Starting phenix.real_space_refine on Wed Jul 30 07:24:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o17_12692/07_2025/7o17_12692.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o17_12692/07_2025/7o17_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7o17_12692/07_2025/7o17_12692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o17_12692/07_2025/7o17_12692.map" model { file = "/net/cci-nas-00/data/ceres_data/7o17_12692/07_2025/7o17_12692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o17_12692/07_2025/7o17_12692.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG: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: 7.32, per 1000 atoms: 0.63 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: 2.72 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.32 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: 3.95 Time building geometry restraints manager: 3.31 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: 6099 17.91 - 35.82: 731 35.82 - 53.73: 174 53.73 - 71.65: 37 71.65 - 89.56: 10 Dihedral angle restraints: 7051 sinusoidal: 2740 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 7048 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.430 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 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 : 16.813 89.557 4305 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.002 TRP A 98 HIS 0.009 0.003 HIS B 120 PHE 0.022 0.003 PHE D 185 TYR 0.019 0.003 TYR C 13 ARG 0.027 0.003 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.30593 ( 379) hydrogen bonds : angle 10.49186 ( 1086) covalent geometry : bond 0.00692 (11901) covalent geometry : angle 1.21770 (16190) *********************** 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 : 1.244 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: 0.9641 (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: 0.8797 (mtp) REVERT: B 295 MET cc_start: 0.9136 (mmm) cc_final: 0.8874 (mmm) REVERT: C 46 MET cc_start: 0.9090 (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: 0.8656 (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: 0.8689 (t80) outliers start: 13 outliers final: 5 residues processed: 166 average time/residue: 0.2494 time to fit residues: 58.6252 Evaluate side-chains 105 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 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 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 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** ** C 154 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 = 0.2840 r_free = 0.2840 target = 0.036202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.026837 restraints weight = 99942.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.027687 restraints weight = 64101.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.028289 restraints weight = 46624.078| |-----------------------------------------------------------------------------| r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11901 Z= 0.188 Angle : 0.736 9.787 16190 Z= 0.384 Chirality : 0.045 0.205 1876 Planarity : 0.005 0.056 2067 Dihedral : 9.126 86.622 1727 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.25 % Allowed : 7.38 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.19), residues: 1519 helix: -2.39 (0.16), residues: 619 sheet: -2.57 (0.31), residues: 219 loop : -2.79 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 343 HIS 0.014 0.002 HIS C 97 PHE 0.014 0.002 PHE D 157 TYR 0.023 0.002 TYR C 168 ARG 0.005 0.001 ARG C 269 Details of bonding type rmsd hydrogen bonds : bond 0.04997 ( 379) hydrogen bonds : angle 