Starting phenix.real_space_refine on Sat Sep 12 11:38:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ch0_30367/09_2026/7ch0_30367.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ch0_30367/09_2026/7ch0_30367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ch0_30367/09_2026/7ch0_30367.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ch0_30367/09_2026/7ch0_30367.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ch0_30367/09_2026/7ch0_30367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ch0_30367/09_2026/7ch0_30367.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ch0_30367/09_2026/7ch0_30367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ch0_30367/09_2026/7ch0_30367.map" } resolution = 3.7 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 68 5.16 5 C 10164 2.51 5 N 2666 2.21 5 O 2952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15856 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1934 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "B" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1995 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 244} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1995 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 244} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1934 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "C" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 725 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "F" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 725 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "G" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "H" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "I" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1033 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "J" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "K" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "L" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1033 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.78, per 1000 atoms: 0.24 Number of scatterers: 15856 At special positions: 0 Unit cell: (108.7, 105.439, 150.006, 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 68 16.00 P 6 15.00 O 2952 8.00 N 2666 7.00 C 10164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 714.5 milliseconds 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3824 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 22 sheets defined 38.9% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 3 through 32 removed outlier: 3.538A pdb=" N SER A 8 " --> pdb=" O ASN A 4 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 52 removed outlier: 3.617A pdb=" N VAL A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 77 removed outlier: 3.623A pdb=" N ILE A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.617A pdb=" N TYR A 81 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 87 through 98 removed outlier: 4.001A pdb=" N LEU A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 126 removed outlier: 3.538A pdb=" N VAL A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.523A pdb=" N GLU A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 144 through 174 removed outlier: 3.586A pdb=" N TRP A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Proline residue: A 156 - end of helix removed outlier: 4.034A pdb=" N VAL A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 191 removed outlier: 3.913A pdb=" N ASN A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 220 removed outlier: 3.806A pdb=" N LYS A 205 " --> pdb=" O ASN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 243 removed outlier: 3.868A pdb=" N ILE A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 257 removed outlier: 3.950A pdb=" N LEU A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.733A pdb=" N ILE B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 84 removed outlier: 3.795A pdb=" N TYR B 81 " --> pdb=" O ARG B 77 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 124 through 132 removed outlier: 4.013A pdb=" N GLU B 130 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 157 removed outlier: 3.756A pdb=" N ARG B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 189 removed outlier: 3.681A pdb=" N ILE B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 261 through 266 Processing helix chain 'E' and resid 47 through 55 removed outlier: 3.732A pdb=" N ILE E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 84 removed outlier: 3.794A pdb=" N TYR E 81 " --> pdb=" O ARG E 77 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR E 82 " --> pdb=" O SER E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 124 through 132 removed outlier: 4.014A pdb=" N GLU E 130 " --> pdb=" O MET E 126 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL E 132 " --> pdb=" O LYS E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 157 removed outlier: 3.756A pdb=" N ARG E 152 " --> pdb=" O GLY E 148 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA E 154 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA E 156 " --> pdb=" O ARG E 152 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 removed outlier: 3.680A pdb=" N ILE E 187 " --> pdb=" O LEU E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 211 Processing helix chain 'D' and resid 4 through 32 removed outlier: 3.537A pdb=" N SER D 8 " --> pdb=" O ASN D 4 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU D 9 " --> pdb=" O ALA D 5 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY D 10 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR D 16 " --> pdb=" O LYS D 12 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 52 removed outlier: 3.617A pdb=" N VAL D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG D 46 " --> pdb=" O PRO D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 77 removed outlier: 3.622A pdb=" N ILE D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE D 66 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY D 74 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 3.618A pdb=" N TYR D 81 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 86 Processing helix chain 'D' and resid 87 through 98 removed outlier: 4.001A pdb=" N LEU D 93 " --> pdb=" O MET D 89 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 126 removed outlier: 3.538A pdb=" N VAL D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 134 removed outlier: 3.523A pdb=" N GLU D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 144 through 174 removed outlier: 3.586A pdb=" N TRP D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY D 151 " --> pdb=" O ARG D 147 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 155 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Proline