Starting phenix.real_space_refine on Fri Mar 6 17:53:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fes_31562/03_2026/7fes_31562.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fes_31562/03_2026/7fes_31562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fes_31562/03_2026/7fes_31562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fes_31562/03_2026/7fes_31562.map" model { file = "/net/cci-nas-00/data/ceres_data/7fes_31562/03_2026/7fes_31562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fes_31562/03_2026/7fes_31562.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.021 sd= 0.119 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 98 5.16 5 C 10641 2.51 5 N 2819 2.21 5 O 3220 1.98 5 H 17095 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33873 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2402 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2422 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "C" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2411 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2426 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2419 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2422 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "G" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2422 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "H" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2422 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "I" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2418 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "J" Number of atoms: 2380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2380 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "K" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2422 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "L" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2422 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "M" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2463 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Chain: "N" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2422 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Time building chain proxies: 6.27, per 1000 atoms: 0.19 Number of scatterers: 33873 At special positions: 0 Unit cell: (120.4, 123.84, 102.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 O 3220 8.00 N 2819 7.00 C 10641 6.00 H 17095 1.00 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: 3.14 Conformation dependent library (CDL) restraints added in 962.1 milliseconds 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4116 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 18 sheets defined 49.1% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 removed outlier: 3.679A pdb=" N LYS A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 52 removed outlier: 3.614A pdb=" N ALA A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 81 removed outlier: 4.210A pdb=" N MET A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 75 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 141 through 154 removed outlier: 3.888A pdb=" N LEU A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 170 removed outlier: 3.588A pdb=" N ILE A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG A 170 " --> pdb=" O ARG A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.518A pdb=" N ALA A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 36 through 53 removed outlier: 3.704A pdb=" N ALA B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 83 removed outlier: 4.105A pdb=" N MET B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 83 " --> pdb=" O THR B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 104 Processing helix chain 'B' and resid 139 through 155 removed outlier: 3.986A pdb=" N LEU B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 170 removed outlier: 3.680A pdb=" N ASP B 167 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 181 removed outlier: 3.586A pdb=" N GLU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 25 removed outlier: 3.613A pdb=" N LYS C 25 " --> pdb=" O SER C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 54 removed outlier: 3.660A pdb=" N ALA C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 83 removed outlier: 4.470A pdb=" N THR C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN C 81 " --> pdb=" O TYR C 77 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE C 83 " --> pdb=" O THR C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 104 Processing helix chain 'C' and resid 139 through 156 removed outlier: 3.825A pdb=" N LEU C 144 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 146 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP C 147 " --> pdb=" O LEU C 143 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 167 removed outlier: 3.725A pdb=" N ASP C 167 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 181 removed outlier: 3.531A pdb=" N LEU C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 24 Processing helix chain 'D' and resid 36 through 53 removed outlier: 3.640A pdb=" N ALA D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 42 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU D 53 " --> pdb=" O PHE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 75 Processing helix chain 'D' and resid 76 through 83 removed outlier: 3.788A pdb=" N ILE D 83 " --> pdb=" O THR D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 104 removed outlier: 3.779A pdb=" N LEU D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 158 removed outlier: 3.924A pdb=" N LEU D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP D 147 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR D 157 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 169 removed outlier: 3.610A pdb=" N ILE D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP D 167 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 181 removed outlier: 3.869A pdb=" N GLU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 26 removed outlier: 3.966A pdb=" N ASP E 26 " --> pdb=" O ARG E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 50 removed outlier: 3.558A pdb=" N SER E 42 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 83 removed outlier: 4.414A pdb=" N MET E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE E 83 " --> pdb=" O THR E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 104 Processing helix chain 'E' and resid 105 through 106 No H-bonds generated for 'chain 'E' and resid 105 through 106' Processing helix chain 'E' and resid 107 through 109 No H-bonds generated for 'chain 'E' and resid 107 through 109' Processing helix chain 'E' and resid 139 through 158 removed outlier: 4.644A pdb=" N LEU E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG E 146 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 153 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 170 removed outlier: 3.595A pdb=" N ILE E 164 " --> pdb=" O PRO E 160 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG E 170 " --> pdb=" O ARG E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 181 removed outlier: 3.565A pdb=" N LEU E 180 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 25 removed outlier: 3.623A pdb=" N LEU F 24 " --> pdb=" O TYR F 20 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS F 25 " --> pdb=" O SER F 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 20 through 25' Processing helix chain 'F' and resid 36 through 52 removed outlier: 3.515A pdb=" N ALA F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER F 42 " --> pdb=" O ASN F 38 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER F 45 " --> pdb=" O ASN F 41 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 83 removed outlier: 3.953A pdb=" N MET F 74 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR F 79 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN F 81 " --> pdb=" O TYR F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.800A pdb=" N GLY F 106 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 154 removed outlier: 3.836A pdb=" N LEU F 145 " --> pdb=" O ARG F 141 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG F 146 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP F 147 " --> pdb=" O LEU F 143 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 168 removed outlier: 3.547A pdb=" N ASP F 167 " --> pdb=" O VAL F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 181 removed outlier: 3.696A pdb=" N GLU F 181 " --> pdb=" O GLU F 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 24 Processing helix chain 'G' and resid 36 through 54 removed outlier: 3.551A pdb=" N SER G 42 " --> pdb=" O ASN G 38 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER G 45 " --> pdb=" O ASN G 41 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA G 52 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 75 Processing helix chain 'G' and resid 76 through 81 Processing helix chain 'G' and resid 96 through 104 Processing helix chain 'G' and resid 139 through 158 removed outlier: 4.060A pdb=" N LEU G 143 " --> pdb=" O ALA G 139 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU G 144 " --> pdb=" O LYS G 140 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU G 145 " --> pdb=" O ARG G 141 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG G 146 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP G 147 " --> pdb=" O LEU G 143 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU G 153 " --> pdb=" O LEU G 149 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA G 154 " --> pdb=" O ASN G 150 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 169 removed outlier: 3.700A pdb=" N GLU G 165 " --> pdb=" O LEU G 161 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG G 166 " --> pdb=" O GLU G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 181 removed outlier: 3.788A pdb=" N GLU G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 24 removed outlier: 3.532A pdb=" N LEU H 24 " --> pdb=" O TYR H 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 