6.41523 ( 1086) covalent geometry : bond 0.00390 (11901) covalent geometry : angle 0.73604 (16190) *********************** 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 139 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8384 (tpp) cc_final: 0.8117 (tpt) REVERT: A 209 MET cc_start: 0.9343 (mmm) cc_final: 0.8915 (mmm) REVERT: A 386 VAL cc_start: 0.9582 (p) cc_final: 0.9127 (p) REVERT: A 390 MET cc_start: 0.9748 (mmp) cc_final: 0.9442 (mmm) REVERT: A 402 GLN cc_start: 0.9740 (OUTLIER) cc_final: 0.9281 (mm110) REVERT: B 22 LEU cc_start: 0.9588 (tp) cc_final: 0.9382 (tt) REVERT: B 85 PHE cc_start: 0.9422 (m-80) cc_final: 0.9151 (m-80) REVERT: B 133 MET cc_start: 0.9288 (mtp) cc_final: 0.9081 (mtp) REVERT: B 295 MET cc_start: 0.9041 (mmm) cc_final: 0.8754 (mmp) REVERT: C 47 LYS cc_start: 0.9597 (mtmm) cc_final: 0.9352 (mtmt) REVERT: C 127 LYS cc_start: 0.9271 (pttm) cc_final: 0.8925 (pttm) REVERT: C 133 MET cc_start: 0.9422 (mtp) cc_final: 0.8985 (mtp) REVERT: D 66 MET cc_start: 0.9521 (tpp) cc_final: 0.8841 (tpp) REVERT: D 72 LEU cc_start: 0.9270 (pp) cc_final: 0.9043 (pp) REVERT: D 101 LEU cc_start: 0.9382 (mt) cc_final: 0.9154 (mt) REVERT: D 189 PHE cc_start: 0.9005 (t80) cc_final: 0.8547 (t80) REVERT: D 221 TYR cc_start: 0.8933 (t80) cc_final: 0.8630 (t80) REVERT: E 20 TRP cc_start: 0.7233 (m-10) cc_final: 0.6777 (m-90) REVERT: E 66 MET cc_start: 0.9269 (tpp) cc_final: 0.8648 (tpp) REVERT: E 72 LEU cc_start: 0.9680 (mm) cc_final: 0.9261 (tt) REVERT: E 76 ASP cc_start: 0.8959 (p0) cc_final: 0.8502 (p0) REVERT: E 88 MET cc_start: 0.9529 (ptp) cc_final: 0.9110 (mpp) REVERT: E 104 LYS cc_start: 0.9697 (mmmt) cc_final: 0.9398 (tptp) REVERT: E 223 LEU cc_start: 0.9718 (mt) cc_final: 0.9430 (mt) outliers start: 3 outliers final: 0 residues processed: 139 average time/residue: 0.2433 time to fit residues: 49.4628 Evaluate side-chains 99 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 38 optimal weight: 0.0870 chunk 128 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 30.0000 chunk 37 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 50.0000 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 A 324 ASN ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.036612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.027198 restraints weight = 97818.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.027954 restraints weight = 64287.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.028606 restraints weight = 47460.001| |-----------------------------------------------------------------------------| r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11901 Z= 0.142 Angle : 0.671 8.865 16190 Z= 0.344 Chirality : 0.045 0.210 1876 Planarity : 0.005 0.051 2067 Dihedral : 8.409 89.774 1727 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.08 % Allowed : 7.71 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.20), residues: 1519 helix: -1.45 (0.19), residues: 632 sheet: -2.62 (0.29), residues: 246 loop : -2.52 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 343 HIS 0.007 0.001 HIS C 97 PHE 0.027 0.002 PHE E 143 TYR 0.023 0.002 TYR C 168 ARG 0.003 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 379) hydrogen bonds : angle 5.77175 ( 1086) covalent geometry : bond 0.00299 (11901) covalent geometry : angle 0.67106 (16190) *********************** 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 138 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 1.373 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: 0.8253 (tpp) cc_final: 0.7995 (tpt) REVERT: A 209 MET cc_start: 0.9286 (mmm) cc_final: 0.8838 (mmm) REVERT: A 386 VAL cc_start: 0.9574 (p) cc_final: 0.9185 (p) REVERT: A 391 ASN cc_start: 0.9603 (t0) cc_final: 0.9322 (p0) REVERT: B 34 LEU cc_start: 0.9630 (mp) cc_final: 0.9413 (tp) REVERT: B 82 ASN cc_start: 0.9017 (p0) cc_final: 0.8798 (p0) REVERT: B 85 PHE cc_start: 0.9381 (m-80) cc_final: 0.9107 (m-80) REVERT: B 102 LYS cc_start: 0.9599 (mmpt) cc_final: 0.9168 (mmmt) REVERT: B 127 LYS cc_start: 0.9404 (ptmm) cc_final: 0.8861 (pttm) REVERT: B 295 MET cc_start: 0.9093 (mmm) cc_final: 0.8748 (mmm) REVERT: C 37 HIS cc_start: 0.9282 (m90) cc_final: 0.9077 (m90) REVERT: C 46 MET cc_start: 0.9593 (mmp) cc_final: 0.9359 (mmm) REVERT: C 47 LYS cc_start: 0.9586 (mtmm) cc_final: 0.9285 (mtmt) REVERT: C 133 MET cc_start: 0.9503 (mtp) cc_final: 0.9055 (mtp) REVERT: D 66 MET cc_start: 0.9502 (tpp) cc_final: 0.9002 (tpp) REVERT: D 72 LEU cc_start: 0.9182 (pp) cc_final: 0.8957 (pp) REVERT: D 101 LEU cc_start: 0.9334 (mt) cc_final: 0.9105 (mt) REVERT: D 189 PHE cc_start: 0.8971 (t80) cc_final: 0.8559 (t80) REVERT: D 221 TYR cc_start: 0.8946 (t80) cc_final: 0.8655 (t80) REVERT: E 20 TRP cc_start: 0.7196 (m-10) cc_final: 0.6731 (m-90) REVERT: E 66 MET cc_start: 0.9220 (tpp) cc_final: 0.8669 (tpp) REVERT: E 72 LEU cc_start: 0.9668 (mm) cc_final: 0.9359 (tt) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.2401 time to fit residues: 49.0953 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 : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 20 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 8 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 133 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** 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 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.035763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.026502 restraints weight = 99875.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.027254 restraints weight = 66002.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.027827 restraints weight = 49196.264| |-----------------------------------------------------------------------------| r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11901 Z= 0.210 Angle : 0.714 9.161 16190 Z= 0.369 Chirality : 0.045 0.195 1876 Planarity : 0.005 0.048 2067 Dihedral : 8.052 86.602 1727 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.08 % Allowed : 5.70 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.21), residues: 1519 helix: -0.92 (0.20), residues: 640 sheet: -2.53 (0.30), residues: 239 loop : -2.43 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 236 HIS 0.007 0.002 HIS B 120 PHE 0.017 0.002 PHE D 157 TYR 0.015 0.002 TYR C 168 ARG 0.008 0.000 ARG C 73 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 379) hydrogen bonds : angle 5.63731 ( 1086) covalent geometry : bond 0.00433 (11901) covalent geometry : angle 0.71403 (16190) *********************** 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 126 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 1.635 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: 0.8290 (tpp) cc_final: 0.8049 (tpt) REVERT: A 209 MET cc_start: 0.9170 (mmm) cc_final: 0.8677 (mmm) REVERT: A 231 MET cc_start: 0.8390 (mpp) cc_final: 0.7979 (mpp) REVERT: A 386 VAL cc_start: 0.9652 (p) cc_final: 0.9107 (p) REVERT: A 390 MET cc_start: 0.9739 (mmp) cc_final: 0.9465 (mmm) REVERT: A 391 ASN cc_start: 0.9684 (t0) cc_final: 0.9431 (t0) REVERT: A 396 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8658 (mm-30) REVERT: B 34 LEU cc_start: 0.9699 (mp) cc_final: 0.9466 (mp) REVERT: B 85 PHE cc_start: 0.9477 (m-80) cc_final: 0.9189 (m-80) REVERT: B 127 LYS cc_start: 0.9447 (ptmm) cc_final: 0.8962 (pttm) REVERT: B 133 MET cc_start: 0.9589 (mtm) cc_final: 0.9321 (mtp) REVERT: B 295 MET cc_start: 0.9098 (mmm) cc_final: 0.8760 (mmm) REVERT: C 37 HIS cc_start: 0.9293 (m90) cc_final: 0.9066 (m90) REVERT: C 46 MET cc_start: 0.9594 (mmp) cc_final: 0.9345 (mmm) REVERT: C 47 LYS cc_start: 0.9584 (mtmm) cc_final: 0.9372 (mtmt) REVERT: C 127 LYS cc_start: 0.9301 (pttm) cc_final: 0.8868 (pttm) REVERT: C 133 MET cc_start: 0.9447 (mtp) cc_final: 0.9001 (mtp) REVERT: D 66 MET cc_start: 0.9507 (tpp) cc_final: 0.9112 (tpp) REVERT: D 72 LEU cc_start: 0.9167 (pp) cc_final: 0.8927 (pp) REVERT: D 101 LEU cc_start: 0.9351 (mt) cc_final: 0.9116 (mt) REVERT: D 189 PHE cc_start: 0.9144 (t80) cc_final: 0.8672 (t80) REVERT: D 221 TYR cc_start: 0.8989 (t80) cc_final: 0.8676 (t80) REVERT: E 66 MET cc_start: 0.9258 (tpp) cc_final: 0.8762 (tpp) REVERT: E 72 LEU cc_start: 0.9681 (mm) cc_final: 0.9322 (tt) REVERT: E 76 ASP cc_start: 0.8879 (p0) cc_final: 0.8519 (p0) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.2260 time to fit residues: 42.1645 Evaluate side-chains 96 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 144 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 110 optimal weight: 0.1980 chunk 118 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.035735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.026393 restraints weight = 98762.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.027187 restraints weight = 64111.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.027755 restraints weight = 46990.351| |-----------------------------------------------------------------------------| r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11901 Z= 0.194 Angle : 0.701 8.937 16190 Z= 0.357 Chirality : 0.045 0.207 1876 Planarity : 0.005 0.080 2067 Dihedral : 7.747 83.821 1727 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.21), residues: 1519 helix: -0.68 (0.20), residues: 642 sheet: -2.51 (0.29), residues: 244 loop : -2.37 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 358 HIS 0.006 0.002 HIS B 120 PHE 0.039 0.002 PHE E 183 TYR 0.017 0.002 TYR C 168 ARG 0.005 0.000 ARG C 73 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 379) hydrogen bonds : angle 5.50250 ( 1086) covalent geometry : bond 0.00404 (11901) covalent geometry : angle 0.70101 (16190) *********************** 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 129 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.479 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: 0.8275 (tpp) cc_final: 0.8039 (tpt) REVERT: A 209 MET cc_start: 0.9201 (mmm) cc_final: 0.8592 (mmm) REVERT: A 386 VAL cc_start: 0.9664 (p) cc_final: 0.9172 (p) REVERT: A 390 MET cc_start: 0.9713 (mmp) cc_final: 0.9465 (mmm) REVERT: A 391 ASN cc_start: 0.9718 (t0) cc_final: 0.9340 (t0) REVERT: A 396 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8716 (mm-30) REVERT: B 34 LEU cc_start: 0.9699 (mp) cc_final: 0.9427 (mp) REVERT: B 46 MET cc_start: 0.9231 (mmp) cc_final: 0.9021 (mmm) REVERT: B 85 PHE cc_start: 0.9446 (m-80) cc_final: 0.9150 (m-80) REVERT: B 127 LYS cc_start: 0.9456 (ptmm) cc_final: 0.8959 (pttm) REVERT: B 133 MET cc_start: 0.9620 (mtm) cc_final: 0.9346 (mtp) REVERT: B 295 MET cc_start: 0.9113 (mmm) cc_final: 0.8732 (mmm) REVERT: C 37 HIS cc_start: 0.9251 (m90) cc_final: 0.8966 (m90) REVERT: C 46 MET cc_start: 0.9578 (mmp) cc_final: 0.9300 (mmm) REVERT: C 127 LYS cc_start: 0.9310 (pttm) cc_final: 0.8835 (pttm) REVERT: C 133 MET cc_start: 0.9474 (mtp) cc_final: 0.9060 (mtp) REVERT: C 295 MET cc_start: 0.9515 (tmm) cc_final: 