residue: D 156 - end of helix removed outlier: 4.034A pdb=" N VAL D 160 " --> pdb=" O PRO D 156 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL D 173 " --> pdb=" O GLY D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 191 removed outlier: 3.913A pdb=" N ASN D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 220 removed outlier: 3.805A pdb=" N LYS D 205 " --> pdb=" O ASN D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 243 removed outlier: 3.868A pdb=" N ILE D 231 " --> pdb=" O THR D 227 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 236 " --> pdb=" O SER D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 257 removed outlier: 3.950A pdb=" N LEU D 247 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 31 removed outlier: 4.022A pdb=" N MET C 31 " --> pdb=" O PRO C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 62 removed outlier: 5.122A pdb=" N LEU C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C 58 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.723A pdb=" N LYS C 67 " --> pdb=" O ASP C 63 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 31 removed outlier: 4.022A pdb=" N MET F 31 " --> pdb=" O PRO F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 62 removed outlier: 5.121A pdb=" N LEU F 57 " --> pdb=" O GLY F 53 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU F 58 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 68 removed outlier: 3.723A pdb=" N LYS F 67 " --> pdb=" O ASP F 63 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 28 removed outlier: 4.001A pdb=" N TRP G 9 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL G 10 " --> pdb=" O ASN G 6 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU G 15 " --> pdb=" O GLY G 11 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA G 28 " --> pdb=" O VAL G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 152 removed outlier: 3.606A pdb=" N ILE G 147 " --> pdb=" O LEU G 143 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN G 149 " --> pdb=" O ASP G 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 24 removed outlier: 3.658A pdb=" N TRP H 9 " --> pdb=" O LYS H 5 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY H 11 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE H 13 " --> pdb=" O TRP H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 151 Processing helix chain 'I' and resid 8 through 28 removed outlier: 4.015A pdb=" N LEU I 14 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA I 28 " --> pdb=" O VAL I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 151 removed outlier: 3.694A pdb=" N LEU I 146 " --> pdb=" O VAL I 142 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY I 148 " --> pdb=" O GLU I 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 28 removed outlier: 3.796A pdb=" N GLY J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE J 13 " --> pdb=" O TRP J 9 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA J 21 " --> pdb=" O ALA J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 152 removed outlier: 3.526A pdb=" N GLY J 148 " --> pdb=" O GLU J 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 28 removed outlier: 4.494A pdb=" N PHE K 13 " --> pdb=" O TRP K 9 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU K 15 " --> pdb=" O GLY K 11 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 152 removed outlier: 3.618A pdb=" N LEU K 146 " --> pdb=" O VAL K 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 18 removed outlier: 3.700A pdb=" N ALA L 17 " --> pdb=" O PHE L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 28 removed outlier: 4.190A pdb=" N CYS L 25 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU L 26 " --> pdb=" O LEU L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 152 Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 32 removed outlier: 3.587A pdb=" N VAL B 9 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 14 through 18 removed outlier: 3.723A pdb=" N ILE B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N PHE B 16 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP B 25 " --> pdb=" O PHE B 16 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG B 18 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE B 23 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 37 through 39 removed outlier: 6.309A pdb=" N THR B 37 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 217 through 218 removed outlier: 3.840A pdb=" N ALA B 225 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 30 through 32 removed outlier: 3.587A pdb=" N VAL E 9 " --> pdb=" O VAL E 31 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 14 through 18 removed outlier: 3.723A pdb=" N ILE E 27 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N PHE E 16 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP E 25 " --> pdb=" O PHE E 16 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG E 18 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE E 23 " --> pdb=" O ARG E 18 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 37 through 39 removed outlier: 6.310A pdb=" N THR E 37 " --> pdb=" O VAL E 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 215 through 218 removed outlier: 3.653A pdb=" N ALA E 215 " --> pdb=" O GLY E 227 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY E 227 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA E 225 " --> pdb=" O ILE E 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 9 removed outlier: 3.665A pdb=" N MET C 8 " --> pdb=" O ALA C 15 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA C 15 " --> pdb=" O MET C 8 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N ARG C 46 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU C 16 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N SER C 48 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLY C 18 " --> pdb=" O SER C 48 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL C 50 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU C 20 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AB2, first strand: chain 'F' and resid 6 through 9 removed outlier: 3.665A pdb=" N MET F 8 " --> pdb=" O ALA F 15 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA F 15 " --> pdb=" O MET F 8 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N ARG F 46 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU F 16 " --> pdb=" O ARG F 46 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N SER F 48 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N GLY F 18 " --> pdb=" O SER F 48 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL F 50 " --> pdb=" O GLY F 18 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU F 20 