20 through 24' Processing helix chain 'H' and resid 36 through 49 removed outlier: 3.525A pdb=" N ALA H 40 " --> pdb=" O ASP H 36 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN H 41 " --> pdb=" O ASP H 37 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER H 42 " --> pdb=" O ASN H 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE H 43 " --> pdb=" O VAL H 39 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE H 49 " --> pdb=" O SER H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 81 removed outlier: 4.007A pdb=" N MET H 74 " --> pdb=" O ILE H 70 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR H 79 " --> pdb=" O ALA H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 105 removed outlier: 3.713A pdb=" N ALA H 100 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE H 101 " --> pdb=" O SER H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 157 removed outlier: 3.940A pdb=" N LEU H 143 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU H 144 " --> pdb=" O LYS H 140 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG H 146 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASP H 147 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS H 148 " --> pdb=" O LEU H 144 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL H 152 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA H 154 " --> pdb=" O ASN H 150 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU H 155 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 168 removed outlier: 3.503A pdb=" N ARG H 166 " --> pdb=" O GLU H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 181 removed outlier: 4.032A pdb=" N GLU H 181 " --> pdb=" O GLU H 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 26 Processing helix chain 'I' and resid 36 through 54 removed outlier: 3.511A pdb=" N ALA I 40 " --> pdb=" O ASP I 36 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN I 41 " --> pdb=" O ASP I 37 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER I 42 " --> pdb=" O ASN I 38 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER I 45 " --> pdb=" O ASN I 41 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU I 48 " --> pdb=" O VAL I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 75 Processing helix chain 'I' and resid 76 through 83 Processing helix chain 'I' and resid 96 through 104 removed outlier: 3.759A pdb=" N ALA I 100 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE I 101 " --> pdb=" O SER I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 109 No H-bonds generated for 'chain 'I' and resid 107 through 109' Processing helix chain 'I' and resid 139 through 149 removed outlier: 3.766A pdb=" N LEU I 143 " --> pdb=" O ALA I 139 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU I 144 " --> pdb=" O LYS I 140 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU I 149 " --> pdb=" O LEU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 158 removed outlier: 4.393A pdb=" N ALA I 154 " --> pdb=" O ASN I 150 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLU I 155 " --> pdb=" O LYS I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 169 removed outlier: 3.590A pdb=" N GLU I 165 " --> pdb=" O LEU I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 181 removed outlier: 3.724A pdb=" N GLU I 181 " --> pdb=" O GLU I 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 52 removed outlier: 3.597A pdb=" N ASN J 41 " --> pdb=" O ASP J 37 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU J 50 " --> pdb=" O GLN J 46 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA J 52 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 76 removed outlier: 3.710A pdb=" N ILE J 76 " --> pdb=" O GLY J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 105 Processing helix chain 'J' and resid 139 through 153 removed outlier: 4.178A pdb=" N LEU J 144 " --> pdb=" O LYS J 140 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN J 150 " --> pdb=" O ARG J 146 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU J 153 " --> pdb=" O LEU J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 162 No H-bonds generated for 'chain 'J' and resid 160 through 162' Processing helix chain 'J' and resid 163 through 169 removed outlier: 3.651A pdb=" N ASP J 167 " --> pdb=" O VAL J 163 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP J 169 " --> pdb=" O GLU J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 181 removed outlier: 3.847A pdb=" N GLU J 181 " --> pdb=" O GLU J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 25 Processing helix chain 'K' and resid 36 through 53 removed outlier: 3.899A pdb=" N ALA K 40 " --> pdb=" O ASP K 36 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN K 41 " --> pdb=" O ASP K 37 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER K 42 " --> pdb=" O ASN K 38 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER K 45 " --> pdb=" O ASN K 41 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU K 50 " --> pdb=" O GLN K 46 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA K 51 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA K 52 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU K 53 " --> pdb=" O PHE K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 75 Processing helix chain 'K' and resid 76 through 83 removed outlier: 3.874A pdb=" N GLN K 81 " --> pdb=" O TYR K 77 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE K 83 " --> pdb=" O THR K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 105 Processing helix chain 'K' and resid 139 through 158 removed outlier: 4.850A pdb=" N LEU K 144 " --> pdb=" O LYS K 140 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG K 146 " --> pdb=" O ILE K 142 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP K 147 " --> pdb=" O LEU K 143 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN K 150 " --> pdb=" O ARG K 146 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL K 152 " --> pdb=" O LYS K 148 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA K 154 " --> pdb=" O ASN K 150 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU K 155 " --> pdb=" O LYS K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 169 removed outlier: 3.586A pdb=" N ASP K 169 " --> pdb=" O GLU K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 181 Processing helix chain 'L' and resid 20 through 25 Processing helix chain 'L' and resid 38 through 54 removed outlier: 3.697A pdb=" N SER L 42 " --> pdb=" O ASN L 38 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER L 45 " --> pdb=" O ASN L 41 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLN L 46 " --> pdb=" O SER L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 76 removed outlier: 3.595A pdb=" N ILE L 76 " --> pdb=" O GLY L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 removed outlier: 3.989A pdb=" N ILE L 83 " --> pdb=" O THR L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 105 Processing helix chain 'L' and resid 141 through 151 removed outlier: 3.679A pdb=" N ARG L 146 " --> pdb=" O ILE L 142 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASP L 147 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 157 Processing helix chain 'L' and resid 161 through 169 removed outlier: 3.715A pdb=" N ARG L 166 " --> pdb=" O GLU L 162 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP L 169 " --> pdb=" O GLU L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 181 removed outlier: 3.808A pdb=" N GLU L 181 " --> pdb=" O GLU L 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 24 Processing helix chain 'M' and resid 39 through 54 removed outlier: 3.900A pdb=" N SER M 45 " --> pdb=" O ASN M 41 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN M 46 " --> pdb=" O SER M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 75 Processing helix chain 'M' and resid 76 through 83 removed outlier: 3.592A pdb=" N GLN M 81 " --> pdb=" O TYR M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 103 Processing helix chain 'M' and resid 139 through 157 removed outlier: 3.530A pdb=" N LEU M 143 " --> pdb=" O ALA M 139 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU M 144 " --> pdb=" O LYS M 140 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU M 145 " --> pdb=" O ARG M 141 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG M 146 " --> pdb=" O ILE M 142 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASP M 147 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN M 150 " --> pdb=" O ARG M 146 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL M 152 " --> pdb=" O LYS M 148 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA M 154 " --> pdb=" O ASN M 150 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLU M 155 " --> pdb=" O LYS M 151 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG M 156 " --> pdb=" O VAL M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 169 removed outlier: 3.538A pdb=" N GLU M 165 " --> pdb=" O LEU M 161 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG M 166 " --> pdb=" O GLU M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 181 removed outlier: 4.003A pdb=" N GLU M 181 " --> pdb=" O GLU M 177 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 25 Processing helix chain 'N' and resid 36 through 52 removed outlier: 3.819A pdb=" N ASN N 41 " --> pdb=" O ASP N 37 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER N 42 " --> pdb=" O ASN N 38 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU N 50 " --> pdb=" O GLN N 46 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA N 52 " --> pdb=" O LEU N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 75 Processing helix chain 'N' and resid 76 through 83 Processing helix chain 'N' and resid 98 through 105 Processing helix chain 'N' and resid 139 through 149 removed outlier: 3.698A pdb=" N LEU N 143 " --> pdb=" O ALA N 139 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU N 144 " --> pdb=" O LYS N 140 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU N 145 " --> pdb=" O ARG N 141 