Starting phenix.real_space_refine on Sat Sep 12 11:47:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cgn_30358/09_2026/7cgn_30358.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cgn_30358/09_2026/7cgn_30358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7cgn_30358/09_2026/7cgn_30358.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cgn_30358/09_2026/7cgn_30358.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cgn_30358/09_2026/7cgn_30358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cgn_30358/09_2026/7cgn_30358.map" model { file = "/net/cci-nas-00/data/ceres_data/7cgn_30358/09_2026/7cgn_30358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cgn_30358/09_2026/7cgn_30358.cif" } resolution = 4.3 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= 0.004 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 2950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 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: 15854 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: "C" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 724 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} 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: "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: "F" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 724 Classifications: {'peptide': 94} 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: 3.56, per 1000 atoms: 0.22 Number of scatterers: 15854 At special positions: 0 Unit cell: (104.352, 116.309, 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 2950 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: 1.14 Conformation dependent library (CDL) restraints added in 620.7 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: 64 helices and 20 sheets defined 42.9% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 5 through 31 removed outlier: 3.752A pdb=" N LEU A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 12 " --> pdb=" O SER A 8 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU A 17 " --> pdb=" O GLY A 13 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 52 removed outlier: 3.710A pdb=" N VAL A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.804A pdb=" N ILE A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 87 through 96 removed outlier: 3.822A pdb=" N ALA A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 126 removed outlier: 3.705A pdb=" N VAL A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 133 removed outlier: 3.533A 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 153 removed outlier: 3.588A pdb=" N VAL A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 174 removed outlier: 4.001A pdb=" N LEU A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 191 removed outlier: 3.686A pdb=" N TRP A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 221 removed outlier: 4.022A pdb=" N LEU A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 258 removed outlier: 4.136A pdb=" N SER A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.769A pdb=" N LEU B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 removed outlier: 3.863A pdb=" N ALA B 74 " --> pdb=" O ASN B 71 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET B 75 " --> pdb=" O ILE B 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 through 75' Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 109 through 114 Processing helix chain 'B' and resid 117 through 132 removed outlier: 3.878A pdb=" N LYS B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 130 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.539A pdb=" N ARG B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 193 removed outlier: 3.520A pdb=" N LYS B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN B 191 " --> pdb=" O ILE B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 237 through 246 Processing helix chain 'C' and resid 25 through 31 Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 80 through 88 removed outlier: 3.669A pdb=" N LYS C 86 " --> pdb=" O TYR C 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 31 removed outlier: 3.752A pdb=" N LEU D 9 " --> pdb=" O ALA D 5 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS D 12 " --> pdb=" O SER D 8 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE D 14 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU D 17 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR D 19 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 52 removed outlier: 3.710A pdb=" N VAL D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG D 46 " --> pdb=" O PRO D 42 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR D 49 " --> pdb=" O VAL D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 removed outlier: 3.803A pdb=" N ILE D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU D 76 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 87 through 96 removed outlier: 3.822A pdb=" N ALA D 92 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU D 93 " --> pdb=" O MET D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 126 removed outlier: 3.705A pdb=" N VAL D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA D 104 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 114 " --> pdb=" O GLY D 110 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 133 removed outlier: 3.533A 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 153 removed outlier: 3.589A pdb=" N VAL D 152 " --> pdb=" O PHE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 174 removed outlier: 4.000A pdb=" N LEU D 157 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA D 164 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 173 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY D 174 " --> pdb=" O GLY D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.687A pdb=" N TRP D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA D 188 " --> pdb=" O PHE D 184 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 221 removed outlier: 4.021A pdb=" N LEU D 203 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 208 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 211 " --> pdb=" O VAL D 207 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR D 212 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP D 215 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 258 removed outlier: 4.137A pdb=" N SER D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL D 240 " --> pdb=" O THR D 236 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 244 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU D 247 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE D 258 " --> pdb=" O THR D 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 removed outlier: 3.769A pdb=" N LEU E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 75 removed outlier: 3.864A pdb=" N ALA E 74 " --> pdb=" O ASN E 71 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET E 75 " --> pdb=" O ILE E 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 71 through 75' Processing helix chain 'E' and resid 76 through 84 Processing helix chain 'E' and resid 101 through 107 Processing helix chain 'E' and resid 109 through 114 Processing helix chain 'E' and resid 117 through 132 removed outlier: 3.878A pdb=" N LYS E 128 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU E 130 " --> pdb=" O MET E 126 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL E 132 " --> pdb=" O LYS E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 159 removed outlier: 3.540A pdb=" N ARG E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG E 152 " --> pdb=" O GLY E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 3.520A pdb=" N LYS E 185 " --> pdb=" O GLY E 181 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN E 191 " --> pdb=" O ILE E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 209 Processing helix chain 'E' and resid 237 through 246 Processing helix chain 'F' and resid 25 through 31 Processing helix chain 'F' and resid 51 through 64 Processing helix chain 'F' and resid 80 through 88 removed outlier: 3.669A pdb=" N LYS F 86 " --> pdb=" O TYR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 26 removed outlier: 3.540A pdb=" N TRP G 9 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY G 11 " --> pdb=" O GLU G 7 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 18 " --> pdb=" O LEU G 14 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 150 Processing helix chain 'H' and resid 9 through 28 removed outlier: 3.985A pdb=" N PHE H 13 " --> pdb=" O TRP H 9 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS H 25 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS H 27 " --> pdb=" O PHE H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 152 removed outlier: 3.759A pdb=" N PHE H 150 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU H 151 " --> pdb=" O ILE H 147 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR H 152 " --> pdb=" O GLY H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 28 removed outlier: 4.028A pdb=" N TRP I 9 " --> pdb=" O LYS I 5 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL I 10 " --> pdb=" O ASN I 6 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE I 13 " --> pdb=" O TRP I 9 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 152 removed outlier: 3.515A pdb=" N PHE I 150 " --> pdb=" O LEU I 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 29 removed outlier: 3.702A pdb=" N GLY J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 152 removed outlier: 3.515A pdb=" N PHE J 150 " --> pdb=" O LEU J 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 29 removed outlier: 3.993A pdb=" N ALA K 28 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA K 29 " --> pdb=" O CYS K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 152 removed outlier: 4.568A pdb=" N LEU K 146 " --> pdb=" O VAL K 142 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU K 151 " --> pdb=" O ILE K 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 28 Processing helix chain 'L' and resid 143 through 151 removed outlier: 3.565A pdb=" N PHE L 150 " --> pdb=" O LEU L 146 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 32 removed outlier: 6.033A pdb=" N ILE B 27 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP B 13 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 29 " --> pdb=" O MET B 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.721A pdb=" N SER B 88 " --> pdb=" O MET B 167 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP B 169 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU B 90 " --> pdb=" O ASP B 169 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B 37 " --> pdb=" O CYS B 198 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ILE B 36 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N TRP B 216 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA B 38 " --> pdb=" O TRP B 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AA4, first strand: chain 'E' and resid 27 through 32 removed outlier: 6.033A pdb=" N ILE E 27 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP E 13 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU E 29 " --> pdb=" O MET E 11 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 87 through 90 removed outlier: 6.720A pdb=" N SER E 88 " --> pdb=" O MET E 167 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ASP E 169 " --> pdb=" O SER E 88 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU E 90 " --> pdb=" O ASP E 169 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR E 37 " --> pdb=" O CYS E 198 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE E 36 " --> pdb=" O HIS E 214 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N TRP E 216 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA E 38 " --> pdb=" O TRP E 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 41 through 42 Processing sheet with id=AA7, first strand: chain 'G' and resid 97 through 98 Processing sheet with id=AA8, first strand: chain 'G' and resid 97 through 98 removed outlier: 6.815A pdb=" N VAL G 58 " --> pdb=" O VAL G 65 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N VAL G 65 " --> pdb=" O GLU G 87 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU G 87 " --> pdb=" O VAL G 65 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG G 67 " --> pdb=" O GLU G 85 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU G 85 " --> pdb=" O ARG G 67 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU G 42 " --> pdb=" O LEU G 84 " (cutoff:3.500A) removed outlier: 9.455A pdb=" N ILE G 134 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N TYR G 43 " --> pdb=" O ILE G 134 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 81 through 87 removed outlier: 8.825A pdb=" N ILE H 134 " --> pdb=" O THR H 41 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR H 43 " --> pdb=" O ILE H 134 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 63 through 67 removed outlier: 6.864A pdb=" N VAL H 58 " --> pdb=" O VAL H 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 39 through 40 Processing sheet with id=AB3, first strand: chain 'I' and resid 63 through 68 removed outlier: 3.686A pdb=" N VAL I 63 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL I 58 " --> pdb=" O VAL I 65 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG I 67 " --> pdb=" O SER I 56 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER I 56 " --> pdb=" O ARG I 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 81 through 87 removed outlier: 3.634A pdb=" N LEU J 42 " --> pdb=" O LEU J 84 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ILE J 134 " --> pdb=" O THR J 41 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N TYR J 43 " --> pdb=" O ILE J 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 63 through 67 removed outlier: 3.751A pdb=" N VAL J 63 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL J 58 " --> pdb=" O VAL J 65 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU J 114 " --> pdb=" O PRO J 57 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER J 59 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL J 116 " --> pdb=" O SER J 59 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 39 through 40 Processing sheet with id=AB7, first strand: chain 'K' and resid 81 through 83 removed outlier: 7.754A pdb=" N TYR K 43 " --> pdb=" O ILE K 134 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 63 through 68 removed outlier: 6.382A pdb=" N VAL K 58 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG K 67 " --> pdb=" O SER K 56 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N SER K 56 " --> pdb=" O ARG K 67 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 63 through 68 removed outlier: 6.382A pdb=" N VAL K 58 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG K 67 " --> pdb=" O SER K 56 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N SER K 56 " --> pdb=" O ARG K 67 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 39 through 40 Processing sheet with id=AC2, first strand: chain 'L' and resid 63 through 67 removed outlier: 6.732A pdb=" N VAL L 58 " --> pdb=" O VAL L 65 " (cutoff:3.500A) 609 hydrogen bonds defined for protein. 