Starting phenix.real_space_refine on Fri Jul 3 04:35:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7o17_12692/07_2026/7o17_12692.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o17_12692/07_2026/7o17_12692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7o17_12692/07_2026/7o17_12692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o17_12692/07_2026/7o17_12692.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7o17_12692/07_2026/7o17_12692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o17_12692/07_2026/7o17_12692.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7o17_12692/07_2026/7o17_12692.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7o17_12692/07_2026/7o17_12692.cif" } resolution = 4.5 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 341 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 7456 2.51 5 N 2054 2.21 5 O 2127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11679 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3057 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 16, 'TRANS': 386} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "C" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "D" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2030 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 264} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1938 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.88, per 1000 atoms: 0.25 Number of scatterers: 11679 At special positions: 0 Unit cell: (84.24, 81.648, 195.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 P 6 15.00 Mg 2 11.99 O 2127 8.00 N 2054 7.00 C 7456 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: 1.00 Conformation dependent library (CDL) restraints added in 630.5 milliseconds 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2746 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 12 sheets defined 43.8% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 375 through 383 removed outlier: 4.212A pdb=" N LEU A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 391 removed outlier: 4.066A pdb=" N LEU A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.663A pdb=" N VAL A 397 " --> pdb=" O PRO A 393 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 removed outlier: 3.574A pdb=" N LEU A 427 " --> pdb=" O THR A 424 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR A 429 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 90 through 103 removed outlier: 3.591A pdb=" N ARG B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 101 " --> pdb=" O HIS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 116 removed outlier: 3.632A pdb=" N GLU B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.733A pdb=" N ALA B 122 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 130 through 143 removed outlier: 3.616A pdb=" N GLN B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 173 removed outlier: 4.015A pdb=" N GLN B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 194 removed outlier: 3.750A pdb=" N ALA B 193 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 removed outlier: 3.556A pdb=" N LEU B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 241 removed outlier: 3.692A pdb=" N LEU B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TRP B 240 " --> pdb=" O TRP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 275 removed outlier: 3.838A pdb=" N GLY B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 274 " --> pdb=" O GLN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.674A pdb=" N TYR B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 50 removed outlier: 3.997A pdb=" N MET C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 90 through 103 removed outlier: 3.626A pdb=" N LEU C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 101 " --> pdb=" O HIS C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 removed outlier: 4.472A pdb=" N VAL C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLU C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 130 through 143 removed outlier: 3.804A pdb=" N LEU C 137 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 142 " --> pdb=" O GLY C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 176 removed outlier: 3.749A pdb=" N GLN C 165 " --> pdb=" O PRO C 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.837A pdb=" N ALA C 193 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 removed outlier: 3.755A pdb=" N ALA C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 242 removed outlier: 4.006A pdb=" N THR C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 237 through 242' Processing helix chain 'C' and resid 266 through 272 removed outlier: 3.739A pdb=" N GLN C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 298 Processing helix chain 'D' and resid 4 through 18 removed outlier: 3.742A pdb=" N ALA D 8 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY D 15 " --> pdb=" O GLU D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 36 removed outlier: 4.312A pdb=" N LEU D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 31 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA D 32 " --> pdb=" O PHE D 28 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 62 removed outlier: 3.611A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 59 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 75 removed outlier: 3.849A pdb=" N ALA D 70 " --> pdb=" O MET D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 98 through 120 removed outlier: 3.755A pdb=" N LEU D 102 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY D 103 " --> pdb=" O GLN D 99 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU D 112 " --> pdb=" O HIS D 108 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 130 removed outlier: 3.528A pdb=" N ILE D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA D 128 " --> pdb=" O ALA D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 168 removed outlier: 3.528A pdb=" N LEU D 139 " --> pdb=" O GLU D 135 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR D 151 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D 158 " --> pdb=" O GLY D 154 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 159 " --> pdb=" O TRP D 155 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 164 " --> pdb=" O PHE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 185 