7449 (ttp-170) REVERT: X 101 MET cc_start: 0.8421 (mmt) cc_final: 0.8211 (mmt) outliers start: 63 outliers final: 25 residues processed: 804 average time/residue: 2.0533 time to fit residues: 1868.7675 Evaluate side-chains 648 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 614 time to evaluate : 3.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 103 CYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain K residue 103 CYS Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain W residue 64 ARG Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain X residue 123 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 112 optimal weight: 8.9990 chunk 191 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 292 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 334 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 278 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN B 84 GLN C 84 GLN C 126 ASN D 84 GLN E 76 GLN F 84 GLN G 76 GLN H 76 GLN H 84 GLN I 84 GLN I 126 ASN J 84 GLN K 76 GLN K 84 GLN L 84 GLN M 84 GLN N 84 GLN O 84 GLN P 76 GLN P 84 GLN Q 84 GLN R 76 GLN S 84 GLN T 84 GLN T 126 ASN U 84 GLN V 84 GLN W 84 GLN X 84 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.142160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.130669 restraints weight = 31021.347| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 0.84 r_work: 0.3240 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 31392 Z= 0.211 Angle : 0.593 5.902 42240 Z= 0.326 Chirality : 0.040 0.123 4440 Planarity : 0.004 0.025 5568 Dihedral : 4.675 20.014 4056 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.01 % Allowed : 12.68 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.17 (0.13), residues: 3672 helix: 1.25 (0.09), residues: 2904 sheet: None (None), residues: 0 loop : -0.90 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 94 HIS 0.007 0.002 HIS L 152 PHE 0.012 0.002 PHE H 42 TYR 0.027 0.004 TYR S 138 ARG 0.005 0.001 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.10223 ( 1992) hydrogen bonds : angle 3.66019 ( 5976) covalent geometry : bond 0.00467 (31392) covalent geometry : angle 0.59309 (42240) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 517 time to evaluate : 3.997 Fit side-chains REVERT: A 30 TYR cc_start: 0.9030 (t80) cc_final: 0.8769 (t80) REVERT: B 30 TYR cc_start: 0.9007 (t80) cc_final: 0.8756 (t80) REVERT: B 44 ARG cc_start: 0.8826 (mtp180) cc_final: 0.8622 (mtm180) REVERT: B 64 ARG cc_start: 0.8424 (ptm160) cc_final: 0.7719 (ttt180) REVERT: C 30 TYR cc_start: 0.9020 (t80) cc_final: 0.8774 (t80) REVERT: C 101 MET cc_start: 0.8713 (mmt) cc_final: 0.8419 (mmt) REVERT: C 103 CYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7758 (m) REVERT: D 30 TYR cc_start: 0.9021 (t80) cc_final: 0.8768 (t80) REVERT: E 30 TYR cc_start: 0.9004 (t80) cc_final: 0.8749 (t80) REVERT: F 30 TYR cc_start: 0.9001 (t80) cc_final: 0.8755 (t80) REVERT: G 30 TYR cc_start: 0.9018 (t80) cc_final: 0.8764 (t80) REVERT: G 101 MET cc_start: 0.8689 (mmt) cc_final: 0.8388 (mmt) REVERT: G 103 CYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7769 (m) REVERT: H 30 TYR cc_start: 0.8998 (t80) cc_final: 0.8749 (t80) REVERT: I 30 TYR cc_start: 0.8997 (t80) cc_final: 0.8749 (t80) REVERT: I 64 ARG cc_start: 0.8468 (ttp-110) cc_final: 0.7255 (ttt180) REVERT: I 103 CYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7873 (m) REVERT: J 30 TYR cc_start: 0.9018 (t80) cc_final: 0.8778 (t80) REVERT: K 30 TYR cc_start: 0.9000 (t80) cc_final: 0.8743 (t80) REVERT: K 103 CYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7837 (m) REVERT: L 30 TYR cc_start: 0.8980 (t80) cc_final: 0.8726 (t80) REVERT: M 30 TYR cc_start: 0.9012 (t80) cc_final: 0.8757 (t80) REVERT: M 43 ASP cc_start: 0.8580 (t70) cc_final: 0.8379 (t70) REVERT: M 101 MET cc_start: 0.8753 (mmt) cc_final: 0.8545 (mmt) REVERT: M 103 CYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7841 (m) REVERT: N 30 TYR cc_start: 0.9011 (t80) cc_final: 0.8774 (t80) REVERT: N 44 ARG cc_start: 0.8789 (mtm180) cc_final: 0.8524 (mtm180) REVERT: N 64 ARG cc_start: 0.8391 (ttp-170) cc_final: 0.7780 (ttp-170) REVERT: N 101 MET cc_start: 0.8759 (mmt) cc_final: 0.8507 (mmt) REVERT: O 30 TYR cc_start: 0.9042 (t80) cc_final: 0.8799 (t80) REVERT: O 64 ARG cc_start: 0.8149 (ttp-110) cc_final: 0.7254 (ttt180) REVERT: P 30 TYR cc_start: 0.9016 (t80) cc_final: 0.8768 (t80) REVERT: Q 30 TYR cc_start: 0.9015 (t80) cc_final: 0.8769 (t80) REVERT: Q 103 CYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7760 (m) REVERT: R 30 TYR cc_start: 0.8989 (t80) cc_final: 0.8734 (t80) REVERT: R 103 CYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7841 (m) REVERT: S 30 TYR cc_start: 0.9002 (t80) cc_final: 0.8759 (t80) REVERT: T 30 TYR cc_start: 0.9029 (t80) cc_final: 0.8775 (t80) REVERT: T 101 MET cc_start: 0.8680 (mmt) cc_final: 0.8374 (mmt) REVERT: T 103 CYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7752 (m) REVERT: U 30 TYR cc_start: 0.9006 (t80) cc_final: 0.8751 (t80) REVERT: U 64 ARG cc_start: 0.8458 (ttp-110) cc_final: 0.7341 (ttt180) REVERT: V 30 TYR cc_start: 0.8998 (t80) cc_final: 0.8737 (t80) REVERT: W 30 TYR cc_start: 0.8988 (t80) cc_final: 0.8734 (t80) REVERT: X 30 TYR cc_start: 0.9038 (t80) cc_final: 0.8793 (t80) REVERT: X 64 ARG cc_start: 0.8041 (ttp-170) cc_final: 0.7691 (ttm110) outliers start: 101 outliers final: 53 residues processed: 590 average time/residue: 2.5000 time to fit residues: 1632.7628 Evaluate side-chains 525 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 464 time to evaluate : 3.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 64 ARG Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 103 CYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 69 LYS Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 103 CYS Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 69 LYS Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain O residue 18 GLU Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain P residue 18 GLU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 69 LYS Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain U residue 18 GLU Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain V residue 18 GLU Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain W residue 18 GLU Chi-restraints excluded: chain W residue 64 ARG Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain X residue 18 GLU Chi-restraints excluded: chain X residue 123 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 229 optimal weight: 6.9990 chunk 311 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 310 optimal weight: 5.9990 chunk 151 optimal weight: 20.0000 chunk 353 optimal weight: 4.9990 chunk 288 optimal weight: 8.9990 chunk 136 optimal weight: 20.0000 chunk 332 optimal weight: 9.9990 chunk 260 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN B 84 GLN C 84 GLN D 84 GLN E 76 GLN F 84 GLN G 76 GLN H 76 GLN H 84 GLN I 84 GLN J 84 GLN K 76 GLN K 84 GLN L 84 GLN M 84 GLN N 84 GLN O 84 GLN P 76 GLN P 84 GLN Q 84 GLN R 76 GLN S 84 GLN T 84 GLN U 84 GLN V 84 GLN W 84 GLN X 84 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.145766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.137032 restraints weight = 31130.777| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 0.67 r_work: 0.3338 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 31392 Z= 0.151 Angle : 0.478 4.146 42240 Z= 0.270 Chirality : 0.037 0.119 4440 Planarity : 0.003 0.023 5568 Dihedral : 4.356 18.159 4056 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.27 % Allowed : 12.44 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 2.49 (0.13), residues: 3672 helix: 2.21 (0.09), residues: 2904 sheet: None (None), residues: 0 loop : -0.52 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP B 94 HIS 0.005 0.001 HIS I 152 PHE 0.010 0.002 PHE U 42 TYR 0.018 0.003 TYR I 33 ARG 0.004 0.001 ARG W 64 Details of bonding type rmsd hydrogen bonds : bond 0.08090 ( 1992) hydrogen bonds : angle 3.31728 ( 5976) covalent geometry : bond 0.00310 (31392) covalent geometry : angle 0.47849 (42240) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 547 time to evaluate : 3.587 Fit side-chains REVERT: A 30 TYR cc_start: 0.8956 (t80) cc_final: 0.8715 (t80) REVERT: B 30 TYR cc_start: 0.8946 (t80) cc_final: 0.8721 (t80) REVERT: B 44 ARG cc_start: 0.8802 (mtp180) cc_final: 0.8350 (mtm180) REVERT: B 64 ARG cc_start: 0.8445 (ptm160) cc_final: 0.7742 (ttt180) REVERT: C 30 TYR cc_start: 0.8946 (t80) cc_final: 0.8742 (t80) REVERT: D 30 TYR cc_start: 0.8958 (t80) cc_final: 0.8743 (t80) REVERT: E 30 TYR cc_start: 0.8940 (t80) cc_final: 0.8715 (t80) REVERT: E 141 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7320 (mp0) REVERT: F 30 TYR cc_start: 0.8942 (t80) cc_final: 0.8740 (t80) REVERT: G 30 TYR cc_start: 0.8941 (t80) cc_final: 0.8721 (t80) REVERT: H 30 TYR cc_start: 0.8948 (t80) cc_final: 0.8729 (t80) REVERT: I 64 ARG cc_start: 0.8406 (ttp-110) cc_final: 0.7995 (ttt180) REVERT: J 30 TYR cc_start: 0.8967 (t80) cc_final: 0.8765 (t80) REVERT: K 30 TYR cc_start: 0.8944 (t80) cc_final: 0.8738 (t80) REVERT: L 30 TYR cc_start: 0.8914 (t80) cc_final: 0.8701 (t80) REVERT: M 30 TYR cc_start: 0.8928 (t80) cc_final: 0.8714 (t80) REVERT: M 43 ASP cc_start: 0.8381 (t70) cc_final: 0.8111 (t70) REVERT: N 30 TYR cc_start: 0.8963 (t80) cc_final: 0.8762 (t80) REVERT: N 64 ARG cc_start: 0.8078 (ttp-170) cc_final: 0.7818 (ttp-170) REVERT: N 101 MET cc_start: 0.8532 (mmt) cc_final: 