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG N 146 " --> pdb=" O ILE N 142 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP N 147 " --> pdb=" O LEU N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 157 Processing helix chain 'N' and resid 160 through 170 Processing helix chain 'N' and resid 175 through 181 removed outlier: 3.503A pdb=" N ALA N 179 " --> pdb=" O SER N 175 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU N 181 " --> pdb=" O GLU N 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 90 removed outlier: 6.423A pdb=" N THR A 89 " --> pdb=" O TYR A 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 89 through 90 removed outlier: 6.299A pdb=" N THR B 89 " --> pdb=" O TYR B 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 89 through 90 removed outlier: 6.453A pdb=" N THR C 89 " --> pdb=" O TYR C 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 94 through 95 Processing sheet with id=AA5, first strand: chain 'E' and resid 89 through 90 removed outlier: 6.462A pdb=" N THR E 89 " --> pdb=" O TYR E 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 89 through 90 removed outlier: 6.611A pdb=" N THR F 89 " --> pdb=" O TYR F 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 94 through 95 Processing sheet with id=AA8, first strand: chain 'G' and resid 89 through 90 removed outlier: 6.477A pdb=" N THR G 89 " --> pdb=" O TYR G 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 94 through 95 Processing sheet with id=AB1, first strand: chain 'H' and resid 89 through 90 removed outlier: 6.734A pdb=" N THR H 89 " --> pdb=" O TYR H 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'H' and resid 94 through 95 Processing sheet with id=AB3, first strand: chain 'I' and resid 89 through 90 removed outlier: 6.771A pdb=" N THR I 89 " --> pdb=" O TYR I 112 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS I 187 " --> pdb=" O ARG I 111 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA I 113 " --> pdb=" O LYS I 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'J' and resid 89 through 90 removed outlier: 6.881A pdb=" N THR J 89 " --> pdb=" O TYR J 112 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS J 187 " --> pdb=" O ARG J 111 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA J 113 " --> pdb=" O LYS J 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'J' and resid 94 through 95 Processing sheet with id=AB6, first strand: chain 'K' and resid 89 through 90 removed outlier: 6.688A pdb=" N THR K 89 " --> pdb=" O TYR K 112 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS K 187 " --> pdb=" O ARG K 111 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA K 113 " --> pdb=" O LYS K 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'L' and resid 89 through 90 removed outlier: 6.608A pdb=" N THR L 89 " --> pdb=" O TYR L 112 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS L 187 " --> pdb=" O ARG L 111 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA L 113 " --> pdb=" O LYS L 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'M' and resid 89 through 90 removed outlier: 6.951A pdb=" N THR M 89 " --> pdb=" O TYR M 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'N' and resid 89 through 90 removed outlier: 6.715A pdb=" N THR N 89 " --> pdb=" O TYR N 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 434 hydrogen bonds defined for protein. 1191 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: 7.04 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 17081 1.03 - 1.23: 1137 1.23 - 1.43: 5572 1.43 - 1.63: 10083 1.63 - 1.83: 182 Bond restraints: 34055 Sorted by residual: bond pdb=" C ARG N 166 " pdb=" O ARG N 166 " ideal model delta sigma weight residual 1.237 1.306 -0.069 1.17e-02 7.31e+03 3.50e+01 bond pdb=" N ARG N 170 " pdb=" CA ARG N 170 " ideal model delta sigma weight residual 1.452 1.509 -0.057 1.22e-02 6.72e+03 2.17e+01 bond pdb=" CA ALA M 105 " pdb=" CB ALA M 105 " ideal model delta sigma weight residual 1.527 1.495 0.033 7.60e-03 1.73e+04 1.83e+01 bond pdb=" C ILE M 28 " pdb=" O ILE M 28 " ideal model delta sigma weight residual 1.234 1.194 0.041 1.11e-02 8.12e+03 1.35e+01 bond pdb=" C ALA M 100 " pdb=" O ALA M 100 " ideal model delta sigma weight residual 1.235 1.279 -0.044 1.26e-02 6.30e+03 1.23e+01 ... (remaining 34050 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.03: 61727 10.03 - 20.06: 14 20.06 - 30.09: 35 30.09 - 40.12: 25 40.12 - 50.15: 5 Bond angle restraints: 61806 Sorted by residual: angle pdb=" C ASN J 116 " pdb=" N SER J 117 " pdb=" H SER J 117 " ideal model delta sigma weight residual 124.67 74.53 50.15 3.00e+00 1.11e-01 2.79e+02 angle pdb=" CA SER J 117 " pdb=" N SER J 117 " pdb=" H SER J 117 " ideal model delta sigma weight residual 114.38 65.04 49.33 3.00e+00 1.11e-01 2.70e+02 angle pdb=" C PHE J 82 " pdb=" CA PHE J 82 " pdb=" HA PHE J 82 " ideal model delta sigma weight residual 109.00 68.21 40.79 3.00e+00 1.11e-01 1.85e+02 angle pdb=" N ASP J 37 " pdb=" CA ASP J 37 " pdb=" HA ASP J 37 " ideal model delta sigma weight residual 110.00 69.38 40.62 3.00e+00 1.11e-01 1.83e+02 angle pdb=" C ASP J 26 " pdb=" CA ASP J 26 " pdb=" HA ASP J 26 " ideal model delta sigma weight residual 109.00 68.83 40.17 3.00e+00 1.11e-01 1.79e+02 ... (remaining 61801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.15: 13627 18.15 - 36.30: 1655 36.30 - 54.46: 442 54.46 - 72.61: 86 72.61 - 90.76: 21 Dihedral angle restraints: 15831 sinusoidal: 8877 harmonic: 6954 Sorted by residual: dihedral pdb=" CA SER F 97 " pdb=" C SER F 97 " pdb=" N MET F 98 " pdb=" CA MET F 98 " ideal model delta harmonic sigma weight residual 180.00 -151.21 -28.79 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ILE M 63 " pdb=" C ILE M 63 " pdb=" N ASN M 64 " pdb=" CA ASN M 64 " ideal model delta harmonic sigma weight residual 180.00 152.13 27.87 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA ILE I 63 " pdb=" C ILE I 63 " pdb=" N ASN I 64 " pdb=" CA ASN I 64 " ideal model delta harmonic sigma weight residual 180.00 152.29 27.71 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 15828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.366: 2703 0.366 - 0.732: 6 0.732 - 1.098: 0 1.098 - 1.464: 3 1.464 - 1.830: 4 Chirality restraints: 2716 Sorted by residual: chirality pdb=" CG LEU F 31 " pdb=" CB LEU F 31 " pdb=" CD1 LEU F 31 " pdb=" CD2 LEU F 31 " both_signs ideal model delta sigma weight residual False -2.59 -0.76 -1.83 2.00e-01 2.50e+01 8.38e+01 chirality pdb=" CG LEU F 103 " pdb=" CB LEU F 103 " pdb=" CD1 LEU F 103 " pdb=" CD2 LEU F 103 " both_signs ideal model delta sigma weight residual False -2.59 -0.82 -1.77 2.00e-01 2.50e+01 7.81e+01 chirality pdb=" CG LEU M 50 " pdb=" CB LEU M 50 " pdb=" CD1 LEU M 50 " pdb=" CD2 LEU M 50 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.53e+01 ... (remaining 2713 not shown) Planarity restraints: 5020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN N 159 " -0.240 2.00e-02 2.50e+03 2.88e-01 1.24e+03 pdb=" CD GLN N 159 " 0.024 2.00e-02 2.50e+03 pdb=" OE1 GLN N 159 " 0.228 2.00e-02 2.50e+03 pdb=" NE2 GLN N 159 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN N 159 " 0.433 2.00e-02 2.50e+03 pdb="HE22 GLN N 159 " -0.447 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 81 " 0.092 2.00e-02 2.50e+03 9.49e-02 1.35e+02 pdb=" CD GLN A 81 " -0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN A 81 " -0.082 2.00e-02 2.50e+03 pdb=" NE2 GLN A 81 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 81 " 0.142 2.00e-02 2.50e+03 pdb="HE22 GLN A 81 " -0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 121 " -0.035 2.00e-02 2.50e+03 6.87e-02 4.72e+01 pdb=" N HIS E 122 " 0.118 2.00e-02 2.50e+03 pdb=" CA HIS E 122 " -0.030 2.00e-02 2.50e+03 pdb=" H HIS E 122 " -0.053 2.00e-02 2.50e+03 ... (remaining 5017 not shown) Histogram of nonbonded interaction distances: 0.51 - 1.33: 30 1.33 - 2.15: 1651 2.15 - 2.96: 94075 2.96 - 3.78: 122377 3.78 - 4.60: 207644 Warning: very small nonbonded interaction distances. Nonbonded interactions: 425777 Sorted by model distance: nonbonded pdb=" CD1 ILE A 83 " pdb=" HD2 PRO A 85 " model vdw 0.512 2.920 nonbonded pdb="HD11 LEU F 50 " pdb=" HE2 LYS F 57 " model vdw 0.612 2.440 nonbonded pdb="HD12 ILE A 83 " pdb=" HD2 PRO A 85 " model vdw 0.670 2.440 nonbonded pdb=" CD1 LEU F 50 " pdb=" HE2 LYS F 57 " model vdw 0.745 2.920 nonbonded pdb="HD12 LEU F 50 " pdb=" HD2 LYS F 57 " model vdw 0.825 2.440 ... (remaining 425772 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 26 or (resid 27 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2 or name H or name HA )) or resid 28 through 55 or (resid 56 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name OE1 o \ r name OE2 or name H or name HA )) or (resid 57 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ ame HA )) or resid 58 through 106 or (resid 107 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H or \ name HA )) or resid 108 through 119 or (resid 120 and (name N or name CA or nam \ e C or name O or name CB or name CG or name SD or name CE or name H or name HA ) \ ) or resid 121 through 156 or (resid 157 and (name N or name CA or name C or nam \ e O or name CB or name OG1 or name CG2)) or (resid 158 and (name N or name CA or \ name C or name O )) or (resid 159 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name OE1 or name NE2)) or (resid 160 and (name \ N or name CA or name C or name O or name CB or name CG or name CD )) or (resid \ 161 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2)) or (resid 162 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name OE1 or name OE2)) or resid 163 through 189)) selection = (chain 'B' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or (resid 57 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z or name H or name HA )) or resid 58 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or resid 108 through 119 or (resid 120 and (name N o \ r name CA or name C or name O or name CB or name CG or name SD or name CE or nam \ e H or name HA )) or resid 121 through 156 or (resid 157 and (name N or name CA \ or name C or name O or name CB or name OG1 or name CG2)) or (resid 158 and (name \ N or name CA or name C or name O )) or (resid 159 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (res \ id 160 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or (resid 161 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2)) or (resid 162 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 163 \ through 189)) selection = (chain 'C' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 55 or (resid 56 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or (resid 57 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD or name CE or name NZ or name H or name HA \ )) or resid 58 through 106 or (resid 107 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD or name OE1 or name OE2 or name H or name \ HA )) or resid 108 through 119 or (resid 120 and (name N or name CA or name C or \ name O or name CB or name CG or name SD or name CE or name H or name HA )) or r \ esid 121 through 156 or (resid 157 and (name N or name CA or name C or name O or \ name CB or name OG1 or name CG2)) or (resid 158 and (name N or name CA or name \ C or name O )) or (resid 159 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name OE1 or name NE2)) or (resid 160 and (name N or \ name CA or name C or name O or name CB or name CG or name CD )) or (resid 161 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2)) or (resid 162 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name OE1 or name OE2)) or resid 163 through 189)) selection = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or resid 57 through 83 or (re \ sid 84 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 85 through 106 or (resid 107 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD or name OE1 or name OE2 or name H or name \ HA )) or resid 108 through 119 or (resid 120 and (name N or name CA or name C o \ r name O or name CB or name CG or name SD or name CE or name H or name HA )) or \ resid 121 through 156 or (resid 157 and (name N or name CA or name C or name O o \ r name CB or name OG1 or name CG2)) or (resid 158 and (name N or name CA or name \ C or name O )) or (resid 159 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name OE1 or name NE2)) or (resid 160 and (name N or \ name CA or name C or name O or name CB or name CG or name CD )) or (resid 161 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD1 or n \ ame CD2)) or (resid 162 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name OE1 or name OE2)) or resid 163 through 189)) selection = (chain 'E' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or (resid 57 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z or name H or name HA )) or resid 58 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or resid 108 through 156 or (resid 157 and (name N o \ r name CA or name C or name O or name CB or name OG1 or name CG2)) or (resid 158 \ and (name N or name CA or name C or name O )) or (resid 159 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name OE1 or name NE2 \ )) or (resid 160 and (name N or name CA or name C or name O or name CB or name C \ G or name CD )) or (resid 161 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2)) or (resid 162 and (name N or name CA or \ name C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or \ resid 163 through 186 or (resid 187 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 188 through 189)) selection = (chain 'F' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or (resid 57 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z or name H or name HA )) or resid 58 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or resid 108 through 119 or (resid 120 and (name N o \ r name CA or name C or name O or name CB or name CG or name SD or name CE or nam \ e H or name HA )) or resid 121 through 156 or (resid 157 and (name N or name CA \ or name C or name O or name CB or name OG1 or name CG2)) or (resid 158 and (name \ N or name CA or name C or name O )) or (resid 159 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (res \ id 160 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or (resid 161 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2)) or (resid 162 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 163 \ through 189)) selection = (chain 'G' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or (resid 57 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z or name H or name HA )) or resid 58 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or resid 108 through 119 or (resid 120 and (name N o \ r name CA or name C or name O or name CB or name CG or name SD or name CE or nam \ e H or name HA )) or resid 121 through 156 or (resid 157 and (name N or name CA \ or name C or name O or name CB or name OG1 or name CG2)) or (resid 158 and (name \ N or name CA or name C or name O )) or (resid 159 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (res \ id 160 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or (resid 161 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2)) or (resid 162 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 163 \ through 189)) selection = (chain 'H' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or (resid 57 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z or name H or name HA )) or resid 58 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or resid 108 through 119 or (resid 120 and (name N o \ r name CA or name C or name O or name CB or name CG or name SD or name CE or nam \ e H or name HA )) or resid 121 through 156 or (resid 157 and (name N or name CA \ or name C or name O or name CB or name OG1 or name CG2)) or (resid 158 and (name \ N or name CA or name C or name O )) or (resid 159 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (res \ id 160 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or (resid 161 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2)) or (resid 162 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 163 \ through 189)) selection = (chain 'I' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 56 or (re \ sid 57 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name CE or name NZ or name H or name HA )) or resid 58 through 106 or (res \ id 107 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or resid 108 through 119 or ( \ resid 120 and (name N or name CA or name C or name O or name CB or name CG or na \ me SD or name CE or name H or name HA )) or resid 121 through 156 or (resid 157 \ and (name N or name CA or name C or name O or name CB or name OG1 or name CG2)) \ or (resid 158 and (name N or name CA or name C or name O )) or (resid 159 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD or name OE \ 1 or name NE2)) or (resid 160 and (name N or name CA or name C or name O or name \ CB or name CG or name CD )) or (resid 161 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD1 or name CD2)) or (resid 162 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name OE1 or n \ ame OE2)) or resid 163 through 189)) selection = (chain 'J' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or (resid 57 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z or name H or name HA )) or resid 58 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or resid 108 through 119 or (resid 120 and (name N o \ r name CA or name C or name O or name CB or name CG or name SD or name CE or nam \ e H or name HA )) or resid 121 through 189)) selection = (chain 'K' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or (resid 57 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z or name H or name HA )) or resid 58 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or resid 108 through 119 or (resid 120 and (name N o \ r name CA or name C or name O or name CB or name CG or name SD or name CE or nam \ e H or name HA )) or resid 121 through 156 or (resid 157 and (name N or name CA \ or name C or name O or name CB or name OG1 or name CG2)) or (resid 158 and (name \ N or name CA or name C or name O )) or (resid 159 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (res \ id 160 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or (resid 161 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2)) or (resid 162 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 163 \ through 189)) selection = (chain 'L' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or (resid 57 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z or name H or name HA )) or resid 58 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or resid 108 through 119 or (resid 120 and (name N o \ r name CA or name C or name O or name CB or name CG or name SD or name CE or nam \ e H or name HA )) or resid 121 through 156 or (resid 157 and (name N or name CA \ or name C or name O or name CB or name OG1 or name CG2)) or (resid 158 and (name \ N or name CA or name C or name O )) or (resid 159 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (res \ id 160 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or (resid 161 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2)) or (resid 162 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 163 \ through 189)) selection = (chain 'M' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or (resid 57 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z or name H or name HA )) or resid 58 through 83 or (resid 84 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 85 through \ 119 or (resid 120 and (name N or name CA or name C or name O or name CB or name \ CG or name SD or name CE or name H or name HA )) or resid 121 through 139 or (re \ sid 140 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 141 through 156 or (resid 157 and (name N or name CA or name C or \ name O or name CB or name OG1 or name CG2)) or (resid 158 and (name N or name C \ A or name C or name O )) or (resid 159 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name OE1 or name NE2)) or (resid 160 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD )) or (re \ sid 161 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or (resid 162 and (name N or name CA or name C or name O or n \ ame CB or name CG or name CD or name OE1 or name OE2)) or resid 163 through 186 \ or (resid 187 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 188 through 189)) selection = (chain 'N' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or (resid 57 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z or name H or name HA )) or resid 58 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or resid 108 through 119 or (resid 120 and (name N o \ r name CA or name C or name O or name CB or name CG or name SD or name CE or nam \ e H or name HA )) or resid 121 through 156 or (resid 157 and (name N or name CA \ or name C or name O or name CB or name OG1 or name CG2)) or (resid 158 and (name \ N or name CA or name C or name O )) or (resid 159 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (res \ id 160 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or (resid 161 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2)) or (resid 162 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 163 \ through 189)) } 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: 0.530 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: 0.220 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 30.040 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.011 0.077 16960 Z= 0.487 Angle : 1.206 18.600 22854 Z= 0.694 Chirality : 0.101 1.830 2716 Planarity : 0.006 0.061 2926 Dihedral : 15.697 90.760 6418 Min Nonbonded Distance : 1.102 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 1.49 % Allowed : 17.69 % Favored : 80.81 % Rotamer: Outliers : 2.30 % Allowed : 9.93 % Favored : 87.77 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.10 (0.16), residues: 2142 helix: -3.75 (0.12), residues: 720 sheet: -4.08 (0.22), residues: 239 loop : -3.02 (0.19), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 141 TYR 0.035 0.002 TYR I 182 PHE 0.024 0.003 PHE D 49 HIS 0.007 0.003 HIS I 122 Details of bonding type rmsd covalent geometry : bond 0.01062 (16960) covalent geometry : angle 1.20629 (22854) hydrogen bonds : bond 0.35612 ( 434) hydrogen bonds : angle 11.01046 ( 1191) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 691 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 650 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ILE cc_start: 0.8949 (mt) cc_final: 0.8703 (mm) REVERT: C 108 LYS cc_start: 0.7479 (pttt) cc_final: 0.7029 (tttp) REVERT: C 122 HIS cc_start: 0.7863 (t70) cc_final: 0.7316 (t-90) REVERT: C 170 ARG cc_start: 0.7518 (ttm110) cc_final: 0.6921 (ttt90) REVERT: C 173 PHE cc_start: 0.7991 (m-10) cc_final: 0.7176 (m-10) REVERT: D 28 ILE cc_start: 0.8700 (mt) cc_final: 0.8469 (mm) REVERT: D 108 LYS cc_start: 0.7930 (pttp) cc_final: 0.7252 (tttp) REVERT: D 118 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7342 (mt-10) REVERT: D 173 PHE cc_start: 0.7978 (m-80) cc_final: 0.7522 (m-80) REVERT: E 58 GLU cc_start: 0.8400 (pp20) cc_final: 0.7901 (pm20) REVERT: E 163 VAL cc_start: 0.7881 (m) cc_final: 0.6822 (p) REVERT: E 165 GLU cc_start: 0.8648 (tp30) cc_final: 0.8328 (mt-10) REVERT: E 167 ASP cc_start: 0.7853 (p0) cc_final: 0.7621 (p0) REVERT: E 169 ASP cc_start: 0.7435 (t70) cc_final: 0.7142 (p0) REVERT: F 108 LYS cc_start: 0.7634 (ptpp) cc_final: 0.7298 (ptmm) REVERT: F 173 PHE cc_start: 0.7998 (m-80) cc_final: 0.7473 (m-80) REVERT: H 58 GLU cc_start: 0.7756 (pm20) cc_final: 0.7551 (pm20) REVERT: H 81 GLN cc_start: 0.7721 (tp40) cc_final: 0.7466 (tm-30) REVERT: H 101 PHE cc_start: 0.8344 (t80) cc_final: 0.8117 (t80) REVERT: H 165 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7237 (tp30) REVERT: I 58 GLU cc_start: 0.7107 (tp30) cc_final: 0.6523 (tp30) REVERT: I 162 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6662 (tm-30) REVERT: I 173 PHE cc_start: 0.7043 (m-80) cc_final: 0.6633 (m-80) REVERT: J 143 LEU cc_start: 0.8393 (tt) cc_final: 0.8174 (tp) REVERT: J 173 PHE cc_start: 0.7140 (m-80) cc_final: 0.6739 (m-10) REVERT: K 57 LYS cc_start: 0.8257 (mttt) cc_final: 0.8000 (mtpt) REVERT: K 162 GLU cc_start: 0.6554 (mp0) cc_final: 0.6002 (tm-30) REVERT: K 172 ASN cc_start: 0.7732 (p0) cc_final: 0.7503 (p0) REVERT: L 151 LYS cc_start: 0.8520 (tmtt) cc_final: 0.8270 (tptp) REVERT: L 167 ASP cc_start: 0.8722 (m-30) cc_final: 0.8176 (p0) REVERT: M 26 ASP cc_start: 0.8346 (p0) cc_final: 0.8067 (p0) REVERT: M 28 ILE cc_start: 0.9282 (mt) cc_final: 0.8951 (mm) REVERT: M 122 HIS cc_start: 0.7333 (t70) cc_final: 0.7132 (t70) REVERT: M 178 GLU cc_start: 0.8470 (pt0) cc_final: 0.8128 (pm20) REVERT: N 38 ASN cc_start: 0.8081 (m110) cc_final: 0.7812 (m110) REVERT: N 57 LYS cc_start: 0.7703 (mtpp) cc_final: 0.7259 (tttt) REVERT: N 169 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7975 (p0) REVERT: N 178 GLU cc_start: 0.7972 (pt0) cc_final: 0.7636 (pm20) outliers start: 41 outliers final: 27 residues processed: 685 average time/residue: 0.3882 time to fit residues: 368.6705 Evaluate side-chains 454 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 426 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain I residue 182 TYR Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 59 ILE Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 98 MET Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain K residue 101 PHE Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 162 GLU Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 186 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 46 GLN A 122 HIS B 41 ASN C 41 ASN C 159 GLN D 41 ASN D 116 ASN E 41 ASN G 172 ASN H 41 ASN H 150 ASN I 41 ASN I 172 ASN ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 ASN L 172 ASN M 38 ASN N 41 ASN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.133784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.113680 restraints weight = 119608.411| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 5.58 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16960 Z= 0.165 Angle : 0.789 15.435 22854 Z= 0.412 Chirality : 0.093 1.722 2716 Planarity : 0.005 0.060 2926 Dihedral : 8.156 84.021 2416 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.51 % Allowed : 12.84 % Favored : 86.65 % Rotamer: Outliers : 3.42 % Allowed : 19.80 % Favored : 76.78 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.82 (0.15), residues: 2142 helix: -2.84 (0.14), residues: 889 sheet: -3.85 (0.23), residues: 272 loop : -3.28 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 27 TYR 0.017 0.001 TYR M 20 PHE 0.018 0.002 PHE B 173 HIS 0.005 0.001 HIS I 122 Details of bonding type rmsd covalent geometry : bond 0.00344 (16960) covalent geometry : angle 0.78886 (22854) hydrogen bonds : bond 0.08083 ( 434) hydrogen bonds : angle 7.22732 ( 1191) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 557 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 496 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 PHE cc_start: 0.7162 (m-10) cc_final: 0.6901 (m-10) REVERT: C 108 LYS cc_start: 0.7519 (pttt) cc_final: 0.7155 (tttp) REVERT: C 170 ARG cc_start: 0.7577 (ttm110) cc_final: 0.7170 (ttt90) REVERT: D 22 ARG cc_start: 0.8002 (mtt180) cc_final: 0.7787 (ptp-170) REVERT: D 28 ILE cc_start: 0.8786 (mt) cc_final: 0.8574 (mm) REVERT: D 108 LYS cc_start: 0.7858 (pttp) cc_final: 0.6506 (tttp) REVERT: D 118 GLU cc_start: 0.7623 (mt-10) cc_final: 0.6969 (mt-10) REVERT: D 173 PHE cc_start: 0.7829 (m-80) cc_final: 0.7508 (m-80) REVERT: F 108 LYS cc_start: 0.7586 (ptpp) cc_final: 0.7358 (ptmm) REVERT: F 165 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8285 (mt-10) REVERT: G 58 GLU cc_start: 0.8556 (pm20) cc_final: 0.7827 (tt0) REVERT: H 46 GLN cc_start: 0.8918 (mt0) cc_final: 0.8698 (mt0) REVERT: H 162 GLU cc_start: 0.6976 (mp0) cc_final: 0.5493 (tm-30) REVERT: H 178 GLU cc_start: 0.8540 (pt0) cc_final: 0.7949 (pm20) REVERT: H 181 GLU cc_start: 0.8526 (mp0) cc_final: 0.8304 (mp0) REVERT: K 22 ARG cc_start: 0.7188 (ptm160) cc_final: 0.6741 (ptp-170) REVERT: K 57 LYS cc_start: 0.8293 (mttt) cc_final: 0.7955 (mtpt) REVERT: K 74 MET cc_start: 0.7604 (mmm) cc_final: 0.7397 (mmm) REVERT: K 162 GLU cc_start: 0.6731 (mp0) cc_final: 0.6157 (tm-30) REVERT: K 172 ASN cc_start: 0.7851 (p0) cc_final: 0.7581 (p0) REVERT: K 177 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7599 (pm20) REVERT: L 22 ARG cc_start: 0.7822 (mtp180) cc_final: 0.7527 (mtt180) REVERT: L 151 LYS cc_start: 0.8701 (tmtt) cc_final: 0.8478 (tptp) REVERT: L 166 ARG cc_start: 0.7986 (ptm-80) cc_final: 0.7612 (ptm160) REVERT: L 167 ASP cc_start: 0.8714 (m-30) cc_final: 0.8287 (p0) REVERT: L 172 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.7391 (p0) REVERT: L 177 GLU cc_start: 0.7812 (tm-30) cc_final: 0.6960 (tp30) REVERT: N 169 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7694 (p0) REVERT: N 173 PHE cc_start: 0.7277 (m-80) cc_final: 0.6788 (t80) outliers start: 61 outliers final: 40 residues processed: 535 average time/residue: 0.3546 time to fit residues: 271.7050 Evaluate side-chains 459 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 416 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 172 ASN Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain I residue 182 TYR Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain K residue 116 ASN Chi-restraints excluded: chain K residue 177 GLU Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 172 ASN Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 35 ILE Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain N residue 118 GLU Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 169 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 40 optimal weight: 0.2980 chunk 35 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN C 38 ASN F 81 GLN G 172 ASN H 150 ASN I 81 GLN I 172 ASN J 172 ASN L 81 GLN L 159 GLN ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.129285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.109459 restraints weight = 123181.426| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 