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 41 through 42 Processing sheet with id=AB4, first strand: chain 'G' and resid 39 through 45 removed outlier: 3.588A pdb=" N ALA G 44 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR G 83 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N VAL G 65 " --> pdb=" O GLU G 87 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL G 64 " --> pdb=" O ILE G 60 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE G 60 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY G 66 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N SER G 59 " --> pdb=" O LEU G 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 39 through 40 Processing sheet with id=AB6, first strand: chain 'H' and resid 81 through 83 removed outlier: 6.809A pdb=" N TYR H 43 " --> pdb=" O ILE H 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 63 through 64 removed outlier: 3.510A pdb=" N SER H 59 " --> pdb=" O LEU H 112 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 39 through 43 removed outlier: 3.531A pdb=" N ARG I 67 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL I 65 " --> pdb=" O GLU I 87 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL I 63 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL I 58 " --> pdb=" O VAL I 65 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU I 99 " --> pdb=" O LYS I 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 57 through 60 removed outlier: 3.994A pdb=" N GLY J 66 " --> pdb=" O VAL J 58 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE J 60 " --> pdb=" O VAL J 64 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL J 64 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL J 65 " --> pdb=" O GLU J 87 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR J 83 " --> pdb=" O ALA J 69 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA J 44 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP J 132 " --> pdb=" O THR J 41 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 98 through 100 Processing sheet with id=AC2, first strand: chain 'K' and resid 39 through 40 Processing sheet with id=AC3, first strand: chain 'K' and resid 43 through 45 removed outlier: 6.744A pdb=" N THR K 83 " --> pdb=" O ALA K 69 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL K 64 " --> pdb=" O ILE K 60 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE K 60 " --> pdb=" O VAL K 64 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL K 58 " --> pdb=" O GLY K 66 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU K 114 " --> pdb=" O PRO K 57 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N SER K 59 " --> pdb=" O LEU K 114 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG K 102 " --> pdb=" O TYR K 111 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN K 115 " --> pdb=" O SER K 98 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER K 98 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU K 99 " --> pdb=" O LYS K 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 133 through 134 removed outlier: 8.787A pdb=" N ILE L 134 " --> pdb=" O THR L 41 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR L 43 " --> pdb=" O ILE L 134 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG L 67 " --> pdb=" O GLU L 85 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N VAL L 65 " --> pdb=" O GLU L 87 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU L 114 " --> pdb=" O PRO L 57 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER L 59 " --> pdb=" O LEU L 114 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU L 99 " --> pdb=" O LYS L 138 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1482 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: 2.30 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5082 1.34 - 1.46: 2652 1.46 - 1.57: 8266 1.57 - 1.69: 10 1.69 - 1.81: 124 Bond restraints: 16134 Sorted by residual: bond pdb=" C4 ATP E 301 " pdb=" C5 ATP E 301 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.26e+01 bond pdb=" C4 ATP B 301 " pdb=" C5 ATP B 301 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.17e+01 bond pdb=" C5 ATP B 301 " pdb=" C6 ATP B 301 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.48e+01 bond pdb=" C5 ATP E 301 " pdb=" C6 ATP E 301 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.44e+01 bond pdb=" C5 ATP E 301 " pdb=" N7 ATP E 301 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.31e+01 ... (remaining 16129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 21650 3.79 - 7.58: 267 7.58 - 11.37: 30 11.37 - 15.16: 1 15.16 - 18.95: 4 Bond angle restraints: 21952 Sorted by residual: angle pdb=" PB ATP E 301 " pdb=" O3B ATP E 301 " pdb=" PG ATP E 301 " ideal model delta sigma weight residual 139.87 120.92 18.95 1.00e+00 1.00e+00 3.59e+02 angle pdb=" PB ATP B 301 " pdb=" O3B ATP B 301 " pdb=" PG ATP B 301 " ideal model delta sigma weight residual 139.87 120.94 18.93 1.00e+00 1.00e+00 3.58e+02 angle pdb=" PA ATP E 301 " pdb=" O3A ATP E 301 " pdb=" PB ATP E 301 " ideal model delta sigma weight residual 136.83 119.25 17.58 1.00e+00 1.00e+00 3.09e+02 angle pdb=" PA ATP B 301 " pdb=" O3A ATP B 301 " pdb=" PB ATP B 301 " ideal model delta sigma weight residual 136.83 119.31 17.52 1.00e+00 1.00e+00 3.07e+02 angle pdb=" C5 ATP E 301 " pdb=" C4 ATP E 301 " pdb=" N3 ATP E 301 " ideal model delta sigma weight residual 126.80 118.28 8.52 1.00e+00 1.00e+00 7.26e+01 ... (remaining 21947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8508 17.94 - 35.88: 815 35.88 - 53.82: 224 53.82 - 71.77: 53 71.77 - 89.71: 12 Dihedral angle restraints: 9612 sinusoidal: 3658 harmonic: 5954 Sorted by residual: dihedral pdb=" CA THR J 77 " pdb=" C THR J 77 " pdb=" N TYR J 78 " pdb=" CA TYR J 78 " ideal model delta harmonic sigma weight residual -180.00 -153.22 -26.78 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA ASP G 95 " pdb=" C ASP G 95 " pdb=" N THR G 96 " pdb=" CA THR G 96 " ideal model delta harmonic sigma weight residual 180.00 154.56 25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA THR L 77 " pdb=" C THR L 77 " pdb=" N TYR L 78 " pdb=" CA TYR L 78 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 9609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2335 0.083 - 0.165: 298 0.165 - 0.248: 13 0.248 - 0.331: 3 0.331 - 0.414: 3 Chirality restraints: 2652 Sorted by residual: chirality pdb=" CB ILE L 71 " pdb=" CA ILE L 71 " pdb=" CG1 ILE L 71 " pdb=" CG2 ILE L 71 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CB ILE I 71 " pdb=" CA ILE I 71 " pdb=" CG1 ILE I 71 " pdb=" CG2 ILE I 71 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CB ILE H 71 " pdb=" CA ILE H 71 " pdb=" CG1 ILE H 71 " pdb=" CG2 ILE H 71 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 