0.8321 (mmt) REVERT: O 30 TYR cc_start: 0.8968 (t80) cc_final: 0.8753 (t80) REVERT: O 64 ARG cc_start: 0.8007 (ttp-110) cc_final: 0.7265 (ttt180) REVERT: P 30 TYR cc_start: 0.8950 (t80) cc_final: 0.8741 (t80) REVERT: Q 30 TYR cc_start: 0.8962 (t80) cc_final: 0.8756 (t80) REVERT: R 30 TYR cc_start: 0.8915 (t80) cc_final: 0.8701 (t80) REVERT: T 30 TYR cc_start: 0.8962 (t80) cc_final: 0.8748 (t80) REVERT: U 30 TYR cc_start: 0.8941 (t80) cc_final: 0.8724 (t80) REVERT: U 64 ARG cc_start: 0.8374 (ttp-110) cc_final: 0.7979 (ptt180) REVERT: V 30 TYR cc_start: 0.8939 (t80) cc_final: 0.8711 (t80) REVERT: W 30 TYR cc_start: 0.8931 (t80) cc_final: 0.8702 (t80) REVERT: X 30 TYR cc_start: 0.8977 (t80) cc_final: 0.8774 (t80) REVERT: X 64 ARG cc_start: 0.7956 (ttp-170) cc_final: 0.7410 (ttp-170) outliers start: 110 outliers final: 58 residues processed: 618 average time/residue: 2.2493 time to fit residues: 1544.8480 Evaluate side-chains 585 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 527 time to evaluate : 3.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 64 ARG Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain I residue 69 LYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 69 LYS Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 127 ASP Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain O residue 127 ASP Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 127 ASP Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 127 ASP Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain S residue 69 LYS Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain U residue 18 GLU Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain U residue 127 ASP Chi-restraints excluded: chain V residue 18 GLU Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain V residue 127 ASP Chi-restraints excluded: chain W residue 64 ARG Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 127 ASP Chi-restraints excluded: chain X residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 97 optimal weight: 9.9990 chunk 211 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 248 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 219 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 135 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 289 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN B 84 GLN C 84 GLN D 84 GLN E 76 GLN F 84 GLN H 76 GLN H 84 GLN I 84 GLN J 84 GLN K 84 GLN L 84 GLN M 84 GLN N 84 GLN O 84 GLN P 76 GLN P 84 GLN Q 84 GLN R 76 GLN S 84 GLN T 84 GLN U 84 GLN V 84 GLN W 84 GLN X 84 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.141853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.133197 restraints weight = 30916.867| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 0.66 r_work: 0.3272 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 31392 Z= 0.204 Angle : 0.564 5.461 42240 Z= 0.310 Chirality : 0.040 0.122 4440 Planarity : 0.003 0.021 5568 Dihedral : 4.448 18.447 4056 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.42 % Allowed : 13.51 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 2.50 (0.13), residues: 3672 helix: 2.17 (0.09), residues: 2904 sheet: None (None), residues: 0 loop : -0.34 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 94 HIS 0.007 0.002 HIS I 152 PHE 0.013 0.002 PHE H 42 TYR 0.021 0.003 TYR D 40 ARG 0.005 0.001 ARG W 64 Details of bonding type rmsd hydrogen bonds : bond 0.09609 ( 1992) hydrogen bonds : angle 3.49636 ( 5976) covalent geometry : bond 0.00458 (31392) covalent geometry : angle 0.56421 (42240) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 538 time to evaluate : 3.539 Fit side-chains REVERT: A 30 TYR cc_start: 0.8996 (t80) cc_final: 0.8767 (t80) REVERT: B 30 TYR cc_start: 0.8967 (t80) cc_final: 0.8741 (t80) REVERT: B 44 ARG cc_start: 0.8778 (mtp180) cc_final: 0.8569 (mtm180) REVERT: B 64 ARG cc_start: 0.8344 (ptm160) cc_final: 0.7758 (ttt180) REVERT: C 30 TYR cc_start: 0.8958 (t80) cc_final: 0.8730 (t80) REVERT: C 64 ARG cc_start: 0.8051 (ttt180) cc_final: 0.7840 (ttt180) REVERT: D 30 TYR cc_start: 0.8972 (t80) cc_final: 0.8741 (t80) REVERT: E 141 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7437 (mp0) REVERT: F 30 TYR cc_start: 0.8951 (t80) cc_final: 0.8730 (t80) REVERT: G 30 TYR cc_start: 0.8964 (t80) cc_final: 0.8730 (t80) REVERT: G 54 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8716 (mttm) REVERT: H 30 TYR cc_start: 0.8963 (t80) cc_final: 0.8733 (t80) REVERT: I 64 ARG cc_start: 0.8416 (ttp-110) cc_final: 0.7297 (ttt180) REVERT: J 30 TYR cc_start: 0.8966 (t80) cc_final: 0.8753 (t80) REVERT: K 30 TYR cc_start: 0.8952 (t80) cc_final: 0.8727 (t80) REVERT: L 30 TYR cc_start: 0.8944 (t80) cc_final: 0.8707 (t80) REVERT: M 30 TYR cc_start: 0.8963 (t80) cc_final: 0.8743 (t80) REVERT: M 43 ASP cc_start: 0.8295 (t70) cc_final: 0.8094 (t70) REVERT: N 30 TYR cc_start: 0.8970 (t80) cc_final: 0.8763 (t80) REVERT: N 101 MET cc_start: 0.8622 (mmt) cc_final: 0.8388 (mmt) REVERT: O 30 TYR cc_start: 0.8986 (t80) cc_final: 0.8754 (t80) REVERT: O 64 ARG cc_start: 0.7991 (ttp-110) cc_final: 0.7233 (ttt180) REVERT: P 30 TYR cc_start: 0.8964 (t80) cc_final: 0.8738 (t80) REVERT: Q 30 TYR cc_start: 0.8975 (t80) cc_final: 0.8756 (t80) REVERT: R 30 TYR cc_start: 0.8947 (t80) cc_final: 0.8717 (t80) REVERT: T 30 TYR cc_start: 0.8974 (t80) cc_final: 0.8735 (t80) REVERT: U 30 TYR cc_start: 0.8955 (t80) cc_final: 0.8723 (t80) REVERT: U 64 ARG cc_start: 0.8350 (ttp-110) cc_final: 0.7287 (ttt180) REVERT: V 30 TYR cc_start: 0.8960 (t80) cc_final: 0.8718 (t80) REVERT: W 30 TYR cc_start: 0.8951 (t80) cc_final: 0.8709 (t80) REVERT: X 30 TYR cc_start: 0.8973 (t80) cc_final: 0.8749 (t80) REVERT: X 64 ARG cc_start: 0.7978 (ttp-170) cc_final: 0.7404 (ttp-170) outliers start: 115 outliers final: 80 residues processed: 614 average time/residue: 2.5808 time to fit residues: 1752.1744 Evaluate side-chains 622 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 541 time to evaluate : 3.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 64 ARG Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 69 LYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 69 LYS Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 127 ASP Chi-restraints excluded: chain O residue 18 GLU Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain O residue 127 ASP Chi-restraints excluded: chain P residue 18 GLU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 127 ASP Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 127 ASP Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 69 LYS Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 127 ASP Chi-restraints excluded: chain U residue 18 GLU Chi-restraints excluded: chain U residue 54 LYS Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain U residue 127 ASP Chi-restraints excluded: chain V residue 18 GLU Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain V residue 127 ASP Chi-restraints excluded: chain W residue 18 GLU Chi-restraints excluded: chain W residue 64 ARG Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 127 ASP Chi-restraints excluded: chain X residue 18 GLU Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 127 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 270 optimal weight: 20.0000 chunk 262 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 277 optimal weight: 6.9990 chunk 335 optimal weight: 0.9990 chunk 267 optimal weight: 0.8980 chunk 257 optimal weight: 10.0000 chunk 341 optimal weight: 4.9990 chunk 269 optimal weight: 5.9990 chunk 345 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 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 84 GLN C 84 GLN D 84 GLN E 76 GLN F 84 GLN H 76 GLN H 84 GLN I 84 GLN J 84 GLN K 76 GLN L 84 GLN M 84 GLN N 84 GLN O 84 GLN P 76 GLN P 84 GLN R 76 GLN S 84 GLN T 84 GLN U 84 GLN V 84 GLN X 84 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.146586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.138046 restraints weight = 31035.365| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 0.66 r_work: 0.3327 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 31392 Z= 0.144 Angle : 0.463 3.893 42240 Z= 0.262 Chirality : 0.036 0.118 4440 Planarity : 0.002 0.020 5568 Dihedral : 4.209 17.616 4056 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.65 % Allowed : 15.12 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.07 (0.13), residues: 3672 helix: 2.59 (0.09), residues: 2904 sheet: None (None), residues: 0 loop : -0.19 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP T 94 HIS 0.004 0.001 HIS B 152 PHE 0.010 0.001 PHE B 42 TYR 0.017 0.002 TYR I 138 ARG 0.004 0.000 ARG W 64 Details of bonding type rmsd hydrogen bonds : bond 0.07732 ( 1992) hydrogen bonds : angle 3.20550 ( 5976) covalent geometry : bond 0.00294 (31392) covalent geometry : angle 0.46257 (42240) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 600 time to evaluate : 3.390 Fit side-chains REVERT: A 141 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7384 (mp0) REVERT: B 44 ARG cc_start: 0.8793 (mtp180) cc_final: 0.8371 (mtm180) REVERT: B 64 ARG cc_start: 0.8376 (ptm160) cc_final: 0.7710 (ttt180) REVERT: B 141 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7417 (mp0) REVERT: E 141 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7409 (mp0) REVERT: G 141 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7362 (mp0) REVERT: I 54 LYS cc_start: 0.9007 (ttpp) cc_final: 0.8774 (mtpp) REVERT: I 64 ARG cc_start: 0.8434 (ttp-110) cc_final: 0.8029 (ttt180) REVERT: L 141 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7366 (mp0) REVERT: M 43 ASP cc_start: 0.8373 (t70) cc_final: 0.8131 (t70) REVERT: M 141 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7412 (mp0) REVERT: N 101 MET cc_start: 0.8494 (mmt) cc_final: 0.8263 (mmt) REVERT: O 64 ARG cc_start: 0.8027 (ttp-110) cc_final: 0.7237 (ttt180) REVERT: Q 141 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7385 (mp0) REVERT: U 64 ARG cc_start: 0.8261 (ttp-110) cc_final: 0.7863 (ptt180) REVERT: X 64 ARG cc_start: 0.7934 (ttp-170) cc_final: 0.7677 (ttp-170) outliers start: 89 outliers final: 72 residues processed: 672 average time/residue: 2.2800 time to fit residues: 1698.6376 Evaluate side-chains 631 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 559 time to evaluate : 3.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 64 ARG Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 69 LYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 69 LYS Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 127 ASP Chi-restraints excluded: chain O residue 18 GLU Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain P residue 18 GLU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 127 ASP Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 69 LYS Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 127 ASP Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 69 LYS Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 127 ASP Chi-restraints excluded: chain U residue 18 GLU Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain U residue 127 ASP Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain V residue 127 ASP Chi-restraints excluded: chain W residue 18 GLU Chi-restraints excluded: chain W residue 64 ARG Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 127 ASP Chi-restraints excluded: chain X residue 18 GLU Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 127 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 59 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 225 optimal weight: 0.3980 chunk 15 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 325 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 318 optimal weight: 10.0000 chunk 259 optimal weight: 0.7980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN C 84 GLN D 84 GLN F 84 GLN H 84 GLN I 84 GLN J 84 GLN M 84 GLN N 84 GLN O 84 GLN P 84 GLN S 84 GLN T 84 GLN U 84 GLN V 84 GLN X 84 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.149511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.140891 restraints weight = 31018.263| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 0.67 r_work: 0.3381 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 31392 Z= 0.116 Angle : 0.410 3.873 42240 Z= 0.236 Chirality : 0.035 0.115 4440 Planarity : 0.002 0.019 5568 Dihedral : 4.009 16.266 4056 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.50 % Allowed : 15.83 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 3.67 (0.14), residues: 3672 helix: 3.04 (0.09), residues: 2904 sheet: None (None), residues: 0 loop : -0.09 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP I 94 HIS 0.003 0.001 HIS I 152 PHE 0.007 0.001 PHE D 42 TYR 0.013 0.002 TYR I 138 ARG 0.002 0.000 ARG W 64 Details of bonding type rmsd hydrogen bonds : bond 0.06469 ( 1992) hydrogen bonds : angle 2.95721 ( 5976) covalent geometry : bond 0.00217 (31392) covalent geometry : angle 0.40995 (42240) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 600 time to evaluate : 3.466 Fit side-chains REVERT: A 141 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7400 (mp0) REVERT: B 44 ARG cc_start: 0.8783 (mtp180) cc_final: 0.8327 (mtm180) REVERT: B 64 ARG cc_start: 0.8400 (ptm160) cc_final: 0.7787 (ttt180) REVERT: B 141 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7415 (mp0) REVERT: E 141 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7421 (mp0) REVERT: G 141 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7379 (mp0) REVERT: I 64 ARG cc_start: 0.8411 (ttp-110) cc_final: 0.7983 (ttt180) REVERT: L 141 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7374 (mp0) REVERT: M 43 ASP cc_start: 0.8374 (t70) cc_final: 0.8093 (t70) REVERT: M 141 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7398 (mp0) REVERT: N 54 LYS cc_start: 0.9043 (ttpt) cc_final: 0.8605 (mtpp) REVERT: O 64 ARG cc_start: 0.8092 (ttp-110) cc_final: 0.7304 (ttt180) REVERT: Q 141 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7391 (mp0) REVERT: U 64 ARG cc_start: 0.8304 (ttp-110) cc_final: 0.7842 (ptt180) REVERT: X 64 ARG cc_start: 0.7940 (ttp-170) cc_final: 0.7511 (ttp-170) outliers start: 84 outliers final: 50 residues processed: 669 average time/residue: 3.0437 time to fit residues: 2265.5704 Evaluate side-chains 602 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 552 time to evaluate : 7.