1782 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: 2.39 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5142 1.35 - 1.47: 3629 1.47 - 1.60: 7227 1.60 - 1.72: 10 1.72 - 1.84: 124 Bond restraints: 16132 Sorted by residual: bond pdb=" C4 ATP E 301 " pdb=" C5 ATP E 301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.91e+01 bond pdb=" C4 ATP B 301 " pdb=" C5 ATP B 301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.86e+01 bond pdb=" C5 ATP E 301 " pdb=" C6 ATP E 301 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.34e+01 bond pdb=" C5 ATP B 301 " pdb=" C6 ATP B 301 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.33e+01 bond pdb=" C8 ATP E 301 " pdb=" N7 ATP E 301 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.30e+01 ... (remaining 16127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.87: 21687 3.87 - 7.75: 221 7.75 - 11.62: 36 11.62 - 15.49: 0 15.49 - 19.37: 4 Bond angle restraints: 21948 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 139.87 120.50 19.37 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB ATP B 301 " pdb=" O3B ATP B 301 " pdb=" PG ATP B 301 " ideal model delta sigma weight residual 139.87 120.56 19.31 1.00e+00 1.00e+00 3.73e+02 angle pdb=" PA ATP E 301 " pdb=" O3A ATP E 301 " pdb=" PB ATP E 301 " ideal model delta sigma weight residual 136.83 120.47 16.36 1.00e+00 1.00e+00 2.68e+02 angle pdb=" PA ATP B 301 " pdb=" O3A ATP B 301 " pdb=" PB ATP B 301 " ideal model delta sigma weight residual 136.83 120.51 16.32 1.00e+00 1.00e+00 2.66e+02 angle pdb=" C5 ATP E 301 " pdb=" C4 ATP E 301 " pdb=" N3 ATP E 301 " ideal model delta sigma weight residual 126.80 118.64 8.16 1.00e+00 1.00e+00 6.67e+01 ... (remaining 21943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 8401 17.12 - 34.23: 848 34.23 - 51.35: 247 51.35 - 68.47: 92 68.47 - 85.59: 22 Dihedral angle restraints: 9610 sinusoidal: 3656 harmonic: 5954 Sorted by residual: dihedral pdb=" CA GLN J 135 " pdb=" C GLN J 135 " pdb=" N ASP J 136 " pdb=" CA ASP J 136 " ideal model delta harmonic sigma weight residual 180.00 152.81 27.19 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ALA K 140 " pdb=" C ALA K 140 " pdb=" N MET K 141 " pdb=" CA MET K 141 " ideal model delta harmonic sigma weight residual 180.00 155.54 24.46 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA VAL J 142 " pdb=" C VAL J 142 " pdb=" N LEU J 143 " pdb=" CA LEU J 143 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 9607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2114 0.064 - 0.129: 443 0.129 - 0.193: 76 0.193 - 0.257: 15 0.257 - 0.321: 4 Chirality restraints: 2652 Sorted by residual: chirality pdb=" CB ILE B 223 " pdb=" CA ILE B 223 " pdb=" CG1 ILE B 223 " pdb=" CG2 ILE B 223 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB ILE E 223 " pdb=" CA ILE E 223 " pdb=" CG1 ILE E 223 " pdb=" CG2 ILE E 223 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB ILE J 60 " pdb=" CA ILE J 60 " pdb=" CG1 ILE J 60 " pdb=" CG2 ILE J 60 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 2649 not shown) Planarity restraints: 2762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 16 " -0.024 2.00e-02 2.50e+03 2.39e-02 9.99e+00 pdb=" CG PHE E 16 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE E 16 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE E 16 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE E 16 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE E 16 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE E 16 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 16 " 0.024 2.00e-02 2.50e+03 2.38e-02 9.94e+00 pdb=" CG PHE B 16 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE B 16 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE B 16 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 16 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 16 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 16 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 41 " -0.049 5.00e-02 4.00e+02 7.46e-02 8.89e+00 pdb=" N PRO B 42 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 42 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 42 " -0.040 5.00e-02 4.00e+02 ... (remaining 2759 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2668 2.76 - 3.30: 14898 3.30 - 3.83: 26061 3.83 - 4.37: 28802 4.37 - 4.90: 48214 Nonbonded interactions: 120643 Sorted by model distance: nonbonded pdb=" O ALA K 69 " pdb=" N ILE K 71 " model vdw 2.225 3.120 nonbonded pdb=" O GLY A 110 " pdb=" OG SER A 114 " model vdw 2.230 3.040 nonbonded pdb=" O GLY D 110 " pdb=" OG SER D 114 " model vdw 2.231 3.040 nonbonded pdb=" O PRO B 42 " pdb=" CG ASP E 176 " model vdw 2.242 3.270 nonbonded pdb=" OG SER I 100 " pdb=" O ALA I 113 " model vdw 2.252 3.040 ... (remaining 120638 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: 0.03 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: 0.580 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.510 Find NCS groups from input model: 0.320 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 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 : 0.006 0.083 16132 Z= 0.321 Angle : 1.118 19.367 21948 Z= 0.678 Chirality : 0.057 0.321 2652 Planarity : 0.007 0.075 2762 Dihedral : 16.713 85.586 5786 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.44 % Favored : 89.83 % Rotamer: Outliers : 6.36 % Allowed : 9.75 % Favored : 83.89 % 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: -5.60 (0.13), residues: 2056 helix: -4.23 (0.08), residues: 801 sheet: -3.05 (0.28), residues: 254 loop : -3.41 (0.16), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 18 TYR 0.020 0.002 TYR H 40 PHE 0.054 0.002 PHE B 16 TRP 0.012 0.002 TRP B 216 HIS 0.006 0.001 HIS K 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.32 (16132) covalent geometry : angle 1.11757 / 0.68 (21948) hydrogen bonds : bond 0.33197 / 21.86 ( 601) hydrogen bonds : angle 10.71981 / 7.61 ( 1782) *********************** 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 617 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 510 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 TYR cc_start: 0.7525 (m-80) cc_final: 0.7269 (m-80) REVERT: A 189 MET cc_start: 0.6996 (ttm) cc_final: 0.6658 (ttm) REVERT: A 201 ASN cc_start: 0.8626 (t0) cc_final: 0.8267 (t0) REVERT: A 251 PHE cc_start: 0.8406 (t80) cc_final: 0.7976 (t80) REVERT: B 10 ASP cc_start: 0.7381 (t0) cc_final: 0.6881 (t0) REVERT: B 20 ASN cc_start: 0.6980 (OUTLIER) cc_final: 0.6744 (p0) REVERT: B 89 MET cc_start: 0.7195 (mtp) cc_final: 0.6969 (mtp) REVERT: B 100 MET cc_start: 0.7869 (mtt) cc_final: 0.7149 (mtt) REVERT: B 172 PHE cc_start: 0.8292 (m-80) cc_final: 0.7812 (m-80) REVERT: B 224 