removed outlier: 3.611A pdb=" N ALA D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY D 180 " --> pdb=" O GLY D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 197 removed outlier: 3.895A pdb=" N LEU D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU D 193 " --> pdb=" O PHE D 189 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 194 " --> pdb=" O ASP D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 216 removed outlier: 3.678A pdb=" N LEU D 214 " --> pdb=" O TRP D 211 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 215 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 226 removed outlier: 3.594A pdb=" N TYR D 221 " --> pdb=" O PRO D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 248 through 273 removed outlier: 3.862A pdb=" N LEU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 15 removed outlier: 3.966A pdb=" N ILE E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA E 8 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER E 13 " --> pdb=" O ARG E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 23 removed outlier: 3.883A pdb=" N LEU E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 18 through 23' Processing helix chain 'E' and resid 23 through 36 removed outlier: 3.561A pdb=" N LEU E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA E 32 " --> pdb=" O PHE E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 72 removed outlier: 4.003A pdb=" N THR E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 65 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Proline residue: E 67 - end of helix removed outlier: 3.665A pdb=" N ALA E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 85 Processing helix chain 'E' and resid 86 through 93 removed outlier: 3.781A pdb=" N LEU E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.803A pdb=" N GLY E 103 " --> pdb=" O GLN E 99 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 128 removed outlier: 3.531A pdb=" N LEU E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 142 removed outlier: 3.610A pdb=" N TRP E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 166 removed outlier: 4.591A pdb=" N SER E 149 " --> pdb=" O ARG E 145 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU E 164 " --> pdb=" O PHE E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 177 through 187 removed outlier: 4.240A pdb=" N VAL E 181 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 200 removed outlier: 3.502A pdb=" N LEU E 193 " --> pdb=" O PHE E 189 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU E 194 " --> pdb=" O ASP E 190 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU E 199 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 257 removed outlier: 3.547A pdb=" N LEU E 254 " --> pdb=" O ALA E 250 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU E 257 " --> pdb=" O TRP E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 272 removed outlier: 3.833A pdb=" N GLY E 261 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU E 266 " --> pdb=" O VAL E 262 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 46 removed outlier: 6.520A pdb=" N TRP A 45 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU A 64 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL A 142 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA A 170 " --> pdb=" O HIS A 193 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU A 195 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL A 172 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ASN A 192 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE A 217 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU A 194 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU A 216 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL A 238 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N SER A 259 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU A 299 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE A 261 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 322 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 53 removed outlier: 5.691A pdb=" N GLY A 50 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLN A 73 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TYR A 52 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ALA A 70 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N TYR A 96 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A 72 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN A 123 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP A 148 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N MET A 125 " --> pdb=" O ASP A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 58 removed outlier: 7.005A pdb=" N PHE A 56 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A 81 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY A 131 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N HIS A 163 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A 132 " --> pdb=" O HIS A 163 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE A 162 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASP A 187 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE A 184 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N MET A 209 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 186 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR A 204 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ALA A 229 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N MET A 231 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TYR A 208 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR A 226 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N LEU A 252 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR A 228 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ASN A 254 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU A 230 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR A 249 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N PHE A 289 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE A 251 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TYR A 291 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N MET A 253 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE A 310 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N PHE A 289 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU A 308 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LYS A 334 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE A 310 " --> pdb=" O LYS A 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 244 removed outlier: 6.372A pdb=" N VAL A 266 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N PHE A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 24 removed outlier: 5.709A pdb=" N VAL B 18 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG B 12 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N HIS B 20 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N SER B 10 " --> pdb=" O HIS B 20 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 22 " --> pdb=" O GLY B 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 78 through 79 removed outlier: 6.794A pdb=" N LEU B 79 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 32 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL B 31 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ALA B 199 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 33 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.887A pdb=" N GLU B 281 " --> pdb=" O ARG B 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 247 through 248 removed outlier: 3.839A pdb=" N ARG B 248 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU B 256 " --> pdb=" O ARG B 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 24 removed outlier: 6.986A pdb=" N LEU C 24 " --> pdb=" O GLN C 7 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLN C 7 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN C 59 " --> pdb=" O GLN C 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 79 removed outlier: 5.799A pdb=" N LEU C 150 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N CYS C 184 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU C 152 " --> pdb=" O CYS C 184 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 246 through 250 removed outlier: 3.595A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE C 255 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA C 227 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP C 279 " --> pdb=" O SER C 228 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1086 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: 1.97 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3789 1.34 - 1.46: 2430 1.46 - 1.58: 5613 1.58 - 1.70: 11 1.70 - 1.82: 58 Bond restraints: 11901 Sorted by residual: bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.74e+01 bond pdb=" C4 ATP B 401 " pdb=" C5 ATP B 401 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.17e+01 bond pdb=" C5 ATP C 401 " pdb=" C6 ATP C 401 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.94e+01 bond pdb=" C5 ATP B 401 " pdb=" C6 ATP B 401 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.90e+01 bond pdb=" C4 ATP B 401 " pdb=" N9 ATP B 401 " ideal model delta sigma weight residual 1.374 1.320 0.054 1.00e-02 1.00e+04 2.92e+01 ... (remaining 11896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 15906 3.81 - 7.62: 245 7.62 - 11.43: 32 11.43 - 15.23: 3 15.23 - 19.04: 4 Bond angle restraints: 16190 Sorted by residual: angle pdb=" PB ATP B 401 " pdb=" O3B ATP B 401 " pdb=" PG ATP B 401 " ideal model delta sigma weight residual 139.87 120.83 19.04 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PA ATP B 401 " pdb=" O3A ATP B 401 " pdb=" PB ATP B 401 " ideal model delta sigma weight residual 136.83 118.04 18.79 1.00e+00 1.00e+00 3.53e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 123.32 16.55 1.00e+00 1.00e+00 2.74e+02 angle pdb=" PA ATP C 401 " pdb=" O3A ATP C 401 " pdb=" PB ATP C 401 " ideal model delta sigma weight residual 136.83 126.48 10.35 1.00e+00 1.00e+00 1.07e+02 angle pdb=" C5 ATP C 401 " pdb=" C4 ATP C 401 " pdb=" N3 ATP C 401 " ideal model delta sigma weight residual 126.80 119.16 7.64 1.00e+00 1.00e+00 5.84e+01 ... (remaining 16185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6072 17.91 - 35.82: 711 35.82 - 53.73: 163 53.73 - 71.65: 35 71.65 - 89.56: 8 Dihedral angle restraints: 6989 sinusoidal: 2678 harmonic: 4311 Sorted by residual: dihedral pdb=" CA GLY A 349 " pdb=" C GLY A 349 " pdb=" N ASN A 350 " pdb=" CA ASN A 350 " ideal model delta harmonic sigma weight residual 180.00 -139.80 -40.20 0 5.00e+00 4.00e-02 6.47e+01 dihedral pdb=" CA ARG A 225 " pdb=" C ARG A 225 " pdb=" N THR A 226 " pdb=" CA THR A 226 " ideal model delta harmonic sigma weight residual 180.00 144.04 35.96 0 5.00e+00 4.00e-02 5.17e+01 dihedral pdb=" CA VAL A 413 " pdb=" C VAL A 413 " pdb=" N GLN A 414 " pdb=" CA GLN A 414 " ideal model delta harmonic sigma weight residual 180.00 145.26 34.74 0 5.00e+00 4.00e-02 4.83e+01 ... (remaining 6986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1470 0.072 - 0.145: 343 0.145 - 0.217: 43 0.217 - 0.289: 14 0.289 - 0.361: 6 Chirality restraints: 1876 Sorted by residual: chirality pdb=" CB ILE A 298 " pdb=" CA ILE A 298 " pdb=" CG1 ILE A 298 " pdb=" CG2 ILE A 298 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA ASN A 248 " pdb=" N ASN A 248 " pdb=" C ASN A 248 " pdb=" CB ASN A 248 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CB VAL D 168 " pdb=" CA VAL D 168 " pdb=" CG1 VAL D 168 " pdb=" CG2 VAL D 168 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 1873 not shown) Planarity restraints: 2067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 112 " 0.052 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO A 113 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 66 " 0.051 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO E 67 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 28 " -0.050 5.00e-02 4.00e+02 7.40e-02 8.76e+00 pdb=" N PRO A 29 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 29 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 29 " -0.042 5.00e-02 4.00e+02 ... (remaining 2064 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 311 2.65 - 3.21: 10782 3.21 - 3.78: 21353 3.78 - 4.34: 27551 4.34 - 4.90: 41656 Nonbonded interactions: 101653 Sorted by model distance: nonbonded pdb=" OG1 THR C 43 " pdb="MG MG C 402 " model vdw 2.089 2.170 nonbonded pdb=" O2B ATP B 401 " pdb="MG MG B 402 " model vdw 2.100 2.170 nonbonded pdb=" O3G ATP C 401 " pdb="MG MG C 402 " model vdw 2.107 2.170 nonbonded pdb=" O3G ATP B 401 " pdb="MG MG B 402 " model vdw 2.114 2.170 nonbonded pdb=" O2B