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 64 ARG Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 69 LYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain O residue 18 GLU Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain P residue 18 GLU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain Q residue 69 LYS Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 127 ASP Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain W residue 18 GLU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain X residue 18 GLU Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 127 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 235 optimal weight: 10.0000 chunk 353 optimal weight: 6.9990 chunk 218 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 223 optimal weight: 9.9990 chunk 254 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 chunk 214 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 189 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN C 84 GLN D 84 GLN F 84 GLN H 84 GLN I 84 GLN J 84 GLN M 84 GLN N 84 GLN O 84 GLN P 84 GLN S 84 GLN T 84 GLN U 84 GLN V 84 GLN X 84 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.142793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.134216 restraints weight = 31109.641| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 0.66 r_work: 0.3272 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 31392 Z= 0.192 Angle : 0.539 5.034 42240 Z= 0.297 Chirality : 0.039 0.116 4440 Planarity : 0.003 0.035 5568 Dihedral : 4.244 17.806 4056 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 0.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.56 % Allowed : 15.60 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 3.25 (0.13), residues: 3672 helix: 2.72 (0.09), residues: 2904 sheet: None (None), residues: 0 loop : -0.19 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP M 94 HIS 0.007 0.002 HIS O 152 PHE 0.011 0.002 PHE O 42 TYR 0.018 0.003 TYR D 40 ARG 0.003 0.001 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.09169 ( 1992) hydrogen bonds : angle 3.30860 ( 5976) covalent geometry : bond 0.00427 (31392) covalent geometry : angle 0.53906 (42240) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 533 time to evaluate : 3.662 Fit side-chains REVERT: A 141 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7406 (mp0) REVERT: B 64 ARG cc_start: 0.8316 (ptm160) cc_final: 0.7738 (ttt180) REVERT: B 141 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7423 (mp0) REVERT: E 141 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7422 (mp0) REVERT: F 141 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7419 (mp0) REVERT: G 141 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7371 (mp0) REVERT: I 64 ARG cc_start: 0.8363 (ttp-110) cc_final: 0.7225 (ttt180) REVERT: L 141 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7366 (mp0) REVERT: N 141 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7647 (mp0) REVERT: O 64 ARG cc_start: 0.8194 (ttp-110) cc_final: 0.7394 (ttt180) REVERT: Q 141 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7381 (mp0) REVERT: U 64 ARG cc_start: 0.8277 (ttp-110) cc_final: 0.7230 (ttt180) REVERT: W 64 ARG cc_start: 0.8269 (tpt170) cc_final: 0.7949 (ttt180) REVERT: X 64 ARG cc_start: 0.7977 (ttp-170) cc_final: 0.7616 (ttm110) outliers start: 86 outliers final: 77 residues processed: 610 average time/residue: 2.7164 time to fit residues: 1822.3171 Evaluate side-chains 634 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 557 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 64 ARG Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 64 ARG Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 69 LYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 69 LYS Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 127 ASP Chi-restraints excluded: chain O residue 18 GLU Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain O residue 127 ASP Chi-restraints excluded: chain P residue 18 GLU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 127 ASP Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 69 LYS Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 127 ASP Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 127 ASP Chi-restraints excluded: chain U residue 18 GLU Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain U residue 127 ASP Chi-restraints excluded: chain V residue 18 GLU Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain V residue 127 ASP Chi-restraints excluded: chain W residue 18 GLU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 127 ASP Chi-restraints