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7792 (p) REVERT: C 59 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.8883 (tt) REVERT: C 74 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7797 (mm) REVERT: C 80 LYS cc_start: 0.9057 (mmtp) cc_final: 0.8822 (mmmt) REVERT: D 14 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8827 (tp) REVERT: D 135 MET cc_start: 0.8937 (mmt) cc_final: 0.8686 (mmp) REVERT: D 243 SER cc_start: 0.9724 (OUTLIER) cc_final: 0.9289 (t) REVERT: E 28 SER cc_start: 0.7412 (OUTLIER) cc_final: 0.6859 (t) REVERT: E 29 LEU cc_start: 0.8551 (pp) cc_final: 0.8164 (pp) REVERT: E 85 LYS cc_start: 0.8750 (mppt) cc_final: 0.8260 (mtpt) REVERT: E 126 MET cc_start: 0.9343 (tpp) cc_final: 0.8887 (tpp) REVERT: E 167 MET cc_start: 0.6955 (mtt) cc_final: 0.5823 (mtt) REVERT: E 202 SER cc_start: 0.8747 (OUTLIER) cc_final: 0.8523 (p) REVERT: F 74 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7213 (tp) REVERT: F 78 ASN cc_start: 0.8518 (p0) cc_final: 0.8305 (p0) REVERT: F 79 ASP cc_start: 0.7664 (t0) cc_final: 0.7450 (t0) REVERT: F 86 LYS cc_start: 0.8700 (pttt) cc_final: 0.8335 (tmtt) REVERT: G 12 ILE cc_start: 0.8905 (mt) cc_final: 0.8278 (tp) REVERT: G 40 TYR cc_start: 0.3456 (p90) cc_final: 0.3085 (p90) REVERT: G 48 ASN cc_start: 0.4710 (t0) cc_final: 0.4154 (p0) REVERT: G 81 ARG cc_start: 0.7324 (tmm160) cc_final: 0.6837 (ttp80) REVERT: G 89 ARG cc_start: 0.7487 (ptt-90) cc_final: 0.7143 (mtm-85) REVERT: G 145 ASP cc_start: 0.8790 (t0) cc_final: 0.8131 (p0) REVERT: H 90 TYR cc_start: 0.4957 (m-80) cc_final: 0.4715 (m-10) REVERT: H 130 ASP cc_start: 0.8383 (p0) cc_final: 0.7821 (p0) REVERT: H 135 GLN cc_start: 0.6918 (mt0) cc_final: 0.6665 (mp-120) REVERT: I 52 LEU cc_start: 0.3370 (tt) cc_final: 0.2828 (tt) REVERT: I 88 GLN cc_start: 0.6454 (mt0) cc_final: 0.5425 (tm-30) REVERT: J 53 LYS cc_start: 0.7304 (mptt) cc_final: 0.6974 (ptpt) REVERT: K 88 GLN cc_start: 0.6898 (tp-100) cc_final: 0.6548 (pp30) REVERT: K 109 GLU cc_start: 0.7961 (mp0) cc_final: 0.7689 (mp0) outliers start: 107 outliers final: 15 residues processed: 569 average time/residue: 0.1402 time to fit residues: 115.3702 Evaluate side-chains 334 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 310 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 73 GLN A 220 ASN A 241 HIS B 105 ASN B 122 HIS B 191 ASN B 226 HIS C 60 HIS C 68 GLN C 75 GLN D 11 HIS D 29 ASN D 220 ASN E 26 ASN E 105 ASN E 122 HIS E 191 ASN E 226 HIS E 262 HIS F 68 GLN F 89 ASN H 88 GLN I 91 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.115479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.087147 restraints weight = 51373.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.088664 restraints weight = 33917.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.089731 restraints weight = 21726.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.090204 restraints weight = 16748.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.090261 restraints weight = 15596.665| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16132 Z= 0.150 Angle : 0.739 9.233 21948 Z= 0.380 Chirality : 0.047 0.264 2652 Planarity : 0.006 0.057 2762 Dihedral : 6.362 89.337 2234 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.95 % Favored : 90.66 % Rotamer: Outliers : 0.36 % Allowed : 5.47 % Favored : 94.17 % 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: -3.79 (0.16), residues: 2056 helix: -1.68 (0.15), residues: 836 sheet: -2.53 (0.30), residues: 277 loop : -3.30 (0.17), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 67 TYR 0.014 0.001 TYR G 78 PHE 0.021 0.002 PHE H 23 TRP 0.012 0.001 TRP E 216 HIS 0.006 0.001 HIS D 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (16132) covalent geometry : angle 0.73938 / 0.38 (21948) hydrogen bonds : bond 0.05121 / 3.32 ( 601) hydrogen bonds : angle 5.50875 / 3.96 ( 1782) *********************** 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 414 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 408 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ILE cc_start: 0.9355 (mm) cc_final: 0.9095 (mt) REVERT: A 180 ILE cc_start: 0.8090 (mt) cc_final: 0.7436 (mt) REVERT: A 201 ASN cc_start: 0.8577 (t0) cc_final: 0.8221 (t0) REVERT: B 10 ASP cc_start: 0.7688 (t0) cc_final: 0.7385 (t0) REVERT: B 89 MET cc_start: 0.7569 (mtp) cc_final: 0.7111 (mtp) REVERT: B 91 PHE cc_start: 0.8400 (m-80) cc_final: 0.8103 (m-80) REVERT: B 172 PHE cc_start: 0.8736 (m-80) cc_final: 0.8358 (m-80) REVERT: C 40 THR cc_start: 0.8295 (t) cc_final: 0.7848 (m) REVERT: C 59 LEU cc_start: 0.8918 (tp) cc_final: 0.8401 (tt) REVERT: C 63 ASP cc_start: 0.8019 (m-30) cc_final: 0.7573 (m-30) REVERT: C 68 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6492 (tm-30) REVERT: D 135 MET cc_start: 0.9074 (mmt) cc_final: 0.8850 (mmp) REVERT: E 11 MET cc_start: 0.8492 (ptp) cc_final: 0.8131 (ptp) REVERT: E 85 LYS cc_start: 0.8791 (mppt) cc_final: 0.8533 (mtpt) REVERT: E 126 MET cc_start: 0.9242 (tpp) cc_final: 0.9022 (tpp) REVERT: E 221 LYS cc_start: 0.8846 (mppt) cc_final: 0.8604 (mppt) REVERT: F 26 LEU cc_start: 0.7736 (pt) cc_final: 0.7452 (tp) REVERT: F 79 ASP cc_start: 0.7903 (t0) cc_final: 0.7645 (t0) REVERT: F 86 LYS cc_start: 0.8831 (pttt) cc_final: 0.8501 (tmtt) REVERT: F 93 ASP cc_start: 0.7411 (p0) cc_final: 0.6915 (t70) REVERT: G 48 ASN cc_start: 0.4265 (t0) cc_final: 0.3914 (p0) REVERT: G 72 THR cc_start: 0.5324 (t) cc_final: 0.4329 (p) REVERT: G 81 ARG cc_start: 0.7545 (tmm160) cc_final: 0.7005 (ttp80) REVERT: G 103 THR cc_start: 0.6469 (m) cc_final: 0.5809 (t) REVERT: G 145 ASP cc_start: 0.8458 (t0) cc_final: 0.7649 (p0) REVERT: J 53 LYS cc_start: 0.7330 (mptt) cc_final: 0.7008 (ptpt) REVERT: K 88 GLN cc_start: 0.6868 (tp-100) cc_final: 0.6373 (pp30) REVERT: K 109 GLU cc_start: 0.7765 (mp0) cc_final: 0.7186 (mp0) REVERT: L 81 ARG cc_start: 0.6775 (ttp80) cc_final: 0.6269 (ttp80) outliers start: 6 outliers final: 0 residues processed: 413 average time/residue: 0.1250 time to fit residues: 76.8732 Evaluate side-chains 290 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 289 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 48 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 177 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 193 optimal weight: 20.0000 chunk 168 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 GLN B 191 ASN B 214 HIS C 9 GLN E 105 ASN E 175 GLN E 214 HIS ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN H 135 GLN I 88 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.115742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.087719 restraints weight = 52682.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.088071 restraints weight = 35999.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.088390 restraints weight = 26761.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.088670 restraints weight = 23989.