0.9289 (tmm) REVERT: D 66 MET cc_start: 0.9513 (tpp) cc_final: 0.9132 (tpp) REVERT: D 72 LEU cc_start: 0.9186 (pp) cc_final: 0.8982 (pp) REVERT: D 101 LEU cc_start: 0.9368 (mt) cc_final: 0.9120 (mt) REVERT: D 221 TYR cc_start: 0.9034 (t80) cc_final: 0.8646 (t80) REVERT: E 66 MET cc_start: 0.9286 (tpp) cc_final: 0.8799 (tpp) REVERT: E 72 LEU cc_start: 0.9682 (mm) cc_final: 0.9315 (tt) REVERT: E 76 ASP cc_start: 0.8852 (p0) cc_final: 0.8507 (p0) REVERT: E 120 PHE cc_start: 0.9092 (t80) cc_final: 0.8772 (t80) REVERT: E 170 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8701 (tm-30) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2528 time to fit residues: 48.7166 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 : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 90 optimal weight: 9.9990 chunk 148 optimal weight: 0.2980 chunk 84 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 119 optimal weight: 0.3980 chunk 64 optimal weight: 40.0000 chunk 101 optimal weight: 10.0000 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 HIS ** 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** D 225 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.035152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.025944 restraints weight = 101344.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.026732 restraints weight = 65395.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.027294 restraints weight = 47774.783| |-----------------------------------------------------------------------------| r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11901 Z= 0.213 Angle : 0.721 9.343 16190 Z= 0.368 Chirality : 0.045 0.214 1876 Planarity : 0.005 0.067 2067 Dihedral : 7.755 80.455 1727 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.21), residues: 1519 helix: -0.58 (0.21), residues: 634 sheet: -2.42 (0.30), residues: 248 loop : -2.26 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 236 HIS 0.007 0.002 HIS B 194 PHE 0.036 0.002 PHE E 183 TYR 0.013 0.002 TYR C 168 ARG 0.006 0.000 ARG C 73 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 379) hydrogen bonds : angle 5.43478 ( 1086) covalent geometry : bond 0.00438 (11901) covalent geometry : angle 0.72066 (16190) *********************** 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 124 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.531 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: 0.8331 (tpp) cc_final: 0.8090 (tpt) REVERT: A 209 MET cc_start: 0.9214 (mmm) cc_final: 0.8813 (mmm) REVERT: A 386 VAL cc_start: 0.9632 (p) cc_final: 0.9198 (p) REVERT: A 390 MET cc_start: 0.9763 (mmp) cc_final: 0.9491 (mmm) REVERT: A 391 ASN cc_start: 0.9714 (t0) cc_final: 0.9409 (t0) REVERT: A 396 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8691 (mm-30) REVERT: B 34 LEU cc_start: 0.9713 (mp) cc_final: 0.9431 (mp) REVERT: B 46 MET cc_start: 0.9246 (mmp) cc_final: 0.9037 (mmm) REVERT: B 85 PHE cc_start: 0.9466 (m-80) cc_final: 0.9174 (m-80) REVERT: B 127 LYS cc_start: 0.9452 (ptmm) cc_final: 0.8968 (pttm) REVERT: B 133 MET cc_start: 0.9608 (mtm) cc_final: 0.9349 (mtp) REVERT: B 295 MET cc_start: 0.9133 (mmm) cc_final: 0.8745 (mmm) REVERT: C 37 HIS cc_start: 0.9286 (m90) cc_final: 0.9014 (m90) REVERT: C 46 MET cc_start: 0.9561 (mmp) cc_final: 0.9291 (mmm) REVERT: C 47 LYS cc_start: 0.9604 (mtmm) cc_final: 0.9320 (mtmt) REVERT: C 133 MET cc_start: 0.9448 (mtp) cc_final: 0.9052 (mtp) REVERT: C 295 MET cc_start: 0.9536 (tmm) cc_final: 0.9336 (tmm) REVERT: D 66 MET cc_start: 0.9533 (tpp) cc_final: 0.9183 (tpp) REVERT: D 101 LEU cc_start: 0.9344 (mt) cc_final: 0.9093 (mt) REVERT: D 158 LEU cc_start: 0.9666 (mt) cc_final: 0.9464 (mt) REVERT: D 189 PHE cc_start: 0.9243 (t80) cc_final: 0.8866 (t80) REVERT: E 66 MET cc_start: 0.9300 (tpp) cc_final: 0.8801 (tpp) REVERT: E 76 ASP cc_start: 0.8837 (p0) cc_final: 0.8507 (p0) REVERT: E 170 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8708 (tm-30) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2706 time to fit residues: 49.1410 Evaluate side-chains 97 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 140 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 138 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 104 optimal weight: 0.0370 chunk 92 optimal weight: 20.0000 chunk 95 optimal weight: 0.9990 chunk 128 optimal weight: 0.5980 overall best weight: 0.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 11 GLN ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 ASN D 225 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.037250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.027553 restraints weight = 96412.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.028403 restraints weight = 62491.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.028993 restraints weight = 45693.207| |-----------------------------------------------------------------------------| r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11901 Z= 0.113 Angle : 0.686 10.207 16190 Z= 0.333 Chirality : 0.045 0.222 1876 Planarity : 0.004 0.061 2067 Dihedral : 7.669 89.218 1727 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.21), residues: 1519 helix: -0.50 (0.21), residues: 643 sheet: -2.36 (0.29), residues: 253 loop : -2.22 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 20 HIS 0.006 0.001 HIS B 194 PHE 0.029 0.002 PHE E 183 TYR 0.013 0.001 TYR E 221 ARG 0.008 0.000 ARG C 74 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 379) hydrogen bonds : angle 5.12021 ( 1086) covalent geometry : bond 0.00250 (11901) covalent geometry : angle 0.68600 (16190) *********************** 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 138 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 2.102 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: 0.8208 (tpp) cc_final: 0.7972 (tpt) REVERT: A 208 TYR cc_start: 0.9183 (m-10) cc_final: 0.8812 (m-10) REVERT: A 209 MET cc_start: 0.9236 (mmm) cc_final: 0.8700 (mmm) REVERT: A 386 VAL cc_start: 0.9595 (p) cc_final: 0.9138 (p) REVERT: A 390 MET cc_start: 0.9730 (mmp) cc_final: 0.9476 (mmm) REVERT: A 391 ASN cc_start: 0.9719 (t0) cc_final: 0.9395 (t0) REVERT: A 396 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8635 (mm-30) REVERT: B 34 LEU cc_start: 0.9754 (mp) cc_final: 0.9463 (mp) REVERT: B 46 MET cc_start: 0.9246 (mmp) cc_final: 0.8972 (mmm) REVERT: B 102 LYS cc_start: 0.9372 (mmpt) cc_final: 0.9056 (mmmt) REVERT: B 127 LYS cc_start: 0.9427 (ptmm) cc_final: 0.8931 (pttm) REVERT: B 295 MET cc_start: 0.9134 (mmm) cc_final: 0.8783 (mmp) REVERT: C 37 HIS cc_start: 0.9331 (m90) cc_final: 0.8978 (m90) REVERT: C 46 MET cc_start: 0.9568 (mmp) cc_final: 0.9278 (mmm) REVERT: C 47 LYS cc_start: 0.9580 (mtmm) cc_final: 0.9307 (mtmt) REVERT: C 133 MET cc_start: 0.9759 (mtp) cc_final: 0.9459 (mtp) REVERT: D 66 MET cc_start: 0.9490 (tpp) cc_final: 0.9133 (tpp) REVERT: D 101 LEU cc_start: 0.9349 (mt) cc_final: 0.9093 (mt) REVERT: D 221 TYR cc_start: 0.8924 (t80) cc_final: 0.8471 (t80) REVERT: E 66 MET cc_start: 0.9224 (tpp) cc_final: 0.8815 (tpp) REVERT: E 72 LEU cc_start: 0.9651 (mm) cc_final: 0.9350 (tt) REVERT: E 75 TYR cc_start: 0.8507 (p90) cc_final: 0.8284 (p90) REVERT: E 76 ASP cc_start: 0.8804 (p0) cc_final: 0.8405 (p0) REVERT: E 118 ILE cc_start: 0.8711 (tp) cc_final: 0.8394 (tp) REVERT: E 170 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8658 (tm-30) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.3669 time to fit residues: 74.2468 Evaluate side-chains 113 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 88 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 131 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 138 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 overall best weight: 6.