excluded: chain X residue 18 GLU Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 127 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 26 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 357 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 275 optimal weight: 9.9990 chunk 289 optimal weight: 5.9990 chunk 319 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN C 84 GLN D 84 GLN F 84 GLN H 84 GLN I 84 GLN J 84 GLN M 84 GLN N 84 GLN O 84 GLN P 84 GLN S 84 GLN T 84 GLN U 84 GLN V 84 GLN X 84 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.143116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.134626 restraints weight = 30956.749| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 0.65 r_work: 0.3277 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 31392 Z= 0.187 Angle : 0.530 5.109 42240 Z= 0.293 Chirality : 0.039 0.119 4440 Planarity : 0.003 0.038 5568 Dihedral : 4.272 18.068 4056 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.47 % Allowed : 15.83 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 3.12 (0.13), residues: 3672 helix: 2.63 (0.09), residues: 2904 sheet: None (None), residues: 0 loop : -0.21 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP H 94 HIS 0.006 0.001 HIS K 152 PHE 0.011 0.002 PHE X 42 TYR 0.018 0.003 TYR D 40 ARG 0.004 0.001 ARG N 80 Details of bonding type rmsd hydrogen bonds : bond 0.08964 ( 1992) hydrogen bonds : angle 3.32039 ( 5976) covalent geometry : bond 0.00413 (31392) covalent geometry : angle 0.53039 (42240) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 557 time to evaluate : 3.546 Fit side-chains REVERT: A 141 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7398 (mp0) REVERT: B 44 ARG cc_start: 0.8754 (mtm180) cc_final: 0.8481 (mtm180) REVERT: B 64 ARG cc_start: 0.8317 (ptm160) cc_final: 0.7742 (ttt180) REVERT: B 141 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7435 (mp0) REVERT: E 141 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7425 (mp0) REVERT: F 141 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7426 (mp0) REVERT: G 141 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7370 (mp0) REVERT: I 64 ARG cc_start: 0.8363 (ttp-110) cc_final: 0.7213 (ttt180) REVERT: L 141 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7362 (mp0) REVERT: Q 141 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7388 (mp0) REVERT: U 64 ARG cc_start: 0.8292 (ttp-110) cc_final: 0.7257 (ttt180) REVERT: W 64 ARG cc_start: 0.8276 (tpt170) cc_final: 0.7959 (ttt180) REVERT: X 64 ARG cc_start: 0.7963 (ttp-170) cc_final: 0.7553 (ttp-170) outliers start: 83 outliers final: 80 residues processed: 629 average time/residue: 2.4330 time to fit residues: 1687.2341 Evaluate side-chains 632 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 552 time to evaluate : 3.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 64 ARG Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 64 ARG Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 69 LYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 69 LYS Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 127 ASP Chi-restraints excluded: chain O residue 18 GLU Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain O residue 127 ASP Chi-restraints excluded: chain P residue 18 GLU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 127 ASP Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 69 LYS Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 127 ASP Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 127 ASP Chi-restraints excluded: chain U residue 18 GLU Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain U residue 127 ASP Chi-restraints excluded: chain V residue 18 GLU Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain V residue 127 ASP Chi-restraints excluded: chain W residue 18 GLU Chi-restraints excluded: chain W residue 92 ASP Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 127 ASP Chi-restraints excluded: chain X residue 18 GLU Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 127 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 94 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 349 optimal weight: 10.0000 chunk 343 optimal weight: 0.9980 chunk 356 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 289 optimal weight: 1.9990 chunk 174 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN D 84 GLN F 84 GLN H 84 GLN I 84 GLN J 84 GLN M 84 GLN N 84 GLN O 84 GLN P 84 GLN S 84 GLN T 84 GLN U 84 GLN V 84 GLN X 84 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.146406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.137796 restraints weight = 31125.620| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 0.67 r_work: 0.3338 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 