5.67 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 16960 Z= 0.167 Angle : 0.731 15.864 22854 Z= 0.382 Chirality : 0.092 1.708 2716 Planarity : 0.005 0.060 2926 Dihedral : 6.736 84.093 2379 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.33 % Allowed : 13.68 % Favored : 85.99 % Rotamer: Outliers : 3.76 % Allowed : 22.66 % Favored : 73.58 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.23 (0.16), residues: 2142 helix: -2.23 (0.15), residues: 880 sheet: -3.59 (0.24), residues: 268 loop : -3.07 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 27 TYR 0.014 0.001 TYR N 20 PHE 0.019 0.002 PHE J 173 HIS 0.004 0.001 HIS I 122 Details of bonding type rmsd covalent geometry : bond 0.00370 (16960) covalent geometry : angle 0.73134 (22854) hydrogen bonds : bond 0.05444 ( 434) hydrogen bonds : angle 6.38112 ( 1191) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 499 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 432 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 HIS cc_start: 0.7887 (OUTLIER) cc_final: 0.7653 (t-90) REVERT: C 108 LYS cc_start: 0.7760 (pttt) cc_final: 0.7359 (tttp) REVERT: C 170 ARG cc_start: 0.7580 (ttm110) cc_final: 0.7137 (ttt90) REVERT: D 28 ILE cc_start: 0.8824 (mt) cc_final: 0.8613 (mm) REVERT: D 108 LYS cc_start: 0.6973 (pttp) cc_final: 0.6569 (tttp) REVERT: D 118 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7256 (mt-10) REVERT: D 173 PHE cc_start: 0.7790 (m-80) cc_final: 0.7444 (m-80) REVERT: E 81 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8497 (mm-40) REVERT: F 108 LYS cc_start: 0.7749 (ptpp) cc_final: 0.7180 (tttm) REVERT: G 177 GLU cc_start: 0.7174 (pm20) cc_final: 0.6418 (pm20) REVERT: H 118 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7784 (pm20) REVERT: I 162 GLU cc_start: 0.7334 (mp0) cc_final: 0.6413 (tm-30) REVERT: K 22 ARG cc_start: 0.7244 (ptm160) cc_final: 0.6851 (ptp-170) REVERT: K 57 LYS cc_start: 0.8245 (mttt) cc_final: 0.7989 (mtpt) REVERT: K 162 GLU cc_start: 0.6774 (mp0) cc_final: 0.6075 (tm-30) REVERT: K 165 GLU cc_start: 0.7479 (mp0) cc_final: 0.6222 (tp30) REVERT: K 166 ARG cc_start: 0.8423 (ttm-80) cc_final: 0.8088 (mtp180) REVERT: K 172 ASN cc_start: 0.7886 (p0) cc_final: 0.7651 (p0) REVERT: L 141 ARG cc_start: 0.8044 (ptm160) cc_final: 0.7818 (ptm160) REVERT: L 151 LYS cc_start: 0.8838 (tmtt) cc_final: 0.8610 (tptp) REVERT: L 166 ARG cc_start: 0.8016 (ptm-80) cc_final: 0.7787 (ptm-80) REVERT: L 167 ASP cc_start: 0.8628 (m-30) cc_final: 0.8252 (p0) REVERT: M 22 ARG cc_start: 0.8505 (mtt180) cc_final: 0.8305 (mtt180) REVERT: N 46 GLN cc_start: 0.8895 (mt0) cc_final: 0.8683 (mt0) REVERT: N 118 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6980 (pt0) REVERT: N 169 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7700 (p0) REVERT: N 178 GLU cc_start: 0.7819 (pt0) cc_final: 0.7571 (pm20) outliers start: 67 outliers final: 47 residues processed: 471 average time/residue: 0.3535 time to fit residues: 238.1927 Evaluate side-chains 442 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 391 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 122 HIS Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 41 ASN Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 182 TYR Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 172 ASN Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 38 ASN Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain N residue 118 GLU Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 169 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 147 optimal weight: 10.0000 chunk 108 optimal weight: 0.5980 chunk 205 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN G 172 ASN H 172 ASN N 41 ASN N 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.129450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.109714 restraints weight = 122429.246| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 5.62 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16960 Z= 0.128 Angle : 0.689 15.557 22854 Z= 0.355 Chirality : 0.092 1.734 2716 Planarity : 0.004 0.053 2926 Dihedral : 6.193 63.977 2375 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.81 % Favored : 87.86 % Rotamer: Outliers : 3.70 % Allowed : 23.44 % Favored : 72.85 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.83 (0.16), residues: 2142 helix: -1.85 (0.16), residues: 878 sheet: -3.33 (0.25), residues: 278 loop : -2.89 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 27 TYR 0.012 0.001 TYR N 20 PHE 0.022 0.002 PHE J 173 HIS 0.003 0.001 HIS I 122 Details of bonding type rmsd covalent geometry : bond 0.00290 (16960) covalent geometry : angle 0.68946 (22854) hydrogen bonds : bond 0.04557 ( 434) hydrogen bonds : angle 5.98004 ( 1191) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 493 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 427 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7323 (tp30) REVERT: C 108 LYS cc_start: 0.7760 (pttt) cc_final: 0.7324 (tttm) REVERT: C 146 ARG cc_start: 0.7218 (tpp80) cc_final: 0.6925 (mtt180) REVERT: C 170 ARG cc_start: 0.7543 (ttm110) cc_final: 0.7032 (tmt170) REVERT: D 28 ILE cc_start: 0.8830 (mt) cc_final: 0.8590 (mm) REVERT: D 108 LYS cc_start: 0.6915 (pttp) cc_final: 0.6497 (tttp) REVERT: D 118 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7194 (mt-10) REVERT: D 173 PHE cc_start: 0.7816 (m-80) cc_final: 0.7452 (m-80) REVERT: E 162 GLU cc_start: 0.8222 (pm20) cc_final: 0.7885 (pm20) REVERT: F 108 LYS cc_start: 0.7663 (ptpp) cc_final: 0.7105 (tttm) REVERT: F 173 PHE cc_start: 0.7297 (m-80) cc_final: 0.7072 (m-10) REVERT: H 118 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7791 (pm20) REVERT: I 162 GLU cc_start: 0.7243 (mp0) cc_final: 0.6538 (tm-30) REVERT: K 22 ARG cc_start: 0.7295 (ptm160) cc_final: 0.6943 (ptp-170) REVERT: K 57 LYS cc_start: 0.8255 (mttt) cc_final: 0.7994 (mtpt) REVERT: K 162 GLU cc_start: 0.6835 (mp0) cc_final: 0.6128 (tm-30) REVERT: K 165 GLU cc_start: 0.7409 (mp0) cc_final: 0.6309 (tp30) REVERT: K 166 ARG cc_start: 0.8430 (ttm-80) cc_final: 0.8127 (mtp180) REVERT: L 151 LYS cc_start: 0.8884 (tmtt) cc_final: 0.8648 (tptp) REVERT: L 166 ARG cc_start: 0.8025 (ptm-80) cc_final: 0.7787 (ptm-80) REVERT: L 167 ASP cc_start: 0.8715 (m-30) cc_final: 0.8305 (p0) REVERT: N 169 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7634 (p0) REVERT: N 178 GLU cc_start: 0.7841 (pt0) cc_final: 0.7602 (pm20) outliers start: 66 outliers final: 45 residues processed: 462 average time/residue: 0.3405 time to fit residues: 226.8648 Evaluate side-chains 441 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 393 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 41 ASN Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 182 TYR Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 46 GLN Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 173 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 151 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN B 172 ASN C 38 ASN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN H 172 ASN I 46 GLN J 41 ASN ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.123345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.103884 restraints weight = 125937.753| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 5.53 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16960 Z= 0.266 Angle : 0.798 16.139 22854 Z= 0.418 Chirality : 0.094 1.756 2716 Planarity : 0.005 0.068 2926 Dihedral : 6.369 60.365 2371 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.28 % Allowed : 16.20 % Favored : 83.52 % Rotamer: Outliers : 5.50 % Allowed : 23.72 % Favored : 70.78 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.16), residues: 2142 helix: -2.05 (0.15), residues: 896 sheet: -3.37 (0.26), residues: 262 loop : -2.92 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 141 TYR 0.018 0.002 TYR M 20 PHE 0.021 0.002 PHE I 173 HIS 0.004 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00554 (16960) covalent geometry : angle 0.79779 (22854) hydrogen bonds : bond 0.04829 ( 434) hydrogen bonds : angle 6.37056 ( 1191) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 504 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 406 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7253 (tp30) REVERT: C 63 ILE cc_start: 0.9113 (mm) cc_final: 0.8821 (mt) REVERT: C 108 LYS cc_start: 0.8003 (pttt) cc_final: 0.7619 (tttm) REVERT: C 170 ARG cc_start: 0.7492 (ttm110) cc_final: 0.6970 (tmt170) REVERT: D 108 LYS cc_start: 0.7247 (pttp) cc_final: 0.6885 (tttm) REVERT: D 118 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7181 (mt-10) REVERT: D 173 PHE cc_start: 0.7733 (m-80) cc_final: 0.7243 (m-80) REVERT: E 19 ILE cc_start: 0.7424 (OUTLIER) cc_final: 0.7142 (tp) REVERT: E 167 ASP cc_start: 0.8135 (p0) cc_final: 0.7915 (p0) REVERT: E 182 TYR cc_start: 0.8132 (m-10) cc_final: 0.7915 (m-80) REVERT: F 57 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7910 (ptpp) REVERT: F 108 LYS cc_start: 0.8136 (ptpp) cc_final: 0.7755 (tttp) REVERT: F 167 ASP cc_start: 0.8265 (p0) cc_final: 0.7967 (p0) REVERT: F 182 TYR cc_start: 0.7841 (m-80) cc_final: 0.7590 (m-80) REVERT: H 166 ARG cc_start: 0.8067 (ptm-80) cc_final: 0.7804 (ptm160) REVERT: I 53 GLU cc_start: 0.6505 (tp30) cc_final: 0.5971 (tm-30) REVERT: I 162 GLU cc_start: 0.7233 (mp0) cc_final: 0.6590 (tm-30) REVERT: K 22 ARG cc_start: 0.7472 (ptm160) cc_final: 0.7240 (ptp-170) REVERT: K 162 GLU cc_start: 0.6831 (mp0) cc_final: 0.5995 (tm-30) REVERT: K 166 ARG cc_start: 0.8516 (ttm-80) cc_final: 0.8296 (mtp180) REVERT: L 167 ASP cc_start: 0.8626 (m-30) cc_final: 0.8304 (p0) REVERT: N 169 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7688 (p0) REVERT: N 178 GLU cc_start: 0.8095 (pt0) cc_final: 0.7785 (pm20) outliers start: 98 outliers final: 68 residues processed: 466 average time/residue: 0.3191 time to fit residues: 215.9209 Evaluate side-chains 457 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 385 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 41 ASN Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 172 ASN Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 182 TYR Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 122 HIS Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 116 ASN Chi-restraints excluded: chain K residue 122 HIS Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 41 ASN Chi-restraints excluded: chain M residue 78 ASP Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain N residue 38 ASN Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 173 PHE Chi-restraints excluded: chain N residue 186 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 109 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 123 optimal weight: 0.0870 chunk 200 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 193 optimal weight: 0.6980 overall best weight: 3.