2649 not shown) Planarity restraints: 2764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 26 " 0.053 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO C 27 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 27 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 27 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 26 " 0.053 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO F 27 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO F 27 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 27 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 41 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PRO D 42 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 42 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 42 " -0.036 5.00e-02 4.00e+02 ... (remaining 2761 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 80 2.51 - 3.11: 10055 3.11 - 3.70: 22639 3.70 - 4.30: 31649 4.30 - 4.90: 53836 Nonbonded interactions: 118259 Sorted by model distance: nonbonded pdb=" O GLY B 259 " pdb=" O ASP B 260 " model vdw 1.910 3.040 nonbonded pdb=" N GLN E 230 " pdb=" OE1 GLN E 230 " model vdw 2.036 3.120 nonbonded pdb=" O HIS B 226 " pdb=" ND1 HIS B 226 " model vdw 2.129 3.120 nonbonded pdb=" OD1 ASP B 260 " pdb=" N TYR B 261 " model vdw 2.232 3.120 nonbonded pdb=" O TYR E 261 " pdb=" N ALA E 263 " model vdw 2.272 3.120 ... (remaining 118254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = (chain 'G' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = (chain 'H' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = chain 'I' selection = (chain 'J' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = (chain 'K' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.840 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 : 0.008 0.079 16134 Z= 0.361 Angle : 1.105 18.950 21952 Z= 0.658 Chirality : 0.056 0.414 2652 Planarity : 0.007 0.079 2764 Dihedral : 16.082 89.707 5788 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.75 % Favored : 89.01 % Rotamer: Outliers : 6.24 % Allowed : 10.34 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.21 (0.12), residues: 2056 helix: -4.84 (0.06), residues: 811 sheet: -3.29 (0.26), residues: 290 loop : -3.65 (0.16), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 233 TYR 0.036 0.002 TYR J 111 PHE 0.020 0.002 PHE B 254 TRP 0.012 0.002 TRP C 7 HIS 0.003 0.001 HIS E 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00780 / 0.36 (16134) covalent geometry : angle 1.10516 / 0.66 (21952) hydrogen bonds : bond 0.31808 / 20.88 ( 522) hydrogen bonds : angle 11.34493 / 7.67 ( 1482) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 387 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6984 (tp) REVERT: A 72 LEU cc_start: 0.8444 (mm) cc_final: 0.8040 (mt) REVERT: A 111 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8629 (tmm160) REVERT: A 122 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8318 (tp) REVERT: A 203 LEU cc_start: 0.8732 (mt) cc_final: 0.8437 (mt) REVERT: B 130 GLU cc_start: 0.8649 (mm-30) cc_final: 0.7888 (tt0) REVERT: B 176 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8417 (p0) REVERT: B 222 LYS cc_start: 0.8345 (pttt) cc_final: 0.7548 (ptmm) REVERT: B 242 GLN cc_start: 0.6892 (tm-30) cc_final: 0.6486 (tm-30) REVERT: E 139 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8325 (mmtp) REVERT: E 207 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7847 (mm-30) REVERT: E 222 LYS cc_start: 0.8292 (pttt) cc_final: 0.7908 (ptpp) REVERT: D 38 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6491 (mmt180) REVERT: D 129 LEU cc_start: 0.9296 (mt) cc_final: 0.9080 (mt) REVERT: D 134 MET cc_start: 0.8799 (tpt) cc_final: 0.8584 (tpt) REVERT: C 32 ARG cc_start: 0.6746 (ptt90) cc_final: 0.6546 (ptt-90) REVERT: C 81 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8649 (m) REVERT: F 83 THR cc_start: 0.8914 (t) cc_final: 0.8714 (m) REVERT: G 74 ASP cc_start: 0.7947 (t0) cc_final: 0.7712 (t0) REVERT: G 134 ILE cc_start: 0.8664 (mt) cc_final: 0.8450 (mp) REVERT: H 102 ARG cc_start: 0.8339 (mtt180) cc_final: 0.7910 (mtm-85) REVERT: J 30 ASN cc_start: 0.6046 (OUTLIER) cc_final: 0.5539 (m-40) REVERT: J 85 GLU cc_start: 0.8112 (tt0) cc_final: 0.7564 (tt0) REVERT: K 48 ASN cc_start: 0.8274 (m110) cc_final: 0.8013 (t0) outliers start: 105 outliers final: 21 residues processed: 457 average time/residue: 0.1408 time to fit residues: 92.7620 Evaluate side-chains 330 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 301 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 230 GLN Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain J residue 30 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 58.6453 > 50:) chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN A 29 ASN A 73 GLN A 128 GLN A 241 HIS B 57 GLN B 230 GLN E 57 GLN E 62 HIS E 203 HIS D 4 ASN D 29 ASN D 73 GLN D 191 ASN D 241 HIS C 70 ASN F 70 ASN G 91 ASN H 149 GLN I 91 ASN K 6 ASN K 48 ASN K 115 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.140547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 174)---------------| | r_work = 0.3250 r_free = 0.3250 target = 0.121252 restraints weight = 21584.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.118962 restraints weight = 21886.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.119970 restraints weight = 17306.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.120343 restraints weight = 14954.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.120589 restraints weight = 13656.342| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16134 Z= 0.150 Angle : 0.667 8.746 21952 Z= 0.347 Chirality : 0.043 0.175 2652 Planarity : 0.006 0.061 2764 Dihedral : 8.169 87.757 2288 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.64 % Favored : 92.32 % Rotamer: Outliers : 3.27 % Allowed : 16.47 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.74 (0.15), residues: 2056 helix: -3.10 (0.13), residues: 834 sheet: -2.85 (0.28), residues: 276 loop : -3.21 (0.17), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 124 TYR 0.016 0.001 TYR K 40 PHE 0.017 0.002 PHE G 13 TRP 0.011 0.001 TRP E 216 HIS 0.015 0.001 HIS E 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (16134) covalent geometry : angle 0.66749 / 0.35 (21952) hydrogen bonds : bond 0.04849 / 3.17 ( 522) hydrogen bonds : angle 5.34561 / 3.61 ( 1482) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 325 time to evaluate : 0.529 Fit side-chains REVERT: A 26 MET cc_start: 0.8996 (ttt) cc_final: 0.8780 (ttp) REVERT: A 72 LEU cc_start: 0.8480 (mm) cc_final: 0.8224 (mt) REVERT: A 158 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8803 (mp) REVERT: B 141 MET cc_start: 0.8309 (mmm) cc_final: 0.7969 (mmm) REVERT: B 222 LYS cc_start: 0.8187 (pttt) cc_final: 0.7501 (ptmm) REVERT: B 242 GLN cc_start: 0.6930 (tm-30) cc_final: 0.6553 (tm-30) REVERT: E 40 MET cc_start: 0.8074 (mtp) cc_final: 0.7828 (mtt) REVERT: E 222 LYS cc_start: 0.8157 (pttt) cc_final: 0.7917 (ptpp) REVERT: D 75 TYR cc_start: 0.8784 (t80) cc_final: 0.8487 (t80) REVERT: D 129 LEU cc_start: 0.9271 (mt) cc_final: 0.9070 (mt) REVERT: D 231 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8690 (mp) REVERT: C 22 GLN cc_start: 0.7506 (pt0) cc_final: 0.7214 (pt0) REVERT: H 88 GLN cc_start: 0.7526 (mm-40) cc_final: 0.7311 (mm-40) REVERT: J 30 ASN cc_start: 0.6124 (OUTLIER) cc_final: 0.5635 (m-40) REVERT: J 77 THR cc_start: 0.8358 (t) cc_final: 0.8130 (t) REVERT: K 6 ASN cc_start: 0.7479 (t0) cc_final: 0.7195 (t0) REVERT: K 9 TRP cc_start: 0.7716 (t-100) cc_final: 0.6768 (t60) outliers start: 55 outliers final: 33 residues processed: 368 average time/residue: 0.1225 time to fit residues: 67.7664 Evaluate side-chains 312 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 276 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 91 ASN Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 111 TYR Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain L residue 100 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 91 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 193 optimal weight: 0.0970 chunk 168 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 overall best weight: 1.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 233 GLN E 62 HIS D 191 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.141700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.125054 restraints weight = 21836.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.122080 restraints weight = 32088.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.121008 restraints weight = 27646.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.121277 restraints weight = 25327.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.121724 restraints weight = 20243.535| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16134 Z= 0.111 Angle : 0.595 8.626 21952 Z= 0.306 Chirality : 0.041 0.246 2652 Planarity : 0.005 0.049 2764 Dihedral : 6.242 64.920 2249 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.88 % Favored : 92.07 % Rotamer: Outliers : 3.57 % Allowed : 18.73 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.16), residues: 2056 helix: -2.04 (0.16), residues: 842 sheet: -2.60 (0.29), residues: 286 loop : -2.93 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 124 TYR 0.013 0.001 TYR K 40 PHE 0.012 0.001 PHE E 254 TRP 0.009 0.001 TRP A 177 HIS 0.013 0.001 HIS E 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (16134) covalent geometry : angle 0.59537 / 0.31 (21952) hydrogen bonds : bond 0.03730 / 2.44 ( 522) hydrogen bonds : angle 4.56837 / 3.10 ( 1482) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 304 time to evaluate : 0.611 Fit side-chains REVERT: A 72 LEU cc_start: 0.8532 (mm) cc_final: 0.8321 (mt) REVERT: B 141 MET cc_start: 0.8287 (mmm) cc_final: 0.7995 (mmm) REVERT: B 170 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7860 (mt0) REVERT: B 222 LYS cc_start: 0.8199 (pttt) cc_final: 0.7682 (ptmm) REVERT: B 242 GLN cc_start: 0.6889 (tm-30) cc_final: 0.6588 (tm-30) REVERT: E 222 LYS cc_start: 0.8177 (pttt) cc_final: 0.7889 (ptpp) REVERT: D 75 TYR cc_start: 0.8797 (t80) cc_final: 0.8320 (t80) REVERT: D 134 MET cc_start: 0.8479 (tpt) cc_final: 0.8268 (tpt) REVERT: C 22 GLN cc_start: 0.7503 (pt0) cc_final: 0.7265 (pt0) REVERT: I 85 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6010 (mp0) REVERT: J 30 ASN cc_start: 0.5848 (OUTLIER) cc_final: 0.5635 (m-40) REVERT: J 77 THR cc_start: 0.8206 (t) cc_final: 0.7989 (p) REVERT: K 9 TRP cc_start: 0.7765 (t-100) cc_final: 0.6856 (t60) REVERT: K 151 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6602 (pp) outliers start: 60 outliers final: 33 residues processed: 346 average time/residue: 0.1260 time to fit residues: 65.9881 Evaluate side-chains 312 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 275 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 142 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 153 optimal weight: 0.0370 chunk 20 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 chunk 110 optimal weight: 0.0020 chunk 41 optimal weight: 1.9990 overall best weight: 0.6668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 HIS D 191 ASN K 6 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.144315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.128927 restraints weight = 21425.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.126628 restraints weight = 27597.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.125204 restraints weight = 25940.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.125299 restraints weight = 25161.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.125602 restraints weight = 21119.064| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16134 Z= 0.097 Angle : 0.566 8.520 21952 Z= 0.289 Chirality : 0.040 0.157 2652 Planarity : 0.004 0.042 2764 Dihedral : 5.712 62.539 2243 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.91 % Allowed : 20.81 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.17), residues: 2056 helix: -1.32 (0.18), residues: 820 sheet: -2.36 (0.29), residues: 288 loop : -2.80 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 124 TYR 0.014 0.001 TYR J 152 PHE 0.020 0.001 PHE A 219 TRP 0.006 0.001 TRP A 177 HIS 0.003 0.000 HIS E 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (16134) covalent geometry : angle 0.56551 / 0.29 (21952) hydrogen bonds : bond 0.03022 / 1.99 ( 522) hydrogen bonds : angle 4.20619 / 2.85 ( 1482) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 296 time to evaluate : 0.611 Fit side-chains REVERT: A 72 LEU cc_start: 0.8528 (mm) cc_final: 0.8306 (mt) REVERT: B 141 MET cc_start: 0.8201 (mmm) cc_final: 0.7931 (mmm) REVERT: B 242 GLN cc_start: 0.6736 (tm-30) cc_final: 0.6526 (tm-30) REVERT: E 222 LYS cc_start: 0.8137 (pttt) cc_final: 0.7844 (ptpp) REVERT: D 26 MET cc_start: 0.8864 (ttp) cc_final: 0.8349 (tmm) REVERT: D 75 TYR cc_start: 0.8779 (t80) cc_final: 0.8291 (t80) REVERT: D 134 MET cc_start: 0.8471 (tpt) cc_final: 0.8190 (mmm) REVERT: H 70 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8372 (t0) REVERT: K 6 ASN cc_start: 0.7387 (t0) cc_final: 0.7044 (t0) REVERT: K 92 HIS cc_start: 0.7643 (t-90) cc_final: 0.7298 (t-90) REVERT: K 151 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6667 (pp) outliers start: 49 outliers final: 35 residues processed: 327 average time/residue: 0.1251 time to fit residues: 61.8620 Evaluate side-chains 305 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 111 TYR Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 123 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 74 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 199 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 139 optimal weight: 0.4980 chunk 173 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 114 optimal weight: 0.3980 chunk 184 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.143881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 135)---------------| | r_work = 0.3321 r_free = 0.3321 target = 0.126475 restraints weight = 21499.