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.088869 restraints weight = 21240.358| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16132 Z= 0.132 Angle : 0.679 8.732 21948 Z= 0.346 Chirality : 0.045 0.208 2652 Planarity : 0.005 0.062 2762 Dihedral : 5.965 85.659 2234 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.75 % Favored : 90.95 % Rotamer: Outliers : 0.12 % Allowed : 5.29 % Favored : 94.59 % 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: -2.83 (0.17), residues: 2056 helix: -0.42 (0.18), residues: 828 sheet: -2.22 (0.31), residues: 257 loop : -3.18 (0.17), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 18 TYR 0.017 0.001 TYR D 49 PHE 0.037 0.001 PHE E 16 TRP 0.014 0.001 TRP C 7 HIS 0.005 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (16132) covalent geometry : angle 0.67935 / 0.35 (21948) hydrogen bonds : bond 0.04152 / 2.69 ( 601) hydrogen bonds : angle 4.82650 / 3.47 ( 1782) *********************** 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 396 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 394 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.8419 (pm20) cc_final: 0.7945 (pm20) REVERT: A 153 ILE cc_start: 0.9376 (mm) cc_final: 0.9082 (mt) REVERT: A 198 ASP cc_start: 0.7508 (m-30) cc_final: 0.7215 (m-30) REVERT: B 10 ASP cc_start: 0.7798 (t0) cc_final: 0.7377 (t0) REVERT: B 75 MET cc_start: 0.7448 (ptp) cc_final: 0.7127 (ptp) REVERT: B 89 MET cc_start: 0.7933 (mtp) cc_final: 0.7335 (mtp) REVERT: B 91 PHE cc_start: 0.8215 (m-80) cc_final: 0.8009 (m-80) REVERT: D 73 GLN cc_start: 0.8883 (tp40) cc_final: 0.8299 (tp-100) REVERT: D 135 MET cc_start: 0.9111 (mmt) cc_final: 0.8884 (mmp) REVERT: E 11 MET cc_start: 0.8729 (ptp) cc_final: 0.8369 (ptp) REVERT: E 105 ASN cc_start: 0.9002 (OUTLIER) cc_final: 0.8535 (t0) REVERT: E 126 MET cc_start: 0.9182 (tpp) cc_final: 0.8978 (tpp) REVERT: E 170 GLN cc_start: 0.8786 (tp-100) cc_final: 0.8198 (tm-30) REVERT: E 237 ASP cc_start: 0.8016 (t70) cc_final: 0.7726 (t0) REVERT: F 26 LEU cc_start: 0.7873 (pt) cc_final: 0.7544 (tp) REVERT: F 86 LYS cc_start: 0.8808 (pttt) cc_final: 0.8378 (tmtt) REVERT: F 93 ASP cc_start: 0.7456 (p0) cc_final: 0.6906 (t70) REVERT: G 48 ASN cc_start: 0.3992 (t0) cc_final: 0.3651 (p0) REVERT: G 103 THR cc_start: 0.6512 (m) cc_final: 0.5851 (t) REVERT: G 145 ASP cc_start: 0.8479 (t0) cc_final: 0.7676 (p0) REVERT: H 147 ILE cc_start: 0.8205 (pt) cc_final: 0.7958 (pt) REVERT: J 53 LYS cc_start: 0.7339 (mptt) cc_final: 0.7033 (ptpt) REVERT: K 56 SER cc_start: 0.5460 (m) cc_final: 0.5013 (m) REVERT: K 88 GLN cc_start: 0.6788 (tp-100) cc_final: 0.6331 (pp30) REVERT: K 109 GLU cc_start: 0.7481 (mp0) cc_final: 0.6851 (mp0) REVERT: L 81 ARG cc_start: 0.6692 (ttp80) cc_final: 0.6206 (ttp80) outliers start: 2 outliers final: 1 residues processed: 396 average time/residue: 0.1191 time to fit residues: 70.8921 Evaluate side-chains 296 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 294 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 48 optimal weight: 1.9990 chunk 168 optimal weight: 0.0470 chunk 127 optimal weight: 8.9990 chunk 202 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 overall best weight: 1.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 GLN B 62 HIS B 191 ASN C 70 ASN C 89 ASN ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.115581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.087586 restraints weight = 52635.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.087876 restraints weight = 35059.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.087966 restraints weight = 25135.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.088353 restraints weight = 23543.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.088508 restraints weight = 21021.897| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16132 Z= 0.124 Angle : 0.667 8.876 21948 Z= 0.333 Chirality : 0.045 0.220 2652 Planarity : 0.005 0.089 2762 Dihedral : 5.778 87.184 2234 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.71 % Favored : 91.10 % Rotamer: Outliers : 0.12 % Allowed : 4.22 % Favored : 95.66 % 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: -2.37 (0.18), residues: 2056 helix: 0.12 (0.18), residues: 830 sheet: -2.19 (0.29), residues: 281 loop : -3.03 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 97 TYR 0.015 0.001 TYR K 40 PHE 0.032 0.002 PHE E 16 TRP 0.009 0.001 TRP D 168 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (16132) covalent geometry : angle 0.66743 / 0.33 (21948) hydrogen bonds : bond 0.03727 / 2.42 ( 601) hydrogen bonds : angle 4.57767 / 3.28 ( 1782) *********************** 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 382 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 380 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7117 (mtt) cc_final: 0.6708 (tmm) REVERT: A 127 GLU cc_start: 0.8372 (pm20) cc_final: 0.7931 (pm20) REVERT: A 153 ILE cc_start: 0.9405 (mm) cc_final: 0.9105 (mt) REVERT: B 10 ASP cc_start: 0.7648 (t0) cc_final: 0.7317 (t0) REVERT: B 75 MET cc_start: 0.7335 (ptp) cc_final: 0.7105 (ptp) REVERT: B 89 MET cc_start: 0.8133 (mtp) cc_final: 0.7723 (mtp) REVERT: B 100 MET cc_start: 0.7681 (mtt) cc_final: 0.7395 (mtt) REVERT: B 220 ASP cc_start: 0.8278 (t0) cc_final: 0.7896 (t0) REVERT: C 6 SER cc_start: 0.9001 (m) cc_final: 0.8690 (p) REVERT: C 43 ASP cc_start: 0.7203 (p0) cc_final: 0.6991 (p0) REVERT: D 250 ASP cc_start: 0.8593 (t0) cc_final: 0.8390 (t70) REVERT: E 11 MET cc_start: 0.8677 (ptp) cc_final: 0.8340 (ptp) REVERT: E 29 LEU cc_start: 0.8884 (pp) cc_final: 0.8667 (pp) REVERT: E 67 PHE cc_start: 0.8272 (t80) cc_final: 0.8056 (t80) REVERT: E 108 TYR cc_start: 0.8655 (t80) cc_final: 0.8389 (t80) REVERT: E 126 MET cc_start: 0.9207 (tpp) cc_final: 0.8899 (tpp) REVERT: F 26 LEU cc_start: 0.7822 (pt) cc_final: 0.7585 (tp) REVERT: F 86 LYS cc_start: 0.8851 (pttt) cc_final: 0.8422 (tmtt) REVERT: F 93 ASP cc_start: 0.7405 (p0) cc_final: 0.6969 (t70) REVERT: G 48 ASN cc_start: 0.4292 (t0) cc_final: 0.4070 (p0) REVERT: G 81 ARG cc_start: 0.7593 (tmm160) cc_final: 0.7023 (ttp80) REVERT: G 103 THR cc_start: 0.6263 (m) cc_final: 0.5531 (t) REVERT: G 134 ILE cc_start: 0.7599 (mp) cc_final: 0.7365 (mt) REVERT: G 135 GLN cc_start: 0.8289 (pm20) cc_final: 0.8088 (pp30) REVERT: G 145 ASP cc_start: 0.8420 (t0) cc_final: 0.7657 (p0) REVERT: J 53 LYS cc_start: 0.7296 (mptt) cc_final: 0.7016 (ptpt) REVERT: K 56 SER cc_start: 0.6584 (m) cc_final: 0.6294 (m) REVERT: K 88 GLN cc_start: 0.6762 (tp-100) cc_final: 0.6370 (pp30) REVERT: K 109 GLU cc_start: 0.7495 (mp0) cc_final: 0.6813 (mp0) REVERT: L 81 ARG cc_start: 0.6856 (ttp80) cc_final: 0.6274 (ttp80) outliers start: 2 outliers final: 0 residues processed: 382 average time/residue: 0.1200 time to fit residues: 69.3101 Evaluate side-chains 282 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 14 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 186 optimal weight: 40.0000 chunk 57 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 105 optimal weight: 0.1980 chunk 199 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS B 191 ASN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.115728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.086342 restraints weight = 52486.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.088023 restraints weight = 35353.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.088750 restraints weight = 21974.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.089141 restraints weight = 19478.