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN C 38 ASN E 81 GLN H 172 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 GLN ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.124810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.105373 restraints weight = 122454.755| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 5.52 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.6184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16960 Z= 0.140 Angle : 0.699 13.944 22854 Z= 0.360 Chirality : 0.092 1.730 2716 Planarity : 0.004 0.052 2926 Dihedral : 6.053 63.593 2371 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.81 % Favored : 88.00 % Rotamer: Outliers : 3.93 % Allowed : 25.29 % Favored : 70.78 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.48 (0.17), residues: 2142 helix: -1.62 (0.16), residues: 896 sheet: -3.03 (0.27), residues: 262 loop : -2.71 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 166 TYR 0.014 0.001 TYR N 77 PHE 0.013 0.002 PHE I 173 HIS 0.003 0.001 HIS L 122 Details of bonding type rmsd covalent geometry : bond 0.00313 (16960) covalent geometry : angle 0.69941 (22854) hydrogen bonds : bond 0.04054 ( 434) hydrogen bonds : angle 5.77257 ( 1191) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 499 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 429 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7348 (tp30) REVERT: B 19 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7547 (tp) REVERT: C 63 ILE cc_start: 0.9097 (mm) cc_final: 0.8826 (mt) REVERT: C 108 LYS cc_start: 0.7891 (pttt) cc_final: 0.7531 (tttm) REVERT: C 120 MET cc_start: 0.7163 (tmm) cc_final: 0.6926 (tmm) REVERT: C 170 ARG cc_start: 0.7463 (ttm110) cc_final: 0.6870 (tmt170) REVERT: D 108 LYS cc_start: 0.7209 (pttp) cc_final: 0.6788 (tttm) REVERT: D 118 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7091 (mt-10) REVERT: D 173 PHE cc_start: 0.7793 (m-80) cc_final: 0.7353 (m-80) REVERT: E 167 ASP cc_start: 0.7997 (p0) cc_final: 0.7766 (p0) REVERT: E 182 TYR cc_start: 0.8053 (m-10) cc_final: 0.7814 (m-80) REVERT: F 108 LYS cc_start: 0.7920 (ptpp) cc_final: 0.7432 (tttp) REVERT: F 165 GLU cc_start: 0.8182 (mp0) cc_final: 0.7965 (mp0) REVERT: F 167 ASP cc_start: 0.8283 (p0) cc_final: 0.7970 (p0) REVERT: F 182 TYR cc_start: 0.7842 (m-80) cc_final: 0.7585 (m-80) REVERT: H 166 ARG cc_start: 0.8036 (ptm-80) cc_final: 0.7791 (ptm160) REVERT: I 182 TYR cc_start: 0.6778 (OUTLIER) cc_final: 0.6434 (t80) REVERT: J 46 GLN cc_start: 0.8642 (mt0) cc_final: 0.8421 (mt0) REVERT: K 22 ARG cc_start: 0.7397 (ptm160) cc_final: 0.7094 (ptp-170) REVERT: K 162 GLU cc_start: 0.6847 (mp0) cc_final: 0.6202 (tm-30) REVERT: N 46 GLN cc_start: 0.8789 (mt0) cc_final: 0.8581 (mt0) REVERT: N 169 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7669 (p0) REVERT: N 178 GLU cc_start: 0.8089 (pt0) cc_final: 0.7773 (pm20) REVERT: N 189 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6952 (pp) outliers start: 70 outliers final: 54 residues processed: 471 average time/residue: 0.3171 time to fit residues: 218.6724 Evaluate side-chains 455 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 396 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 41 ASN Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 182 TYR Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 122 HIS Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 83 ILE Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 173 PHE Chi-restraints excluded: chain N residue 189 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 55 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 96 optimal weight: 0.3980 chunk 83 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 overall best weight: 6.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN C 38 ASN ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.122550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.103153 restraints weight = 127482.676| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 5.56 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.6479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16960 Z= 0.214 Angle : 0.748 14.482 22854 Z= 0.388 Chirality : 0.093 1.731 2716 Planarity : 0.005 0.059 2926 Dihedral : 6.111 62.257 2371 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 15.69 % Favored : 84.17 % Rotamer: Outliers : 4.99 % Allowed : 26.14 % Favored : 68.87 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.17), residues: 2142 helix: -1.65 (0.16), residues: 896 sheet: -3.06 (0.27), residues: 262 loop : -2.71 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 166 TYR 0.017 0.001 TYR D 77 PHE 0.017 0.002 PHE A 82 HIS 0.003 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00453 (16960) covalent geometry : angle 0.74839 (22854) hydrogen bonds : bond 0.04261 ( 434) hydrogen bonds : angle 5.94704 ( 1191) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 492 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 403 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7386 (tp30) REVERT: C 63 ILE cc_start: 0.9073 (mm) cc_final: 0.8804 (mt) REVERT: C 108 LYS cc_start: 0.7992 (pttt) cc_final: 0.7610 (tttm) REVERT: C 120 MET cc_start: 0.7203 (tmm) cc_final: 0.6999 (tmm) REVERT: C 170 ARG cc_start: 0.7468 (ttm110) cc_final: 0.6898 (tmt170) REVERT: D 108 LYS cc_start: 0.7280 (pttp) cc_final: 0.6875 (tttm) REVERT: D 118 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7270 (mt-10) REVERT: D 165 GLU cc_start: 0.7963 (mp0) cc_final: 0.7749 (mp0) REVERT: E 19 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.7100 (tp) REVERT: E 167 ASP cc_start: 0.7992 (p0) cc_final: 0.7750 (p0) REVERT: E 182 TYR cc_start: 0.8144 (m-10) cc_final: 0.7893 (m-80) REVERT: F 108 LYS cc_start: 0.8108 (ptpp) cc_final: 0.7664 (tttp) REVERT: F 165 GLU cc_start: 0.8217 (mp0) cc_final: 0.8016 (mp0) REVERT: F 167 ASP cc_start: 0.8247 (p0) cc_final: 0.7917 (p0) REVERT: F 182 TYR cc_start: 0.8019 (m-80) cc_final: 0.7776 (m-80) REVERT: H 166 ARG cc_start: 0.8112 (ptm-80) cc_final: 0.7843 (ptm160) REVERT: I 182 TYR cc_start: 0.6824 (OUTLIER) cc_final: 0.6515 (t80) REVERT: J 46 GLN cc_start: 0.8703 (mt0) cc_final: 0.8494 (mt0) REVERT: K 22 ARG cc_start: 0.7530 (ptm160) cc_final: 0.7260 (ptp-170) REVERT: L 167 ASP cc_start: 0.8503 (m-30) cc_final: 0.8115 (p0) REVERT: N 169 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7661 (p0) REVERT: N 178 GLU cc_start: 0.8197 (pt0) cc_final: 0.7801 (pm20) REVERT: N 189 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6880 (pp) outliers start: 89 outliers final: 70 residues processed: 456 average time/residue: 0.3128 time to fit residues: 209.6896 Evaluate side-chains 466 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 391 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 41 ASN Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 182 TYR Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 116 ASN Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 41 ASN Chi-restraints excluded: chain M residue 83 ILE Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain N residue 38 ASN Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 173 PHE Chi-restraints excluded: chain N residue 189 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 157 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN C 38 ASN ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 GLN L 41 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.121153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.101982 restraints weight = 126141.886| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 5.47 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.6769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16960 Z= 0.222 Angle : 0.755 14.497 22854 Z= 0.391 Chirality : 0.093 1.729 2716 Planarity : 0.005 0.054 2926 Dihedral : 6.167 63.861 2371 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.85 % Favored : 85.01 % Rotamer: Outliers : 5.33 % Allowed : 26.42 % Favored : 68.26 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.17), residues: 2142 helix: -1.70 (0.16), residues: 896 sheet: -2.91 (0.28), residues: 262 loop : -2.64 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 166 TYR 0.015 0.001 TYR M 20 PHE 0.018 0.002 PHE I 173 HIS 0.005 0.001 HIS G 122 Details of bonding type rmsd covalent geometry : bond 0.00472 (16960) covalent geometry : angle 0.75515 (22854) hydrogen bonds : bond 0.04192 ( 434) hydrogen bonds : angle 5.96487 ( 1191) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 505 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 410 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8207 (mmt) cc_final: 0.7990 (mmt) REVERT: A 165 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7454 (tp30) REVERT: C 63 ILE cc_start: 0.9056 (mm) cc_final: 0.8788 (mt) REVERT: C 108 LYS cc_start: 0.7967 (pttt) cc_final: 0.7599 (tttp) REVERT: C 169 ASP cc_start: 0.7786 (p0) cc_final: 0.7576 (p0) REVERT: C 170 ARG cc_start: 0.7412 (ttm110) cc_final: 0.6784 (tmt170) REVERT: D 108 LYS cc_start: 0.7351 (pttp) cc_final: 0.6895 (tttm) REVERT: D 118 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7174 (mt-10) REVERT: D 173 PHE cc_start: 0.7501 (m-80) cc_final: 