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.122764 restraints weight = 31114.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 76)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.121919 restraints weight = 22495.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.122171 restraints weight = 20546.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.122723 restraints weight = 16975.533| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16134 Z= 0.103 Angle : 0.565 8.648 21952 Z= 0.288 Chirality : 0.041 0.157 2652 Planarity : 0.004 0.043 2764 Dihedral : 5.348 61.913 2240 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.45 % Allowed : 20.87 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.18), residues: 2056 helix: -0.97 (0.19), residues: 820 sheet: -2.15 (0.30), residues: 288 loop : -2.71 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 18 TYR 0.013 0.001 TYR K 40 PHE 0.014 0.001 PHE A 219 TRP 0.005 0.001 TRP E 216 HIS 0.006 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (16134) covalent geometry : angle 0.56467 / 0.29 (21952) hydrogen bonds : bond 0.03012 / 1.99 ( 522) hydrogen bonds : angle 4.14374 / 2.82 ( 1482) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 272 time to evaluate : 0.595 Fit side-chains REVERT: A 72 LEU cc_start: 0.8500 (mm) cc_final: 0.8275 (mt) REVERT: B 141 MET cc_start: 0.8231 (mmm) cc_final: 0.7895 (mmm) REVERT: B 170 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.7925 (mt0) REVERT: B 242 GLN cc_start: 0.6969 (tm-30) cc_final: 0.6601 (tm-30) REVERT: D 26 MET cc_start: 0.8866 (ttp) cc_final: 0.8452 (tmm) REVERT: D 75 TYR cc_start: 0.8791 (t80) cc_final: 0.8290 (t80) REVERT: D 134 MET cc_start: 0.8503 (tpt) cc_final: 0.8268 (mmm) REVERT: G 78 TYR cc_start: 0.8639 (m-80) cc_final: 0.7618 (m-80) REVERT: I 85 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6170 (mp0) REVERT: I 91 ASN cc_start: 0.7924 (OUTLIER) cc_final: 0.7635 (p0) REVERT: K 22 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7278 (mm) REVERT: K 92 HIS cc_start: 0.7779 (t-90) cc_final: 0.7377 (t-90) REVERT: K 151 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6596 (pp) outliers start: 58 outliers final: 36 residues processed: 309 average time/residue: 0.1174 time to fit residues: 55.4367 Evaluate side-chains 305 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 264 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 91 ASN Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 111 TYR Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 142 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 chunk 126 optimal weight: 0.4980 chunk 100 optimal weight: 0.2980 chunk 71 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 195 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.141596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.125168 restraints weight = 21559.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 107)---------------| | r_work = 0.3252 r_free = 0.3252 target = 0.121296 restraints weight = 27442.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 74)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.119385 restraints weight = 32465.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.120360 restraints weight = 26446.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.120680 restraints weight = 20324.897| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16134 Z= 0.111 Angle : 0.571 8.912 21952 Z= 0.290 Chirality : 0.041 0.157 2652 Planarity : 0.004 0.043 2764 Dihedral : 5.207 62.286 2239 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.86 % Allowed : 20.81 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.18), residues: 2056 helix: -0.67 (0.19), residues: 818 sheet: -1.95 (0.30), residues: 288 loop : -2.62 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 18 TYR 0.015 0.001 TYR K 40 PHE 0.016 0.001 PHE A 219 TRP 0.007 0.001 TRP E 216 HIS 0.002 0.001 HIS B 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (16134) covalent geometry : angle 0.57114 / 0.29 (21952) hydrogen bonds : bond 0.03120 / 2.06 ( 522) hydrogen bonds : angle 4.07289 / 2.77 ( 1482) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 286 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8302 (mt) REVERT: B 141 MET cc_start: 0.8196 (mmm) cc_final: 0.7832 (mmm) REVERT: B 242 GLN cc_start: 0.6895 (tm-30) cc_final: 0.6528 (tm-30) REVERT: E 222 LYS cc_start: 0.8108 (pttt) cc_final: 0.7773 (ptpp) REVERT: D 26 MET cc_start: 0.8908 (ttp) cc_final: 0.8568 (tmm) REVERT: D 75 TYR cc_start: 0.8803 (t80) cc_final: 0.8315 (t80) REVERT: D 134 MET cc_start: 0.8555 (tpt) cc_final: 0.8307 (mmm) REVERT: D 231 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8822 (mp) REVERT: C 8 MET cc_start: 0.5670 (mmt) cc_final: 0.5360 (mmt) REVERT: I 84 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8560 (mt) REVERT: I 85 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6303 (mp0) REVERT: K 6 ASN cc_start: 0.7556 (t0) cc_final: 0.6880 (t0) REVERT: K 22 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7283 (mm) REVERT: K 92 HIS cc_start: 0.7698 (t-90) cc_final: 0.7261 (t-90) REVERT: K 151 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6667 (pp) outliers start: 65 outliers final: 38 residues processed: 327 average time/residue: 0.1163 time to fit residues: 58.5128 Evaluate side-chains 321 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 277 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 89 ARG Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 142 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 152 optimal weight: 0.5980 chunk 196 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN I 91 ASN K 6 ASN L 91 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.139359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.122197 restraints weight = 21564.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.118173 restraints weight = 29558.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.118316 restraints weight = 25355.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.118297 restraints weight = 21393.