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.089213 restraints weight = 17091.096| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16132 Z= 0.119 Angle : 0.662 9.365 21948 Z= 0.329 Chirality : 0.045 0.182 2652 Planarity : 0.005 0.058 2762 Dihedral : 5.673 89.519 2234 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.80 % Favored : 91.00 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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: -2.09 (0.18), residues: 2056 helix: 0.48 (0.19), residues: 830 sheet: -2.10 (0.30), residues: 278 loop : -2.98 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 97 TYR 0.023 0.001 TYR B 261 PHE 0.035 0.002 PHE E 16 TRP 0.025 0.001 TRP C 7 HIS 0.005 0.001 HIS B 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (16132) covalent geometry : angle 0.66177 / 0.33 (21948) hydrogen bonds : bond 0.03446 / 2.22 ( 601) hydrogen bonds : angle 4.43173 / 3.17 ( 1782) *********************** 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 378 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7134 (mtt) cc_final: 0.6736 (tmm) REVERT: A 153 ILE cc_start: 0.9409 (mm) cc_final: 0.9116 (mt) REVERT: B 10 ASP cc_start: 0.7537 (t0) cc_final: 0.7213 (t0) REVERT: B 29 LEU cc_start: 0.9112 (pp) cc_final: 0.8890 (pp) REVERT: B 75 MET cc_start: 0.7361 (ptp) cc_final: 0.7075 (ptp) REVERT: B 89 MET cc_start: 0.8064 (mtp) cc_final: 0.7673 (mtp) REVERT: B 190 LEU cc_start: 0.8977 (mt) cc_final: 0.8772 (mt) REVERT: B 220 ASP cc_start: 0.8241 (t0) cc_final: 0.7718 (t0) REVERT: C 43 ASP cc_start: 0.7269 (p0) cc_final: 0.7052 (p0) REVERT: E 66 LEU cc_start: 0.7980 (tt) cc_final: 0.7359 (mt) REVERT: E 67 PHE cc_start: 0.8338 (t80) cc_final: 0.8077 (t80) REVERT: E 108 TYR cc_start: 0.8608 (t80) cc_final: 0.8316 (t80) REVERT: E 126 MET cc_start: 0.9204 (tpp) cc_final: 0.8881 (tpp) REVERT: F 79 ASP cc_start: 0.7262 (t0) cc_final: 0.7021 (t0) REVERT: F 93 ASP cc_start: 0.7459 (p0) cc_final: 0.7017 (t70) REVERT: G 72 THR cc_start: 0.6949 (p) cc_final: 0.5758 (p) REVERT: G 81 ARG cc_start: 0.7774 (tmm160) cc_final: 0.7097 (ttp80) REVERT: G 103 THR cc_start: 0.6446 (m) cc_final: 0.5945 (t) REVERT: G 145 ASP cc_start: 0.8474 (t0) cc_final: 0.7741 (p0) REVERT: H 27 LYS cc_start: 0.6882 (ttmt) cc_final: 0.6665 (ttpt) REVERT: H 90 TYR cc_start: 0.3875 (m-10) cc_final: 0.3335 (m-80) REVERT: I 129 LYS cc_start: 0.6843 (ptpp) cc_final: 0.6603 (mtmm) REVERT: J 53 LYS cc_start: 0.7274 (mptt) cc_final: 0.7021 (ptpt) REVERT: J 90 TYR cc_start: 0.5827 (m-80) cc_final: 0.5487 (m-80) REVERT: J 141 MET cc_start: 0.1790 (pmm) cc_final: -0.0123 (ptp) REVERT: K 56 SER cc_start: 0.6357 (m) cc_final: 0.6011 (m) REVERT: K 68 VAL cc_start: 0.7588 (m) cc_final: 0.7378 (m) REVERT: K 88 GLN cc_start: 0.6782 (tp-100) cc_final: 0.6381 (pp30) REVERT: K 109 GLU cc_start: 0.7366 (mp0) cc_final: 0.6631 (mp0) REVERT: L 49 ILE cc_start: 0.7422 (pt) cc_final: 0.7214 (pt) REVERT: L 81 ARG cc_start: 0.6816 (ttp80) cc_final: 0.6287 (ttp80) REVERT: L 141 MET cc_start: 0.4368 (pmm) cc_final: 0.4092 (pmm) outliers start: 0 outliers final: 0 residues processed: 378 average time/residue: 0.1166 time to fit residues: 66.8960 Evaluate side-chains 287 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 24 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 119 optimal weight: 30.0000 chunk 141 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 160 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 191 ASN D 40 HIS E 214 HIS ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN J 92 HIS ** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.108907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.079964 restraints weight = 53338.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.081378 restraints weight = 35198.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.082434 restraints weight = 22765.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.083103 restraints weight = 16763.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.083045 restraints weight = 15841.194| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16132 Z= 0.261 Angle : 0.843 9.306 21948 Z= 0.424 Chirality : 0.050 0.217 2652 Planarity : 0.006 0.055 2762 Dihedral : 6.241 88.213 2234 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.70 % Favored : 88.96 % Rotamer: Outliers : 0.06 % Allowed : 4.28 % Favored : 95.66 % 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: -2.40 (0.18), residues: 2056 helix: 0.02 (0.18), residues: 843 sheet: -2.22 (0.30), residues: 274 loop : -2.99 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 18 TYR 0.027 0.002 TYR B 261 PHE 0.023 0.003 PHE E 16 TRP 0.018 0.002 TRP C 7 HIS 0.008 0.002 HIS B 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.26 (16132) covalent geometry : angle 0.84263 / 0.42 (21948) hydrogen bonds : bond 0.04611 / 3.05 ( 601) hydrogen bonds : angle 5.26324 / 3.73 ( 1782) *********************** 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 337 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 336 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7371 (mtt) cc_final: 0.6977 (tmm) REVERT: A 127 GLU cc_start: 0.8369 (pm20) cc_final: 0.7984 (pm20) REVERT: B 10 ASP cc_start: 0.8099 (t0) cc_final: 0.7813 (t0) REVERT: B 89 MET cc_start: 0.8031 (mtp) cc_final: 0.7653 (mtp) REVERT: B 91 PHE cc_start: 0.8310 (m-80) cc_final: 0.8009 (m-80) REVERT: C 6 SER cc_start: 0.9063 (m) cc_final: 0.8712 (p) REVERT: E 126 MET cc_start: 0.9265 (tpp) cc_final: 0.8984 (tpp) REVERT: F 22 GLN cc_start: 0.9235 (pp30) cc_final: 0.9027 (pp30) REVERT: F 68 GLN cc_start: 0.7070 (OUTLIER) cc_final: 0.6682 (pp30) REVERT: G 145 ASP cc_start: 0.8649 (t0) cc_final: 0.7670 (p0) REVERT: G 146 LEU cc_start: 0.6934 (pt) cc_final: 0.6709 (pt) REVERT: H 27 LYS cc_start: 0.7128 (ttmt) cc_final: 0.6904 (ttmt) REVERT: I 55 ARG cc_start: 0.5616 (mmt180) cc_final: 0.5406 (tpp80) REVERT: J 53 LYS cc_start: 0.7395 (mptt) cc_final: 0.7089 (ptpt) REVERT: J 141 MET cc_start: 0.2391 (pmm) cc_final: 0.1014 (ptp) REVERT: K 56 SER cc_start: 0.6422 (m) cc_final: 0.6069 (m) REVERT: L 81 ARG cc_start: 0.6862 (ttp80) cc_final: 0.6295 (ttp80) outliers start: 1 outliers final: 0 residues processed: 337 average time/residue: 0.1219 time to fit residues: 61.1963 Evaluate side-chains 259 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 258 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 25 optimal weight: 8.9990 chunk 197 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 188 optimal weight: 50.0000 chunk 156 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 chunk 39 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 181 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 191 ASN D 11 HIS ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.109103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.081434 restraints weight = 52136.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.082361 restraints weight = 34782.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083342 restraints weight = 23637.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.083728 restraints weight = 18454.