0.6741 (m-80) REVERT: E 19 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.7180 (tp) REVERT: E 167 ASP cc_start: 0.8036 (p0) cc_final: 0.7817 (p0) REVERT: E 182 TYR cc_start: 0.8217 (m-10) cc_final: 0.7958 (m-80) REVERT: F 108 LYS cc_start: 0.8106 (ptpp) cc_final: 0.7724 (tttp) REVERT: F 167 ASP cc_start: 0.8162 (p0) cc_final: 0.7790 (p0) REVERT: F 182 TYR cc_start: 0.8069 (m-80) cc_final: 0.7837 (m-80) REVERT: G 178 GLU cc_start: 0.8247 (pm20) cc_final: 0.7748 (pm20) REVERT: H 166 ARG cc_start: 0.8125 (ptm-80) cc_final: 0.7846 (ptm160) REVERT: K 22 ARG cc_start: 0.7642 (ptm160) cc_final: 0.7385 (ptp-170) REVERT: L 167 ASP cc_start: 0.8466 (m-30) cc_final: 0.8122 (p0) REVERT: M 22 ARG cc_start: 0.8673 (mtt180) cc_final: 0.8002 (ttt180) REVERT: N 169 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7583 (p0) REVERT: N 178 GLU cc_start: 0.8203 (pt0) cc_final: 0.7818 (pm20) REVERT: N 189 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6980 (pp) outliers start: 95 outliers final: 74 residues processed: 469 average time/residue: 0.3186 time to fit residues: 219.2178 Evaluate side-chains 472 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 394 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 41 ASN Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 122 HIS Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 122 HIS Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 116 ASN Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain M residue 41 ASN Chi-restraints excluded: chain M residue 78 ASP Chi-restraints excluded: chain M residue 83 ILE Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain M residue 122 HIS Chi-restraints excluded: chain N residue 38 ASN Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 173 PHE Chi-restraints excluded: chain N residue 189 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 180 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 31 optimal weight: 0.0010 chunk 160 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 177 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN B 38 ASN C 38 ASN E 64 ASN H 46 GLN J 46 GLN N 46 GLN N 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.123018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.103555 restraints weight = 124725.186| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 5.58 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.6949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16960 Z= 0.124 Angle : 0.710 14.204 22854 Z= 0.361 Chirality : 0.092 1.748 2716 Planarity : 0.004 0.044 2926 Dihedral : 5.444 58.996 2364 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.72 % Favored : 88.14 % Rotamer: Outliers : 3.76 % Allowed : 28.21 % Favored : 68.03 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.18), residues: 2142 helix: -1.24 (0.17), residues: 900 sheet: -2.58 (0.29), residues: 262 loop : -2.43 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 166 TYR 0.014 0.001 TYR N 77 PHE 0.017 0.001 PHE A 82 HIS 0.004 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00283 (16960) covalent geometry : angle 0.70982 (22854) hydrogen bonds : bond 0.03817 ( 434) hydrogen bonds : angle 5.46858 ( 1191) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 503 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 436 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7543 (tp30) REVERT: B 112 TYR cc_start: 0.8127 (m-80) cc_final: 0.7906 (m-80) REVERT: C 108 LYS cc_start: 0.7875 (pttt) cc_final: 0.7545 (tttp) REVERT: C 122 HIS cc_start: 0.8303 (t70) cc_final: 0.7940 (t-90) REVERT: C 169 ASP cc_start: 0.7724 (p0) cc_final: 0.7383 (p0) REVERT: C 170 ARG cc_start: 0.7362 (ttm110) cc_final: 0.6655 (tmt170) REVERT: D 108 LYS cc_start: 0.7280 (pttp) cc_final: 0.6798 (tttm) REVERT: D 118 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7229 (mt-10) REVERT: D 173 PHE cc_start: 0.7425 (m-80) cc_final: 0.6758 (m-80) REVERT: E 19 ILE cc_start: 0.7395 (OUTLIER) cc_final: 0.7142 (tp) REVERT: E 167 ASP cc_start: 0.8041 (p0) cc_final: 0.7820 (p0) REVERT: E 182 TYR cc_start: 0.8142 (m-10) cc_final: 0.7884 (m-80) REVERT: F 108 LYS cc_start: 0.7978 (ptpp) cc_final: 0.7457 (tttp) REVERT: F 165 GLU cc_start: 0.7982 (mp0) cc_final: 0.7758 (mp0) REVERT: F 167 ASP cc_start: 0.8165 (p0) cc_final: 0.7779 (p0) REVERT: F 182 TYR cc_start: 0.8063 (m-80) cc_final: 0.7811 (m-80) REVERT: G 141 ARG cc_start: 0.7981 (tmm-80) cc_final: 0.7669 (tmm-80) REVERT: H 166 ARG cc_start: 0.8186 (ptm-80) cc_final: 0.7967 (ptm160) REVERT: K 22 ARG cc_start: 0.7687 (ptm160) cc_final: 0.7382 (ptp-170) REVERT: K 30 MET cc_start: 0.7509 (tpt) cc_final: 0.7124 (tpt) REVERT: N 169 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7549 (p0) REVERT: N 178 GLU cc_start: 0.8204 (pt0) cc_final: 0.7827 (pm20) REVERT: N 189 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7028 (pp) outliers start: 67 outliers final: 55 residues processed: 471 average time/residue: 0.3213 time to fit residues: 221.6794 Evaluate side-chains 465 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 406 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 41 ASN Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 116 ASN Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain N residue 81 GLN Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 173 PHE Chi-restraints excluded: chain N residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 209 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN C 38 ASN K 46 GLN ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.123198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.103741 restraints weight = 126579.680| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 5.59 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.7015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 16960 Z= 0.167 Angle : 0.872 59.199 22854 Z= 0.476 Chirality : 0.092 1.746 2716 Planarity : 0.004 0.044 2926 Dihedral : 5.302 43.853 2360 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.67 % Favored : 88.19 % Rotamer: Outliers : 3.37 % Allowed : 28.72 % Favored : 67.92 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.18), residues: 2142 helix: -1.21 (0.17), residues: 900 sheet: -2.56 (0.29), residues: 262 loop : -2.43 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 141 TYR 0.014 0.001 TYR N 77 PHE 0.014 0.001 PHE A 82 HIS 0.004 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00367 (16960) covalent geometry : angle 0.87219 (22854) hydrogen bonds : bond 0.03918 ( 434) hydrogen bonds : angle 5.49795 ( 1191) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 466 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 406 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7546 (tp30) REVERT: B 112 TYR cc_start: 0.8121 (m-80) cc_final: 0.7899 (m-80) REVERT: C 108 LYS cc_start: 0.7901 (pttt) cc_final: 0.7564 (tttp) REVERT: C 122 HIS cc_start: 0.8303 (t70) cc_final: 0.7937 (t-90) REVERT: C 169 ASP cc_start: 0.7730 (p0) cc_final: 0.7388 (p0) REVERT: C 170 ARG cc_start: 0.7383 (ttm110) cc_final: 0.6670 (tmt170) REVERT: D 108 LYS cc_start: 0.7285 (pttp) cc_final: 0.6801 (tttm) REVERT: D 118 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7214 (mt-10) REVERT: D 173 PHE cc_start: 0.7203 (m-80) cc_final: 0.6782 (m-80) REVERT: E 19 ILE cc_start: 0.7386 (OUTLIER) cc_final: 0.7135 (tp) REVERT: E 167 ASP cc_start: 0.8038 (p0) cc_final: 0.7824 (p0) REVERT: E 182 TYR cc_start: 0.8138 (m-10) cc_final: 0.7883 (m-80) REVERT: F 108 LYS cc_start: 0.7982 (ptpp) cc_final: 0.7464 (tttp) REVERT: F 165 GLU cc_start: 0.7977 (mp0) cc_final: 0.7762 (mp0) REVERT: F 167 ASP cc_start: 0.8172 (p0) cc_final: 0.7784 (p0) REVERT: F 182 TYR cc_start: 0.8072 (m-80) cc_final: 0.7819 (m-80) REVERT: H 166 ARG cc_start: 0.8215 (ptm-80) cc_final: 0.7939 (ptm160) REVERT: I 22 ARG cc_start: 0.8181 (mtt-85) cc_final: 0.7773 (mtt-85) REVERT: K 22 ARG cc_start: 0.7643 (ptm160) cc_final: 0.7343 (ptp-170) REVERT: K 30 MET cc_start: 0.7504 (tpt) cc_final: 0.7130 (tpt) REVERT: N 169 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7525 (p0) REVERT: N 178 GLU cc_start: 0.8188 (pt0) cc_final: 0.7814 (pm20) REVERT: N 189 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7026 (pp) outliers start: 60 outliers final: 55 residues processed: 438 average time/residue: 0.3305 time to fit residues: 211.0463 Evaluate side-chains 463 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 404 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 41 ASN Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 116 ASN Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 173 PHE Chi-restraints excluded: chain N residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 198 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 191 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN C 38 ASN ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.123108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.103802 restraints weight = 124718.715| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 5.52 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.7017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 16960 Z= 0.166 Angle : 0.872 59.178 22854 Z= 0.476 Chirality : 0.092 1.746 2716 Planarity : 0.004 0.044 2926 Dihedral : 5.302 43.853 2360 Min Nonbonded Distance : 1.566 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.67 % Favored : 88.19 % Rotamer: Outliers : 3.31 % Allowed : 28.83 % Favored : 67.86 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.18), residues: 2142 helix: -1.21 (0.17), residues: 900 sheet: -2.56 (0.29), residues: 262 loop : -2.43 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 141 TYR 0.014 0.001 TYR N 77 PHE 0.014 0.001 PHE A 82 HIS 0.004 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00366 (16960) covalent geometry : angle 0.87208 (22854) hydrogen bonds : bond 0.03918 ( 434) hydrogen bonds : angle 5.49799 ( 1191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6174.10 seconds wall clock time: 105 minutes 45.72 seconds (6345.72 seconds total)