ATP C 401 " pdb="MG MG C 402 " model vdw 2.115 2.170 ... (remaining 101648 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 200 or (resid 201 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 202 through 204 and \ (name N or name CA or name C or name O or name CB )) or resid 205 through 230 o \ r resid 245 through 274)) selection = chain 'E' } 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.390 Find NCS groups from input model: 0.160 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 11901 Z= 0.371 Angle : 1.218 19.043 16190 Z= 0.689 Chirality : 0.066 0.361 1876 Planarity : 0.009 0.079 2067 Dihedral : 16.508 89.557 4243 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 1.09 % Allowed : 18.69 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -5.33 (0.16), residues: 1519 helix: -4.23 (0.11), residues: 546 sheet: -2.79 (0.31), residues: 214 loop : -3.18 (0.18), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.003 ARG A 399 TYR 0.019 0.003 TYR C 13 PHE 0.022 0.003 PHE D 185 TRP 0.014 0.002 TRP A 98 HIS 0.009 0.003 HIS B 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.37 (11901) covalent geometry : angle 1.21770 / 0.69 (16190) hydrogen bonds : bond 0.30593 / 20.90 ( 379) hydrogen bonds : angle 10.49186 / 7.29 ( 1086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.497 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 62 MET cc_start: 0.8540 (tpp) cc_final: 0.8263 (tpt) REVERT: A 105 MET cc_start: 0.8162 (tpt) cc_final: 0.7433 (tpp) REVERT: A 209 MET cc_start: 0.9416 (mmm) cc_final: 0.9066 (mmm) REVERT: A 386 VAL cc_start: 0.9640 (p) cc_final: 0.9259 (p) REVERT: A 390 MET cc_start: 0.9771 (mmp) cc_final: 0.9506 (mmm) REVERT: B 34 LEU cc_start: 0.9720 (mp) cc_final: 0.9442 (tp) REVERT: B 102 LYS cc_start: 0.9268 (mmmm) cc_final: 0.9019 (mmmt) REVERT: B 133 MET cc_start: 0.9123 (mtp) cc_final: 0.8796 (mtp) REVERT: B 295 MET cc_start: 0.9136 (mmm) cc_final: 0.8874 (mmm) REVERT: C 46 MET cc_start: 0.9091 (mmt) cc_final: 0.8820 (mmm) REVERT: C 127 LYS cc_start: 0.9382 (pttm) cc_final: 0.9093 (pttm) REVERT: C 133 MET cc_start: 0.9447 (mtp) cc_final: 0.9026 (mtp) REVERT: D 81 GLU cc_start: 0.9326 (mp0) cc_final: 0.9075 (mp0) REVERT: D 185 PHE cc_start: 0.9211 (t80) cc_final: 0.8635 (t80) REVERT: D 189 PHE cc_start: 0.9247 (t80) cc_final: 0.8599 (t80) REVERT: E 20 TRP cc_start: 0.7417 (m-10) cc_final: 0.6842 (m-90) REVERT: E 66 MET cc_start: 0.9428 (tpp) cc_final: 0.8655 (tpp) REVERT: E 72 LEU cc_start: 0.9653 (mm) cc_final: 0.9268 (pp) REVERT: E 76 ASP cc_start: 0.8902 (p0) cc_final: 0.8588 (p0) REVERT: E 170 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8443 (tm-30) REVERT: E 221 TYR cc_start: 0.8948 (t80) cc_final: 0.8690 (t80) outliers start: 13 outliers final: 5 residues processed: 166 average time/residue: 0.1171 time to fit residues: 28.0251 Evaluate side-chains 106 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.0470 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.6284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN A 190 ASN A 212 ASN A 219 ASN A 232 GLN A 241 ASN ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN A 301 ASN A 324 ASN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN B 20 HIS B 23 ASN ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN C 20 HIS C 23 ASN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN D 205 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.037040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.027522 restraints weight = 97846.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.028396 restraints weight = 62320.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.029042 restraints weight = 45058.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.029475 restraints weight = 35424.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.029796 restraints weight = 29652.368| |-----------------------------------------------------------------------------| r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11901 Z= 0.143 Angle : 0.718 9.411 16190 Z= 0.366 Chirality : 0.045 0.205 1876 Planarity : 0.005 0.058 2067 Dihedral : 7.057 56.179 1665 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.25 % Allowed : 6.54 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.18 (0.18), residues: 1519 helix: -2.67 (0.16), residues: 620 sheet: -2.55 (0.31), residues: 219 loop : -2.84 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 269 TYR 0.024 0.001 TYR C 168 PHE 0.012 0.002 PHE D 157 TRP 0.011 0.001 TRP A 343 HIS 0.013 0.002 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (11901) covalent geometry : angle 0.71839 / 0.37 (16190) hydrogen bonds : bond 0.05191 / 3.48 ( 379) hydrogen bonds : angle 6.46577 / 4.49 ( 1086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 146 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8318 (tpp) cc_final: 0.8044 (tpt) REVERT: A 105 MET cc_start: 0.8135 (tpt) cc_final: 0.7447 (tpp) REVERT: A 208 TYR cc_start: 0.9156 (m-10) cc_final: 0.8837 (m-10) REVERT: A 209 MET cc_start: 0.9347 (mmm) cc_final: 0.8915 (mmm) REVERT: A 386 VAL cc_start: 0.9581 (p) cc_final: 0.9140 (p) REVERT: A 390 MET cc_start: 0.9760 (mmp) cc_final: 0.9469 (mmm) REVERT: B 22 LEU cc_start: 0.9570 (tp) cc_final: 0.9362 (tt) REVERT: B 102 LYS cc_start: 0.9267 (mmmm) cc_final: 0.9037 (mmmt) REVERT: B 133 MET cc_start: 0.9365 (mtp) cc_final: 0.9125 (mtp) REVERT: B 143 LEU cc_start: 0.9770 (mm) cc_final: 0.9486 (mt) REVERT: B 295 MET cc_start: 0.9064 (mmm) cc_final: 0.8788 (mmp) REVERT: C 46 MET cc_start: 0.9612 (mmt) cc_final: 0.9411 (mmm) REVERT: C 47 LYS cc_start: 0.9586 (mtmm) cc_final: 0.9334 (mtmt) REVERT: C 127 LYS cc_start: 0.9208 (pttm) cc_final: 0.8797 (pttm) REVERT: C 133 MET cc_start: 0.9498 (mtp) cc_final: 0.9004 (mtp) REVERT: D 66 MET cc_start: 0.9500 (tpp) cc_final: 0.8822 (tpp) REVERT: D 72 LEU cc_start: 0.9236 (pp) cc_final: 0.9005 (pp) REVERT: D 101 LEU cc_start: 0.9382 (mt) cc_final: 0.9137 (mt) REVERT: D 189 PHE cc_start: 0.8860 (t80) cc_final: 0.8390 (t80) REVERT: D 221 TYR cc_start: 0.8931 (t80) cc_final: 0.8603 (t80) REVERT: E 20 TRP cc_start: 0.6630 (m-10) cc_final: 0.6218 (m-90) REVERT: E 66 MET cc_start: 0.9243 (tpp) cc_final: 0.8574 (tpp) REVERT: E 72 LEU cc_start: 0.9660 (mm) cc_final: 0.9314 (tt) REVERT: E 75 TYR cc_start: 0.8946 (p90) cc_final: 0.8258 (p90) REVERT: E 76 ASP cc_start: 0.8896 (p0) cc_final: 0.8114 (p0) REVERT: E 88 MET cc_start: 0.9484 (ptp) cc_final: 0.9089 (mpp) REVERT: E 104 LYS cc_start: 0.9675 (mmmt) cc_final: 0.9319 (tptp) REVERT: E 171 LYS cc_start: 0.9386 (ttmt) cc_final: 0.9142 (tppt) REVERT: E 223 LEU cc_start: 0.9713 (mt) cc_final: 0.9373 (mt) outliers start: 3 outliers final: 1 residues processed: 149 average time/residue: 0.1099 time to fit residues: 24.1795 Evaluate side-chains 103 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 136 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 207 GLN ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.035156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.026243 restraints weight = 101725.