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.118403 restraints weight = 20769.666| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16134 Z= 0.138 Angle : 0.599 9.230 21952 Z= 0.303 Chirality : 0.042 0.158 2652 Planarity : 0.004 0.043 2764 Dihedral : 5.280 63.484 2239 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.98 % Allowed : 21.40 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.18), residues: 2056 helix: -0.66 (0.19), residues: 832 sheet: -1.89 (0.31), residues: 286 loop : -2.50 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 18 TYR 0.017 0.001 TYR K 40 PHE 0.024 0.001 PHE A 219 TRP 0.008 0.001 TRP E 216 HIS 0.002 0.001 HIS B 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (16134) covalent geometry : angle 0.59917 / 0.30 (21952) hydrogen bonds : bond 0.03465 / 2.29 ( 522) hydrogen bonds : angle 4.15062 / 2.82 ( 1482) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 281 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8322 (mt) REVERT: B 242 GLN cc_start: 0.7519 (tm-30) cc_final: 0.7156 (tm-30) REVERT: E 162 GLU cc_start: 0.8634 (pm20) cc_final: 0.8415 (pm20) REVERT: E 222 LYS cc_start: 0.8130 (pttt) cc_final: 0.7780 (ptpp) REVERT: D 26 MET cc_start: 0.8916 (ttp) cc_final: 0.8520 (tmm) REVERT: D 75 TYR cc_start: 0.8846 (t80) cc_final: 0.8364 (t80) REVERT: F 37 LYS cc_start: 0.5709 (OUTLIER) cc_final: 0.5451 (pttp) REVERT: I 84 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8577 (mt) REVERT: I 85 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6253 (mp0) REVERT: I 91 ASN cc_start: 0.7806 (OUTLIER) cc_final: 0.7516 (p0) REVERT: K 6 ASN cc_start: 0.7604 (t0) cc_final: 0.6831 (t0) REVERT: K 22 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7317 (mm) REVERT: K 79 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7472 (pp) REVERT: K 92 HIS cc_start: 0.7824 (t-90) cc_final: 0.7336 (t-90) REVERT: K 151 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.6872 (pp) outliers start: 67 outliers final: 49 residues processed: 326 average time/residue: 0.1172 time to fit residues: 58.9579 Evaluate side-chains 332 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 275 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 89 ARG Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 91 ASN Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 142 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 131 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 69 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 ASN ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 ASN L 91 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.143277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.126677 restraints weight = 21495.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 118)---------------| | r_work = 0.3271 r_free = 0.3271 target = 0.122902 restraints weight = 27863.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.122271 restraints weight = 28619.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.122652 restraints weight = 22437.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.122761 restraints weight = 18988.917| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16134 Z= 0.096 Angle : 0.564 9.152 21952 Z= 0.285 Chirality : 0.040 0.150 2652 Planarity : 0.004 0.047 2764 Dihedral : 4.987 60.844 2239 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.03 % Allowed : 22.24 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.19), residues: 2056 helix: -0.29 (0.19), residues: 818 sheet: -1.74 (0.31), residues: 288 loop : -2.46 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 18 TYR 0.013 0.001 TYR I 90 PHE 0.018 0.001 PHE A 219 TRP 0.006 0.001 TRP E 216 HIS 0.004 0.000 HIS L 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (16134) covalent geometry : angle 0.56435 / 0.28 (21952) hydrogen bonds : bond 0.02808 / 1.86 ( 522) hydrogen bonds : angle 3.95472 / 2.68 ( 1482) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 288 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8328 (mt) REVERT: A 242 SER cc_start: 0.8737 (p) cc_final: 0.8278 (p) REVERT: B 141 MET cc_start: 0.8247 (mmm) cc_final: 0.7878 (mmm) REVERT: B 242 GLN cc_start: 0.7211 (tm-30) cc_final: 0.6762 (tm-30) REVERT: E 162 GLU cc_start: 0.8627 (pm20) cc_final: 0.8409 (pm20) REVERT: E 222 LYS cc_start: 0.8097 (pttt) cc_final: 0.7759 (ptpp) REVERT: D 26 MET cc_start: 0.8925 (ttp) cc_final: 0.8599 (tmm) REVERT: D 75 TYR cc_start: 0.8778 (t80) cc_final: 0.8304 (t80) REVERT: F 37 LYS cc_start: 0.5664 (OUTLIER) cc_final: 0.5408 (pttp) REVERT: I 84 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8569 (mt) REVERT: I 85 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6287 (mp0) REVERT: I 91 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7809 (p0) REVERT: K 6 ASN cc_start: 0.7488 (t0) cc_final: 0.7183 (t0) REVERT: K 22 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7236 (mm) REVERT: K 79 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7421 (pp) REVERT: K 92 HIS cc_start: 0.7779 (t-90) cc_final: 0.7480 (t-90) REVERT: K 151 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6789 (pp) outliers start: 51 outliers final: 34 residues processed: 320 average time/residue: 0.1143 time to fit residues: 56.4735 Evaluate side-chains 315 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 273 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 91 ASN Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 111 TYR Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain L residue 123 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 15 optimal weight: 0.6980 chunk 103 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 95 optimal weight: 0.6980 chunk 166 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN D 128 GLN I 91 ASN L 91 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.141091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.124755 restraints weight = 21487.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.122230 restraints weight = 27578.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.120692 restraints weight = 28579.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.120950 restraints weight = 26588.