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.083807 restraints weight = 16689.141| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16132 Z= 0.210 Angle : 0.760 8.664 21948 Z= 0.382 Chirality : 0.048 0.188 2652 Planarity : 0.006 0.083 2762 Dihedral : 6.049 82.576 2234 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.44 % Favored : 90.32 % Rotamer: Outliers : 0.06 % Allowed : 2.02 % Favored : 97.92 % 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: -2.27 (0.18), residues: 2056 helix: 0.17 (0.18), residues: 843 sheet: -2.21 (0.30), residues: 274 loop : -2.94 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 97 TYR 0.026 0.002 TYR B 261 PHE 0.022 0.002 PHE D 185 TRP 0.026 0.002 TRP D 168 HIS 0.005 0.001 HIS D 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (16132) covalent geometry : angle 0.75978 / 0.38 (21948) hydrogen bonds : bond 0.04053 / 2.65 ( 601) hydrogen bonds : angle 4.98747 / 3.52 ( 1782) *********************** 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 328 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 327 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7309 (mtt) cc_final: 0.7048 (tmm) REVERT: B 10 ASP cc_start: 0.8111 (t0) cc_final: 0.7762 (t0) REVERT: B 75 MET cc_start: 0.7622 (ptp) cc_final: 0.6962 (ptp) REVERT: B 89 MET cc_start: 0.8193 (mtp) cc_final: 0.7814 (mtp) REVERT: B 91 PHE cc_start: 0.8372 (m-80) cc_final: 0.8033 (m-80) REVERT: C 6 SER cc_start: 0.9094 (m) cc_final: 0.8727 (p) REVERT: C 63 ASP cc_start: 0.8247 (m-30) cc_final: 0.8040 (m-30) REVERT: D 250 ASP cc_start: 0.8775 (t70) cc_final: 0.8454 (t70) REVERT: E 108 TYR cc_start: 0.8652 (t80) cc_final: 0.8360 (t80) REVERT: E 126 MET cc_start: 0.9281 (tpp) cc_final: 0.8964 (tpp) REVERT: F 97 ARG cc_start: 0.6095 (tmt170) cc_final: 0.5722 (mmp80) REVERT: G 112 LEU cc_start: 0.6347 (tp) cc_final: 0.5454 (tt) REVERT: G 145 ASP cc_start: 0.8552 (t0) cc_final: 0.7599 (p0) REVERT: G 146 LEU cc_start: 0.6850 (pt) cc_final: 0.6615 (pt) REVERT: H 27 LYS cc_start: 0.7047 (ttmt) cc_final: 0.6819 (ttmt) REVERT: H 152 TYR cc_start: 0.7907 (m-80) cc_final: 0.7633 (m-80) REVERT: I 55 ARG cc_start: 0.5753 (mmt180) cc_final: 0.5329 (mmm160) REVERT: J 53 LYS cc_start: 0.7276 (mptt) cc_final: 0.6965 (ptpt) REVERT: J 141 MET cc_start: 0.2839 (pmm) cc_final: 0.1422 (ptp) outliers start: 1 outliers final: 0 residues processed: 328 average time/residue: 0.1186 time to fit residues: 59.5820 Evaluate side-chains 267 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 152 optimal weight: 6.9990 chunk 196 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 201 optimal weight: 0.0060 chunk 162 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 171 optimal weight: 0.0070 chunk 129 optimal weight: 10.0000 overall best weight: 1.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 191 ASN D 11 HIS D 73 GLN E 105 ASN E 175 GLN ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.113130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.083802 restraints weight = 51961.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.085224 restraints weight = 33182.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.086320 restraints weight = 22129.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.086869 restraints weight = 17002.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.086971 restraints weight = 14764.033| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16132 Z= 0.123 Angle : 0.706 10.079 21948 Z= 0.346 Chirality : 0.046 0.191 2652 Planarity : 0.005 0.072 2762 Dihedral : 5.688 82.253 2234 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.24 % Favored : 90.61 % Rotamer: Outliers : 0.12 % Allowed : 1.25 % Favored : 98.63 % 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: -1.93 (0.19), residues: 2056 helix: 0.54 (0.19), residues: 845 sheet: -2.19 (0.30), residues: 282 loop : -2.80 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 79 TYR 0.038 0.001 TYR E 81 PHE 0.027 0.002 PHE B 16 TRP 0.014 0.001 TRP D 168 HIS 0.007 0.001 HIS D 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (16132) covalent geometry : angle 0.70583 / 0.35 (21948) hydrogen bonds : bond 0.03478 / 2.28 ( 601) hydrogen bonds : angle 4.58240 / 3.25 ( 1782) *********************** 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 355 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 353 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7180 (mtt) cc_final: 0.6912 (tmm) REVERT: A 127 GLU cc_start: 0.8359 (pm20) cc_final: 0.7896 (pm20) REVERT: B 75 MET cc_start: 0.7297 (ptp) cc_final: 0.6885 (ptp) REVERT: B 89 MET cc_start: 0.8022 (mtp) cc_final: 0.7787 (mtp) REVERT: C 6 SER cc_start: 0.8906 (m) cc_final: 0.8588 (p) REVERT: D 250 ASP cc_start: 0.8595 (t70) cc_final: 0.8394 (t70) REVERT: E 16 PHE cc_start: 0.6687 (m-80) cc_final: 0.6440 (m-80) REVERT: E 108 TYR cc_start: 0.8653 (t80) cc_final: 0.8434 (t80) REVERT: E 126 MET cc_start: 0.9215 (tpp) cc_final: 0.8890 (tpp) REVERT: E 261 TYR cc_start: 0.7514 (m-80) cc_final: 0.7272 (m-10) REVERT: F 22 GLN cc_start: 0.9219 (pp30) cc_final: 0.8947 (pp30) REVERT: F 79 ASP cc_start: 0.7263 (t0) cc_final: 0.7058 (t0) REVERT: G 109 GLU cc_start: 0.7615 (pm20) cc_final: 0.6216 (tp30) REVERT: G 112 LEU cc_start: 0.6422 (tp) cc_final: 0.5496 (tt) REVERT: G 145 ASP cc_start: 0.8544 (t0) cc_final: 0.7729 (p0) REVERT: G 146 LEU cc_start: 0.6753 (pt) cc_final: 0.6519 (pt) REVERT: H 152 TYR cc_start: 0.8051 (m-80) cc_final: 0.7659 (m-80) REVERT: I 55 ARG cc_start: 0.5761 (mmt180) cc_final: 0.5443 (mmm160) REVERT: I 91 ASN cc_start: 0.8387 (p0) cc_final: 0.7159 (m-40) REVERT: J 53 LYS cc_start: 0.7323 (mptt) cc_final: 0.7022 (ptpt) REVERT: J 90 TYR cc_start: 0.6146 (m-80) cc_final: 0.5747 (m-80) REVERT: J 141 MET cc_start: 0.2788 (pmm) cc_final: 0.1511 (ptp) REVERT: L 141 MET cc_start: 0.4275 (pmm) cc_final: 0.3917 (pmm) outliers start: 2 outliers final: 0 residues processed: 355 average time/residue: 0.1168 time to fit residues: 63.1289 Evaluate side-chains 269 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 60 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 165 optimal weight: 9.9990 chunk 19 optimal weight: 0.1980 chunk 73 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 196 optimal weight: 30.0000 chunk 110 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 65.6524 > 50:) overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 191 ASN C 60 HIS E 175 GLN ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.110671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081434 restraints weight = 53386.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.082973 restraints weight = 33600.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.084088 restraints weight = 22339.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.084614 restraints weight = 16808.