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.026924 restraints weight = 65761.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.027440 restraints weight = 48702.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.027844 restraints weight = 39215.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.028074 restraints weight = 33134.752| |-----------------------------------------------------------------------------| r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11901 Z= 0.230 Angle : 0.732 9.696 16190 Z= 0.381 Chirality : 0.045 0.192 1876 Planarity : 0.005 0.053 2067 Dihedral : 6.672 56.558 1665 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.08 % Allowed : 8.05 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.20 (0.20), residues: 1519 helix: -1.46 (0.19), residues: 633 sheet: -2.57 (0.29), residues: 244 loop : -2.50 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 292 TYR 0.018 0.002 TYR C 168 PHE 0.022 0.002 PHE A 289 TRP 0.009 0.001 TRP A 343 HIS 0.008 0.002 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.23 (11901) covalent geometry : angle 0.73166 / 0.38 (16190) hydrogen bonds : bond 0.04499 / 3.02 ( 379) hydrogen bonds : angle 5.96244 / 4.16 ( 1086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8278 (tpp) cc_final: 0.8032 (tpt) REVERT: A 209 MET cc_start: 0.9272 (mmm) cc_final: 0.8841 (mmm) REVERT: A 231 MET cc_start: 0.8494 (mpp) cc_final: 0.8116 (mpp) REVERT: A 386 VAL cc_start: 0.9641 (p) cc_final: 0.9218 (p) REVERT: A 390 MET cc_start: 0.9774 (mmp) cc_final: 0.9548 (mmm) REVERT: B 22 LEU cc_start: 0.9541 (tp) cc_final: 0.9341 (tt) REVERT: B 85 PHE cc_start: 0.9500 (m-80) cc_final: 0.9187 (m-80) REVERT: B 168 TYR cc_start: 0.9391 (m-10) cc_final: 0.9138 (m-80) REVERT: B 295 MET cc_start: 0.9050 (mmm) cc_final: 0.8736 (mmm) REVERT: C 47 LYS cc_start: 0.9573 (mtmm) cc_final: 0.9299 (mmtp) REVERT: C 127 LYS cc_start: 0.9315 (pttm) cc_final: 0.8860 (pttm) REVERT: C 133 MET cc_start: 0.9474 (mtp) cc_final: 0.9048 (mtp) REVERT: D 66 MET cc_start: 0.9533 (tpp) cc_final: 0.8974 (tpp) REVERT: D 72 LEU cc_start: 0.9307 (pp) cc_final: 0.9083 (pp) REVERT: D 101 LEU cc_start: 0.9329 (mt) cc_final: 0.9105 (mt) REVERT: D 189 PHE cc_start: 0.9062 (t80) cc_final: 0.8647 (t80) REVERT: D 219 ASP cc_start: 0.9534 (p0) cc_final: 0.8681 (p0) REVERT: D 221 TYR cc_start: 0.8946 (t80) cc_final: 0.8686 (t80) REVERT: D 222 ARG cc_start: 0.9586 (mtm-85) cc_final: 0.8846 (mtm-85) REVERT: E 20 TRP cc_start: 0.7289 (m-10) cc_final: 0.6794 (m-90) REVERT: E 66 MET cc_start: 0.9289 (tpp) cc_final: 0.8759 (tpp) REVERT: E 76 ASP cc_start: 0.8939 (p0) cc_final: 0.8425 (p0) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.1094 time to fit residues: 20.6487 Evaluate side-chains 92 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 135 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 147 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 ASN ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 207 GLN ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.035785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.026440 restraints weight = 99538.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.027201 restraints weight = 65442.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.027761 restraints weight = 48519.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.028160 restraints weight = 38731.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.028458 restraints weight = 32730.396| |-----------------------------------------------------------------------------| r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11901 Z= 0.181 Angle : 0.694 9.117 16190 Z= 0.356 Chirality : 0.045 0.209 1876 Planarity : 0.005 0.047 2067 Dihedral : 6.466 51.923 1665 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.77 (0.21), residues: 1519 helix: -0.92 (0.20), residues: 639 sheet: -2.49 (0.30), residues: 244 loop : -2.44 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 73 TYR 0.018 0.002 TYR C 168 PHE 0.016 0.002 PHE D 157 TRP 0.022 0.001 TRP B 236 HIS 0.006 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (11901) covalent geometry : angle 0.69448 / 0.36 (16190) hydrogen bonds : bond 0.03892 / 2.60 ( 379) hydrogen bonds : angle 5.61540 / 3.91 ( 1086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8252 (tpp) cc_final: 0.8005 (tpt) REVERT: A 209 MET cc_start: 0.9166 (mmm) cc_final: 0.8707 (mmm) REVERT: A 386 VAL cc_start: 0.9657 (p) cc_final: 0.9105 (p) REVERT: A 390 MET cc_start: 0.9784 (mmp) cc_final: 0.9399 (mmm) REVERT: A 391 ASN cc_start: 0.9710 (t0) cc_final: 0.9309 (p0) REVERT: A 396 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8653 (mm-30) REVERT: B 85 PHE cc_start: 0.9488 (m-80) cc_final: 0.9127 (m-80) REVERT: B 102 LYS cc_start: 0.9327 (mmmm) cc_final: 0.9098 (mmmt) REVERT: B 127 LYS cc_start: 0.9383 (ptmm) cc_final: 0.8846 (pttm) REVERT: B 143 LEU cc_start: 0.9744 (mm) cc_final: 0.9443 (mt) REVERT: B 168 TYR cc_start: 0.9408 (m-10) cc_final: 0.9139 (m-80) REVERT: B 295 MET cc_start: 0.9101 (mmm) cc_final: 0.8732 (mmm) REVERT: C 37 HIS cc_start: 0.9249 (m90) cc_final: 0.9013 (m90) REVERT: C 46 MET cc_start: 0.9626 (mmp) cc_final: 0.9385 (mmm) REVERT: C 133 MET cc_start: 0.9513 (mtp) cc_final: 0.9095 (mtp) REVERT: C 295 MET cc_start: 0.9488 (tmm) cc_final: 0.9265 (tmm) REVERT: D 66 MET cc_start: 0.9448 (tpp) cc_final: 0.8959 (tpp) REVERT: D 101 LEU cc_start: 0.9320 (mt) cc_final: 0.9080 (mt) REVERT: D 189 PHE cc_start: 0.9109 (t80) cc_final: 0.8669 (t80) REVERT: D 221 TYR cc_start: 0.8941 (t80) cc_final: 0.8685 (t80) REVERT: E 66 MET cc_start: 0.9239 (tpp) cc_final: 0.8741 (tpp) REVERT: E 72 LEU cc_start: 0.9669 (mm) cc_final: 0.9353 (tt) REVERT: E 171 LYS cc_start: 0.9265 (tptp) cc_final: 0.8787 (tptp) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1039 time to fit residues: 20.5698 Evaluate side-chains 99 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 35 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS A 176 HIS ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.034262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.025263 restraints weight = 105629.