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.121260 restraints weight = 21374.062| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16134 Z= 0.117 Angle : 0.581 9.060 21952 Z= 0.293 Chirality : 0.042 0.152 2652 Planarity : 0.004 0.047 2764 Dihedral : 5.009 61.319 2239 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.33 % Allowed : 22.12 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.19), residues: 2056 helix: -0.25 (0.19), residues: 820 sheet: -1.65 (0.31), residues: 288 loop : -2.44 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 18 TYR 0.014 0.001 TYR K 40 PHE 0.017 0.001 PHE A 219 TRP 0.007 0.001 TRP E 216 HIS 0.002 0.000 HIS B 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (16134) covalent geometry : angle 0.58061 / 0.29 (21952) hydrogen bonds : bond 0.03119 / 2.06 ( 522) hydrogen bonds : angle 4.00635 / 2.72 ( 1482) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 276 time to evaluate : 0.618 Fit side-chains REVERT: A 72 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8332 (mt) REVERT: A 242 SER cc_start: 0.8829 (p) cc_final: 0.8367 (p) REVERT: B 141 MET cc_start: 0.8291 (mmm) cc_final: 0.7891 (mmm) REVERT: B 242 GLN cc_start: 0.7423 (tm-30) cc_final: 0.7088 (tm-30) REVERT: E 162 GLU cc_start: 0.8711 (pm20) cc_final: 0.8434 (pm20) REVERT: E 222 LYS cc_start: 0.8136 (pttt) cc_final: 0.7820 (ptpp) REVERT: D 26 MET cc_start: 0.8918 (ttp) cc_final: 0.8615 (tmm) REVERT: D 75 TYR cc_start: 0.8824 (t80) cc_final: 0.8335 (t80) REVERT: F 37 LYS cc_start: 0.5816 (OUTLIER) cc_final: 0.5539 (pttp) REVERT: I 84 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8580 (mt) REVERT: I 85 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6292 (mp0) REVERT: I 91 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7666 (p0) REVERT: K 6 ASN cc_start: 0.7552 (t0) cc_final: 0.7292 (t0) REVERT: K 22 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7356 (mm) REVERT: K 79 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7414 (pp) REVERT: K 151 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6815 (pp) outliers start: 56 outliers final: 39 residues processed: 312 average time/residue: 0.1218 time to fit residues: 58.0202 Evaluate side-chains 321 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 274 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 89 ARG Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 91 ASN Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 111 TYR Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain L residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 158 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 181 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.143780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 137)---------------| | r_work = 0.3316 r_free = 0.3316 target = 0.126180 restraints weight = 21520.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.122176 restraints weight = 32142.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.121838 restraints weight = 22431.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.122036 restraints weight = 20873.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.122125 restraints weight = 17925.950| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16134 Z= 0.099 Angle : 0.567 9.082 21952 Z= 0.288 Chirality : 0.041 0.148 2652 Planarity : 0.004 0.049 2764 Dihedral : 4.838 60.110 2238 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.79 % Allowed : 22.77 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.19), residues: 2056 helix: -0.06 (0.19), residues: 820 sheet: -1.58 (0.30), residues: 308 loop : -2.36 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 18 TYR 0.012 0.001 TYR K 40 PHE 0.016 0.001 PHE A 219 TRP 0.006 0.001 TRP E 216 HIS 0.003 0.000 HIS I 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (16134) covalent geometry : angle 0.56661 / 0.29 (21952) hydrogen bonds : bond 0.02828 / 1.88 ( 522) hydrogen bonds : angle 3.91046 / 2.66 ( 1482) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 280 time to evaluate : 0.583 Fit side-chains REVERT: A 18 ARG cc_start: 0.7042 (mpt180) cc_final: 0.6800 (mpt180) REVERT: A 72 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8359 (mt) REVERT: A 242 SER cc_start: 0.8866 (p) cc_final: 0.8428 (p) REVERT: B 141 MET cc_start: 0.8285 (mmm) cc_final: 0.7927 (mmm) REVERT: B 242 GLN cc_start: 0.7554 (tm-30) cc_final: 0.7071 (tm-30) REVERT: E 162 GLU cc_start: 0.8595 (pm20) cc_final: 0.8391 (pm20) REVERT: E 222 LYS cc_start: 0.8137 (pttt) cc_final: 0.7761 (ptpp) REVERT: D 26 MET cc_start: 0.8925 (ttp) cc_final: 0.8625 (tmm) REVERT: D 75 TYR cc_start: 0.8778 (t80) cc_final: 0.8286 (t80) REVERT: F 37 LYS cc_start: 0.6191 (OUTLIER) cc_final: 0.5931 (pttp) REVERT: I 84 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8575 (mt) REVERT: I 85 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6333 (mp0) REVERT: I 91 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7665 (p0) REVERT: K 6 ASN cc_start: 0.7507 (t0) cc_final: 0.7258 (t0) REVERT: K 22 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7204 (mm) REVERT: K 151 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6763 (pp) outliers start: 47 outliers final: 36 residues processed: 309 average time/residue: 0.1178 time to fit residues: 55.6622 Evaluate side-chains 319 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 276 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 91 ASN Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 111 TYR Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 118 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 164 optimal weight: 0.0570 chunk 184 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 84 optimal weight: 0.0170 chunk 65 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN L 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.144523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.128348 restraints weight = 21240.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.126398 restraints weight = 27225.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.124449 restraints weight = 26708.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.124676 restraints weight = 25451.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.124968 restraints weight = 21351.680| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16134 Z= 0.098 Angle : 0.564 9.025 21952 Z= 0.285 Chirality : 0.040 0.147 2652 Planarity : 0.004 0.056 2764 Dihedral : 4.700 58.690 2238 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.50 % Allowed : 22.95 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.19), residues: 2056 helix: 0.10 (0.20), residues: 824 sheet: -1.54 (0.30), residues: 316 loop : -2.28 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 18 TYR 0.011 0.001 TYR G 152 PHE 0.015 0.001 PHE A 219 TRP 0.006 0.001 TRP K 9 HIS 0.008 0.000 HIS B 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (16134) covalent geometry : angle 0.56371 / 0.29 (21952) hydrogen bonds : bond 0.02654 / 1.76 ( 522) hydrogen bonds : angle 3.82560 / 2.60 ( 1482) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2822.69 seconds wall clock time: 49 minutes 24.11 seconds (2964.11 seconds total)