31392 Z= 0.133 Angle : 0.444 3.910 42240 Z= 0.253 Chirality : 0.036 0.116 4440 Planarity : 0.002 0.022 5568 Dihedral : 4.082 17.150 4056 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.41 % Allowed : 16.10 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 3.71 (0.13), residues: 3672 helix: 3.06 (0.09), residues: 2904 sheet: None (None), residues: 0 loop : -0.08 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 94 HIS 0.004 0.001 HIS K 152 PHE 0.008 0.001 PHE B 42 TYR 0.014 0.002 TYR I 138 ARG 0.003 0.000 ARG P 44 Details of bonding type rmsd hydrogen bonds : bond 0.07223 ( 1992) hydrogen bonds : angle 3.07241 ( 5976) covalent geometry : bond 0.00261 (31392) covalent geometry : angle 0.44407 (42240) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 602 time to evaluate : 3.618 Fit side-chains REVERT: A 141 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7384 (mp0) REVERT: B 64 ARG cc_start: 0.8409 (ptm160) cc_final: 0.7796 (ttt180) REVERT: B 141 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7408 (mp0) REVERT: E 141 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7411 (mp0) REVERT: F 141 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7397 (mp0) REVERT: G 141 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7357 (mp0) REVERT: I 64 ARG cc_start: 0.8360 (ttp-110) cc_final: 0.7091 (ttt180) REVERT: L 141 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7348 (mp0) REVERT: Q 141 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7376 (mp0) REVERT: T 141 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7371 (mp0) REVERT: U 64 ARG cc_start: 0.8296 (ttp-110) cc_final: 0.7207 (ttt180) REVERT: W 64 ARG cc_start: 0.8264 (tpt170) cc_final: 0.7919 (ttt180) REVERT: X 64 ARG cc_start: 0.7933 (ttp-170) cc_final: 0.7534 (ttp-170) outliers start: 81 outliers final: 78 residues processed: 674 average time/residue: 2.3965 time to fit residues: 1793.5286 Evaluate side-chains 657 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 579 time to evaluate : 3.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 64 ARG Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 69 LYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain L residue 69 LYS Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 127 ASP Chi-restraints excluded: chain O residue 18 GLU Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain O residue 127 ASP Chi-restraints excluded: chain P residue 18 GLU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 127 ASP Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 69 LYS Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 127 ASP Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 127 ASP Chi-restraints excluded: chain U residue 18 GLU Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain U residue 127 ASP Chi-restraints excluded: chain V residue 18 GLU Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain V residue 127 ASP Chi-restraints excluded: chain W residue 18 GLU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 127 ASP Chi-restraints excluded: chain X residue 18 GLU Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 127 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 116 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 332 optimal weight: 10.0000 chunk 195 optimal weight: 0.7980 chunk 183 optimal weight: 10.0000 chunk 226 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 GLN F 84 GLN H 84 GLN I 84 GLN J 84 GLN M 84 GLN N 84 GLN O 84 GLN P 84 GLN S 84 GLN T 84 GLN U 84 GLN X 84 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.146604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.137946 restraints weight = 30907.161| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 0.67 r_work: 0.3332 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 31392 Z= 0.139 Angle : 0.456 3.851 42240 Z= 0.258 Chirality : 0.036 0.116 4440 Planarity : 0.002 0.022 5568 Dihedral : 4.070 17.105 4056 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 0.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.35 % Allowed : 17.08 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.83 (0.13), residues: 3672 helix: 3.16 (0.09), residues: 2904 sheet: None (None), residues: 0 loop : -0.12 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP S 94 HIS 0.004 0.001 HIS I 152 PHE 0.009 0.001 PHE E 42 TYR 0.014 0.002 TYR I 138 ARG 0.005 0.001 ARG T 23 Details of bonding type rmsd hydrogen bonds : bond 0.07456 ( 1992) hydrogen bonds : angle 3.08451 ( 5976) covalent geometry : bond 0.00281 (31392) covalent geometry : angle 0.45565 (42240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30503.63 seconds wall clock time: 531 minutes 39.82 seconds (31899.82 seconds total)