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.026019 restraints weight = 68894.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.026527 restraints weight = 50024.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.026946 restraints weight = 39754.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.027227 restraints weight = 33092.526| |-----------------------------------------------------------------------------| r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11901 Z= 0.307 Angle : 0.801 10.020 16190 Z= 0.415 Chirality : 0.046 0.193 1876 Planarity : 0.005 0.079 2067 Dihedral : 6.734 60.386 1665 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.60 (0.21), residues: 1519 helix: -0.75 (0.20), residues: 623 sheet: -2.47 (0.30), residues: 239 loop : -2.33 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 73 TYR 0.015 0.002 TYR C 86 PHE 0.020 0.003 PHE D 157 TRP 0.027 0.002 TRP A 358 HIS 0.010 0.002 HIS B 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.31 (11901) covalent geometry : angle 0.80053 / 0.41 (16190) hydrogen bonds : bond 0.04507 / 3.03 ( 379) hydrogen bonds : angle 5.83607 / 4.09 ( 1086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.513 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 62 MET cc_start: 0.8427 (tpp) cc_final: 0.8189 (tpt) REVERT: A 209 MET cc_start: 0.9182 (mmm) cc_final: 0.8667 (mmm) REVERT: A 231 MET cc_start: 0.8408 (mpp) cc_final: 0.8085 (mpp) REVERT: A 386 VAL cc_start: 0.9697 (p) cc_final: 0.9223 (p) REVERT: A 390 MET cc_start: 0.9747 (mmp) cc_final: 0.9459 (mmm) REVERT: A 391 ASN cc_start: 0.9713 (t0) cc_final: 0.9339 (t0) REVERT: B 85 PHE cc_start: 0.9496 (m-80) cc_final: 0.9204 (m-80) REVERT: B 102 LYS cc_start: 0.9273 (mmmm) cc_final: 0.8978 (mmmt) REVERT: B 168 TYR cc_start: 0.9384 (m-10) cc_final: 0.9129 (m-80) REVERT: B 295 MET cc_start: 0.9117 (mmm) cc_final: 0.8745 (mmm) REVERT: C 46 MET cc_start: 0.9605 (mmp) cc_final: 0.9384 (mmm) REVERT: C 133 MET cc_start: 0.9443 (mtp) cc_final: 0.9055 (mtp) REVERT: C 295 MET cc_start: 0.9508 (tmm) cc_final: 0.9297 (tmm) REVERT: D 66 MET cc_start: 0.9489 (tpp) cc_final: 0.9092 (tpp) REVERT: D 101 LEU cc_start: 0.9322 (mt) cc_final: 0.9070 (mt) REVERT: D 158 LEU cc_start: 0.9660 (mt) cc_final: 0.9419 (mt) REVERT: E 66 MET cc_start: 0.9301 (tpp) cc_final: 0.8823 (tpp) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1082 time to fit residues: 20.4723 Evaluate side-chains 88 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.035746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.026486 restraints weight = 99005.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.027223 restraints weight = 64676.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.027755 restraints weight = 47773.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.028134 restraints weight = 38289.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.028373 restraints weight = 32445.168| |-----------------------------------------------------------------------------| r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11901 Z= 0.148 Angle : 0.694 8.904 16190 Z= 0.347 Chirality : 0.045 0.237 1876 Planarity : 0.004 0.067 2067 Dihedral : 6.426 60.935 1665 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.21), residues: 1519 helix: -0.50 (0.21), residues: 623 sheet: -2.42 (0.31), residues: 244 loop : -2.27 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 73 TYR 0.012 0.001 TYR C 86 PHE 0.039 0.002 PHE E 183 TRP 0.014 0.001 TRP B 236 HIS 0.009 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (11901) covalent geometry : angle 0.69448 / 0.35 (16190) hydrogen bonds : bond 0.03654 / 2.44 ( 379) hydrogen bonds : angle 5.43651 / 3.78 ( 1086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8298 (tpp) cc_final: 0.8052 (tpt) REVERT: A 209 MET cc_start: 0.9182 (mmm) cc_final: 0.8647 (mmm) REVERT: A 231 MET cc_start: 0.8436 (mpp) cc_final: 0.8204 (mpp) REVERT: A 386 VAL cc_start: 0.9649 (p) cc_final: 0.9181 (p) REVERT: A 390 MET cc_start: 0.9744 (mmp) cc_final: 0.9393 (mmm) REVERT: A 391 ASN cc_start: 0.9687 (t0) cc_final: 0.9405 (t0) REVERT: A 396 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8705 (mm-30) REVERT: B 85 PHE cc_start: 0.9449 (m-80) cc_final: 0.9129 (m-80) REVERT: B 102 LYS cc_start: 0.9280 (mmmm) cc_final: 0.8931 (mmmt) REVERT: B 127 LYS cc_start: 0.9370 (ptmm) cc_final: 0.8874 (pttm) REVERT: B 295 MET cc_start: 0.9128 (mmm) cc_final: 0.8711 (mmp) REVERT: C 37 HIS cc_start: 0.9241 (m90) cc_final: 0.9037 (m90) REVERT: C 46 MET cc_start: 0.9584 (mmp) cc_final: 0.9350 (mmm) REVERT: C 133 MET cc_start: 0.9527 (mtp) cc_final: 0.9119 (mtp) REVERT: C 295 MET cc_start: 0.9515 (tmm) cc_final: 0.9311 (tmm) REVERT: D 66 MET cc_start: 0.9405 (tpp) cc_final: 0.9006 (tpp) REVERT: D 72 LEU cc_start: 0.9236 (pp) cc_final: 0.9034 (pp) REVERT: D 101 LEU cc_start: 0.9318 (mt) cc_final: 0.9054 (mt) REVERT: D 158 LEU cc_start: 0.9637 (mt) cc_final: 0.9401 (mt) REVERT: E 66 MET cc_start: 0.9315 (tpp) cc_final: 0.8914 (tpp) REVERT: E 72 LEU cc_start: 0.9676 (mm) cc_final: 0.9362 (tt) REVERT: E 75 TYR cc_start: 0.8671 (p90) cc_final: 0.8023 (p90) REVERT: E 76 ASP cc_start: 0.8899 (p0) cc_final: 0.8363 (p0) REVERT: E 120 PHE cc_start: 0.9041 (t80) cc_final: 0.8603 (t80) REVERT: E 170 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8647 (tm-30) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1107 time to fit residues: 21.3851 Evaluate side-chains 100 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 60 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 122 optimal weight: 0.0570 overall best weight: 3.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.035399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.026054 restraints weight = 100072.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.026843 restraints weight = 64649.