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.084730 restraints weight = 14640.112| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16132 Z= 0.158 Angle : 0.730 10.140 21948 Z= 0.360 Chirality : 0.047 0.179 2652 Planarity : 0.005 0.069 2762 Dihedral : 5.709 81.932 2234 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.53 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: -1.86 (0.19), residues: 2056 helix: 0.59 (0.19), residues: 845 sheet: -2.13 (0.31), residues: 267 loop : -2.76 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 46 TYR 0.020 0.001 TYR B 261 PHE 0.024 0.002 PHE B 16 TRP 0.015 0.001 TRP D 168 HIS 0.005 0.001 HIS E 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (16132) covalent geometry : angle 0.73027 / 0.36 (21948) hydrogen bonds : bond 0.03653 / 2.39 ( 601) hydrogen bonds : angle 4.69103 / 3.33 ( 1782) *********************** 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 333 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7241 (mtt) cc_final: 0.6944 (tmm) REVERT: A 127 GLU cc_start: 0.8376 (pm20) cc_final: 0.7892 (pm20) REVERT: B 75 MET cc_start: 0.7236 (ptp) cc_final: 0.6935 (ptp) REVERT: C 6 SER cc_start: 0.9012 (m) cc_final: 0.8638 (p) REVERT: D 250 ASP cc_start: 0.8622 (t70) cc_final: 0.8317 (t70) REVERT: E 108 TYR cc_start: 0.8672 (t80) cc_final: 0.8425 (t80) REVERT: E 126 MET cc_start: 0.9249 (tpp) cc_final: 0.8904 (tpp) REVERT: E 177 PRO cc_start: 0.8941 (Cg_exo) cc_final: 0.8700 (Cg_endo) REVERT: E 261 TYR cc_start: 0.7695 (m-80) cc_final: 0.7471 (m-10) REVERT: F 22 GLN cc_start: 0.9246 (pp30) cc_final: 0.8992 (pp30) REVERT: F 79 ASP cc_start: 0.7382 (t0) cc_final: 0.7120 (t0) REVERT: G 90 TYR cc_start: 0.6357 (m-80) cc_final: 0.5933 (m-80) REVERT: G 109 GLU cc_start: 0.7743 (pm20) cc_final: 0.6413 (tp30) REVERT: G 112 LEU cc_start: 0.6433 (tp) cc_final: 0.5559 (tt) REVERT: G 145 ASP cc_start: 0.8573 (t0) cc_final: 0.7719 (p0) REVERT: G 146 LEU cc_start: 0.6791 (pt) cc_final: 0.6566 (pt) REVERT: H 152 TYR cc_start: 0.8106 (m-80) cc_final: 0.7737 (m-80) REVERT: I 55 ARG cc_start: 0.5738 (mmt180) cc_final: 0.5263 (mmm160) REVERT: I 91 ASN cc_start: 0.8380 (p0) cc_final: 0.7103 (m-40) REVERT: J 53 LYS cc_start: 0.7352 (mptt) cc_final: 0.6997 (ptpt) REVERT: J 141 MET cc_start: 0.2887 (pmm) cc_final: 0.1642 (ptp) REVERT: L 141 MET cc_start: 0.4741 (pmm) cc_final: 0.3798 (ttt) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.1155 time to fit residues: 59.0084 Evaluate side-chains 269 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 127 optimal weight: 20.0000 chunk 195 optimal weight: 0.0040 chunk 110 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 171 optimal weight: 30.0000 chunk 106 optimal weight: 3.9990 chunk 109 optimal weight: 0.0010 chunk 39 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 191 ASN B 214 HIS C 60 HIS D 11 HIS ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 GLN ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.112681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.083596 restraints weight = 52469.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.085073 restraints weight = 33162.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.085873 restraints weight = 24190.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.086615 restraints weight = 18420.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.086817 restraints weight = 14970.872| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16132 Z= 0.123 Angle : 0.711 9.820 21948 Z= 0.346 Chirality : 0.045 0.172 2652 Planarity : 0.005 0.090 2762 Dihedral : 5.577 82.714 2234 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.39 % Favored : 90.47 % Rotamer: Outliers : 0.06 % Allowed : 0.48 % Favored : 99.46 % 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: -1.65 (0.19), residues: 2056 helix: 0.84 (0.19), residues: 837 sheet: -1.95 (0.32), residues: 258 loop : -2.72 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 46 TYR 0.017 0.001 TYR K 40 PHE 0.025 0.001 PHE B 16 TRP 0.020 0.001 TRP B 216 HIS 0.008 0.001 HIS D 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (16132) covalent geometry : angle 0.71125 / 0.35 (21948) hydrogen bonds : bond 0.03397 / 2.22 ( 601) hydrogen bonds : angle 4.51424 / 3.20 ( 1782) ********************** 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 343 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 342 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7238 (mtt) cc_final: 0.6898 (tmm) REVERT: A 127 GLU cc_start: 0.8283 (pm20) cc_final: 0.7893 (pm20) REVERT: B 75 MET cc_start: 0.7127 (ptp) cc_final: 0.6903 (ptp) REVERT: B 127 MET cc_start: 0.8462 (tmm) cc_final: 0.8222 (tmm) REVERT: C 6 SER cc_start: 0.8928 (m) cc_final: 0.8560 (p) REVERT: D 250 ASP cc_start: 0.8557 (t70) cc_final: 0.8321 (t70) REVERT: E 29 LEU cc_start: 0.8994 (pp) cc_final: 0.8637 (pp) REVERT: E 108 TYR cc_start: 0.8599 (t80) cc_final: 0.8332 (t80) REVERT: E 126 MET cc_start: 0.9223 (tpp) cc_final: 0.8865 (tpp) REVERT: E 170 GLN cc_start: 0.8997 (tp-100) cc_final: 0.8666 (tp-100) REVERT: E 216 TRP cc_start: 0.8426 (m100) cc_final: 0.7680 (m-10) REVERT: E 261 TYR cc_start: 0.7481 (m-80) cc_final: 0.7261 (m-10) REVERT: F 22 GLN cc_start: 0.9214 (pp30) cc_final: 0.8925 (pp30) REVERT: F 79 ASP cc_start: 0.7268 (t0) cc_final: 0.7040 (t0) REVERT: G 90 TYR cc_start: 0.6304 (m-80) cc_final: 0.5942 (m-80) REVERT: G 109 GLU cc_start: 0.7620 (pm20) cc_final: 0.6463 (tp30) REVERT: G 112 LEU cc_start: 0.6645 (tp) cc_final: 0.5839 (tt) REVERT: G 145 ASP cc_start: 0.8604 (t0) cc_final: 0.7771 (p0) REVERT: H 152 TYR cc_start: 0.8175 (m-80) cc_final: 0.7782 (m-80) REVERT: I 55 ARG cc_start: 0.5801 (mmt180) cc_final: 0.5419 (mmm160) REVERT: I 91 ASN cc_start: 0.8408 (p0) cc_final: 0.7096 (m-40) REVERT: J 53 LYS cc_start: 0.7314 (mptt) cc_final: 0.6979 (ptpt) REVERT: J 90 TYR cc_start: 0.6340 (m-80) cc_final: 0.5756 (m-80) REVERT: J 141 MET cc_start: 0.2901 (pmm) cc_final: 0.1637 (ptp) REVERT: L 141 MET cc_start: 0.4979 (pmm) cc_final: 0.4208 (ttt) outliers start: 1 outliers final: 0 residues processed: 343 average time/residue: 0.1189 time to fit residues: 62.0956 Evaluate side-chains 266 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 44 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 chunk 123 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 145 optimal weight: 0.0000 chunk 108 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 85 optimal weight: 0.0970 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 191 ASN E 105 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 GLN ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.114128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.084696 restraints weight = 52120.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.086543 restraints weight = 33686.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.087728 restraints weight = 20845.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.088154 restraints weight = 16308.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.088306 restraints weight = 14482.318| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.6061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16132 Z= 0.116 Angle : 0.708 11.432 21948 Z= 0.338 Chirality : 0.046 0.243 2652 Planarity : 0.005 0.082 2762 Dihedral : 5.452 85.024 2234 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.46 % Favored : 91.39 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.47 (0.19), residues: 2056 helix: 1.01 (0.19), residues: 821 sheet: -1.76 (0.33), residues: 258 loop : -2.61 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 81 TYR 0.016 0.001 TYR K 40 PHE 0.026 0.001 PHE J 13 TRP 0.022 0.001 TRP B 216 HIS 0.005 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (16132) covalent geometry : angle 0.70769 / 0.34 (21948) hydrogen bonds : bond 0.03156 / 2.07 ( 601) hydrogen bonds : angle 4.35834 / 3.10 ( 1782) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2621.13 seconds wall clock time: 46 minutes 4.17 seconds (2764.17 seconds total)