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.027408 restraints weight = 47420.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.027808 restraints weight = 37720.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.028055 restraints weight = 31680.854| |-----------------------------------------------------------------------------| r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11901 Z= 0.177 Angle : 0.699 10.522 16190 Z= 0.354 Chirality : 0.045 0.237 1876 Planarity : 0.004 0.059 2067 Dihedral : 6.390 68.751 1665 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.31 (0.22), residues: 1519 helix: -0.46 (0.21), residues: 629 sheet: -2.35 (0.31), residues: 249 loop : -2.22 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 74 TYR 0.011 0.002 TYR C 86 PHE 0.037 0.002 PHE E 183 TRP 0.011 0.001 TRP D 20 HIS 0.006 0.002 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (11901) covalent geometry : angle 0.69907 / 0.35 (16190) hydrogen bonds : bond 0.03681 / 2.47 ( 379) hydrogen bonds : angle 5.41673 / 3.78 ( 1086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8315 (tpp) cc_final: 0.8073 (tpt) REVERT: A 209 MET cc_start: 0.9186 (mmm) cc_final: 0.8614 (mmm) REVERT: A 231 MET cc_start: 0.8448 (mpp) cc_final: 0.8171 (mpp) REVERT: A 386 VAL cc_start: 0.9652 (p) cc_final: 0.9201 (p) REVERT: A 390 MET cc_start: 0.9759 (mmp) cc_final: 0.9385 (mmm) REVERT: A 391 ASN cc_start: 0.9707 (t0) cc_final: 0.9402 (t0) REVERT: A 396 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8688 (mm-30) REVERT: B 85 PHE cc_start: 0.9441 (m-80) cc_final: 0.9116 (m-80) REVERT: B 127 LYS cc_start: 0.9374 (ptmm) cc_final: 0.8849 (pttm) REVERT: B 295 MET cc_start: 0.9158 (mmm) cc_final: 0.8825 (mmm) REVERT: C 37 HIS cc_start: 0.9259 (m90) cc_final: 0.9053 (m90) REVERT: C 46 MET cc_start: 0.9584 (mmp) cc_final: 0.9375 (mmm) REVERT: C 133 MET cc_start: 0.9490 (mtp) cc_final: 0.9129 (mtp) REVERT: D 66 MET cc_start: 0.9435 (tpp) cc_final: 0.9053 (tpp) REVERT: D 101 LEU cc_start: 0.9369 (mt) cc_final: 0.9124 (mt) REVERT: D 158 LEU cc_start: 0.9641 (mt) cc_final: 0.9399 (mt) REVERT: D 189 PHE cc_start: 0.9267 (t80) cc_final: 0.8876 (t80) REVERT: D 221 TYR cc_start: 0.8920 (t80) cc_final: 0.8712 (t80) REVERT: E 66 MET cc_start: 0.9271 (tpp) cc_final: 0.8783 (tpp) REVERT: E 72 LEU cc_start: 0.9666 (mm) cc_final: 0.9352 (tt) REVERT: E 75 TYR cc_start: 0.8433 (p90) cc_final: 0.8228 (p90) REVERT: E 76 ASP cc_start: 0.8803 (p0) cc_final: 0.8455 (p0) REVERT: E 170 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8675 (tm-30) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1084 time to fit residues: 20.6131 Evaluate side-chains 98 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 65 optimal weight: 40.0000 chunk 3 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 64 optimal weight: 40.0000 chunk 116 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 2 ASN ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.034455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.025361 restraints weight = 104963.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.026143 restraints weight = 67525.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.026707 restraints weight = 49161.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.027116 restraints weight = 38743.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.027393 restraints weight = 32349.771| |-----------------------------------------------------------------------------| r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11901 Z= 0.295 Angle : 0.810 9.659 16190 Z= 0.415 Chirality : 0.047 0.229 1876 Planarity : 0.005 0.062 2067 Dihedral : 6.772 81.271 1665 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.45 (0.21), residues: 1519 helix: -0.64 (0.20), residues: 636 sheet: -2.33 (0.31), residues: 231 loop : -2.30 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 74 TYR 0.017 0.002 TYR C 86 PHE 0.044 0.003 PHE C 85 TRP 0.016 0.002 TRP D 20 HIS 0.010 0.002 HIS B 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.30 (11901) covalent geometry : angle 0.80955 / 0.41 (16190) hydrogen bonds : bond 0.04342 / 2.92 ( 379) hydrogen bonds : angle 5.74900 / 4.03 ( 1086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.9218 (mmm) cc_final: 0.8503 (mmm) REVERT: A 231 MET cc_start: 0.8368 (mpp) cc_final: 0.8099 (mpp) REVERT: A 390 MET cc_start: 0.9724 (mmp) cc_final: 0.9512 (mmm) REVERT: A 391 ASN cc_start: 0.9701 (t0) cc_final: 0.9441 (t0) REVERT: B 85 PHE cc_start: 0.9445 (m-80) cc_final: 0.9150 (m-80) REVERT: B 102 LYS cc_start: 0.9302 (mmmm) cc_final: 0.9046 (mmmt) REVERT: B 143 LEU cc_start: 0.9760 (mm) cc_final: 0.9492 (mt) REVERT: B 295 MET cc_start: 0.9112 (mmm) cc_final: 0.8740 (mmp) REVERT: C 37 HIS cc_start: 0.9246 (m90) cc_final: 0.9014 (m90) REVERT: C 46 MET cc_start: 0.9575 (mmp) cc_final: 0.9346 (mmm) REVERT: C 133 MET cc_start: 0.9516 (mtp) cc_final: 0.9197 (mtp) REVERT: D 66 MET cc_start: 0.9484 (tpp) cc_final: 0.9127 (tpp) REVERT: D 101 LEU cc_start: 0.9307 (mt) cc_final: 0.9029 (mt) REVERT: D 158 LEU cc_start: 0.9668 (mt) cc_final: 0.9403 (mt) REVERT: D 189 PHE cc_start: 0.9311 (t80) cc_final: 0.8853 (t80) REVERT: E 66 MET cc_start: 0.9293 (tpp) cc_final: 0.8820 (tpp) REVERT: E 170 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8706 (tm-30) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1062 time to fit residues: 20.3289 Evaluate side-chains 92 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 145 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.036401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.026923 restraints weight = 98206.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.027742 restraints weight = 63855.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.028324 restraints weight = 46928.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.028737 restraints weight = 37236.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.029040 restraints weight = 31421.969| |-----------------------------------------------------------------------------| r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11901 Z= 0.133 Angle : 0.703 8.899 16190 Z= 0.346 Chirality : 0.045 0.247 1876 Planarity : 0.004 0.062 2067 Dihedral : 6.311 70.304 1665 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.22), residues: 1519 helix: -0.48 (0.20), residues: 637 sheet: -2.31 (0.31), residues: 249 loop : -2.16 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 399 TYR 0.023 0.002 TYR A 249 PHE 0.032 0.002 PHE E 183 TRP 0.026 0.001 TRP A 358 HIS 0.009 0.001 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (11901) covalent geometry : angle 0.70344 / 0.35 (16190) hydrogen bonds : bond 0.03510 / 2.33 ( 379) hydrogen bonds : angle 5.29729 / 3.69 ( 1086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.436 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 208 TYR cc_start: 0.8901 (m-10) cc_final: 0.8585 (m-10) REVERT: A 209 MET cc_start: 0.9222 (mmm) cc_final: 0.8633 (mmm) REVERT: A 390 MET cc_start: 0.9731 (mmp) cc_final: 0.9523 (mmm) REVERT: A 391 ASN cc_start: 0.9690 (t0) cc_final: 0.9353 (t0) REVERT: B 46 MET cc_start: 0.9349 (mmp) cc_final: 0.9112 (mmm) REVERT: B 85 PHE cc_start: 0.9348 (m-80) cc_final: 0.9100 (m-80) REVERT: B 102 LYS cc_start: 0.9364 (mmmm) cc_final: 0.8939 (mmmt) REVERT: B 127 LYS cc_start: 0.9359 (ptmm) cc_final: 0.8815 (pttm) REVERT: B 295 MET cc_start: 0.9055 (mmm) cc_final: 0.8669 (mmm) REVERT: C 37 HIS cc_start: 0.9251 (m90) cc_final: 0.8968 (m90) REVERT: C 46 MET cc_start: 0.9571 (mmp) cc_final: 0.9323 (mmm) REVERT: C 133 MET cc_start: 0.9602 (mtp) cc_final: 0.9221 (mtp) REVERT: D 66 MET cc_start: 0.9410 (tpp) cc_final: 0.9056 (tpp) REVERT: D 101 LEU cc_start: 0.9357 (mt) cc_final: 0.9126 (mt) REVERT: D 158 LEU cc_start: 0.9646 (mt) cc_final: 0.9384 (mt) REVERT: D 189 PHE cc_start: 0.9282 (t80) cc_final: 0.8909 (t80) REVERT: E 66 MET cc_start: 0.9249 (tpp) cc_final: 0.8818 (tpp) REVERT: E 72 LEU cc_start: 0.9624 (mm) cc_final: 0.9376 (tt) REVERT: E 75 TYR cc_start: 0.8463 (p90) cc_final: 0.8204 (p90) REVERT: E 76 ASP cc_start: 0.8831 (p0) cc_final: 0.8382 (p0) REVERT: E 171 LYS cc_start: 0.9191 (tptp) cc_final: 0.8952 (tptp) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1032 time to fit residues: 20.4602 Evaluate side-chains 104 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 70 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 113 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.035907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.026511 restraints weight = 101739.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.027349 restraints weight = 64736.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.027951 restraints weight = 46978.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.028374 restraints weight = 36818.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.028691 restraints weight = 30634.391| |-----------------------------------------------------------------------------| r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11901 Z= 0.164 Angle : 0.713 9.236 16190 Z= 0.354 Chirality : 0.046 0.261 1876 Planarity : 0.004 0.060 2067 Dihedral : 6.278 75.955 1665 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.20 (0.22), residues: 1519 helix: -0.43 (0.20), residues: 639 sheet: -2.24 (0.31), residues: 249 loop : -2.12 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 399 TYR 0.016 0.002 TYR A 351 PHE 0.033 0.002 PHE E 183 TRP 0.015 0.001 TRP D 20 HIS 0.010 0.002 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (11901) covalent geometry : angle 0.71294 / 0.35 (16190) hydrogen bonds : bond 0.03597 / 2.41 ( 379) hydrogen bonds : angle 5.31026 / 3.71 ( 1086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.516 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 208 TYR cc_start: 0.8931 (m-10) cc_final: 0.8635 (m-10) REVERT: A 209 MET cc_start: 0.9221 (mmm) cc_final: 0.8731 (mmm) REVERT: A 231 MET cc_start: 0.8255 (mpp) cc_final: 0.7862 (mpp) REVERT: A 391 ASN cc_start: 0.9619 (t0) cc_final: 0.9407 (t0) REVERT: B 46 MET cc_start: 0.9378 (mmp) cc_final: 0.9151 (mmm) REVERT: B 85 PHE cc_start: 0.9359 (m-80) cc_final: 0.9095 (m-80) REVERT: B 127 LYS cc_start: 0.9355 (ptmm) cc_final: 0.8817 (pttm) REVERT: B 295 MET cc_start: 0.9068 (mmm) cc_final: 0.8802 (mmm) REVERT: C 37 HIS cc_start: 0.9263 (m90) cc_final: 0.9000 (m90) REVERT: C 46 MET cc_start: 0.9586 (mmp) cc_final: 0.9355 (mmm) REVERT: C 133 MET cc_start: 0.9563 (mtp) cc_final: 0.9253 (mtp) REVERT: D 66 MET cc_start: 0.9446 (tpp) cc_final: 0.9095 (tpp) REVERT: D 101 LEU cc_start: 0.9357 (mt) cc_final: 0.9125 (mt) REVERT: D 158 LEU cc_start: 0.9641 (mt) cc_final: 0.9392 (mt) REVERT: D 189 PHE cc_start: 0.9316 (t80) cc_final: 0.8945 (t80) REVERT: E 66 MET cc_start: 0.9240 (tpp) cc_final: 0.8821 (tpp) REVERT: E 72 LEU cc_start: 0.9616 (mm) cc_final: 0.9333 (tt) REVERT: E 75 TYR cc_start: 0.8458 (p90) cc_final: 0.8207 (p90) REVERT: E 76 ASP cc_start: 0.8824 (p0) cc_final: 0.8395 (p0) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1017 time to fit residues: 19.5854 Evaluate side-chains 99 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 110 optimal weight: 6.9990 chunk 129 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 114 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.035108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.026009 restraints weight = 101484.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.026808 restraints weight = 64989.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.027396 restraints weight = 47289.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.027744 restraints weight = 36861.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.028076 restraints weight = 31280.977| |-----------------------------------------------------------------------------| r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11901 Z= 0.214 Angle : 0.740 9.207 16190 Z= 0.373 Chirality : 0.046 0.244 1876 Planarity : 0.005 0.059 2067 Dihedral : 6.385 78.853 1665 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.25 (0.21), residues: 1519 helix: -0.44 (0.20), residues: 635 sheet: -2.32 (0.31), residues: 249 loop : -2.15 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 399 TYR 0.019 0.002 TYR C 13 PHE 0.034 0.002 PHE E 183 TRP 0.016 0.001 TRP D 20 HIS 0.011 0.002 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.21 (11901) covalent geometry : angle 0.73977 / 0.37 (16190) hydrogen bonds : bond 0.03772 / 2.53 ( 379) hydrogen bonds : angle 5.39785 / 3.78 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1714.51 seconds wall clock time: 30 minutes 52.86 seconds (1852.86 seconds total)