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 25 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** D 6 ASN D 225 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.034378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.025467 restraints weight = 103902.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.026208 restraints weight = 68526.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.026725 restraints weight = 50869.383| |-----------------------------------------------------------------------------| r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11901 Z= 0.298 Angle : 0.811 9.500 16190 Z= 0.416 Chirality : 0.047 0.199 1876 Planarity : 0.005 0.059 2067 Dihedral : 7.861 84.956 1727 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 23.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.21), residues: 1519 helix: -0.59 (0.20), residues: 629 sheet: -2.39 (0.30), residues: 245 loop : -2.17 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 141 HIS 0.011 0.003 HIS B 120 PHE 0.034 0.003 PHE E 183 TYR 0.022 0.002 TYR A 351 ARG 0.005 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 379) hydrogen bonds : angle 5.62038 ( 1086) covalent geometry : bond 0.00601 (11901) covalent geometry : angle 0.81137 (16190) *********************** 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 124 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.420 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: 0.8355 (tpp) cc_final: 0.8079 (tpt) REVERT: A 208 TYR cc_start: 0.9042 (m-10) cc_final: 0.8732 (m-10) REVERT: A 209 MET cc_start: 0.9206 (mmm) cc_final: 0.8665 (mmm) REVERT: A 231 MET cc_start: 0.8272 (mpp) cc_final: 0.7868 (mpp) REVERT: A 305 LYS cc_start: 0.9595 (mmtt) cc_final: 0.9338 (tmtt) REVERT: A 386 VAL cc_start: 0.9637 (p) cc_final: 0.9215 (p) REVERT: A 390 MET cc_start: 0.9763 (mmp) cc_final: 0.9452 (mmm) REVERT: A 391 ASN cc_start: 0.9708 (t0) cc_final: 0.9362 (t0) REVERT: A 396 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8622 (mm-30) REVERT: B 34 LEU cc_start: 0.9709 (mp) cc_final: 0.9447 (mp) REVERT: B 46 MET cc_start: 0.9259 (mmp) cc_final: 0.9059 (mmm) REVERT: B 127 LYS cc_start: 0.9450 (ptmm) cc_final: 0.8894 (pttm) REVERT: B 133 MET cc_start: 0.9613 (mtm) cc_final: 0.9293 (mtp) REVERT: B 295 MET cc_start: 0.9142 (mmm) cc_final: 0.8844 (mmm) REVERT: C 37 HIS cc_start: 0.9273 (m90) cc_final: 0.8973 (m90) REVERT: C 46 MET cc_start: 0.9550 (mmp) cc_final: 0.9295 (mmm) REVERT: C 133 MET cc_start: 0.9521 (mtp) cc_final: 0.9116 (mtp) REVERT: D 14 ASP cc_start: 0.9200 (p0) cc_final: 0.8988 (p0) REVERT: D 66 MET cc_start: 0.9565 (tpp) cc_final: 0.9211 (tpp) REVERT: D 101 LEU cc_start: 0.9319 (mt) cc_final: 0.9033 (mt) REVERT: D 189 PHE cc_start: 0.9350 (t80) cc_final: 0.8916 (t80) REVERT: D 221 TYR cc_start: 0.8923 (t80) cc_final: 0.8566 (t80) REVERT: E 66 MET cc_start: 0.9301 (tpp) cc_final: 0.8862 (tpp) REVERT: E 72 LEU cc_start: 0.9687 (mm) cc_final: 0.9316 (tt) REVERT: E 76 ASP cc_start: 0.8966 (p0) cc_final: 0.8456 (p0) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2397 time to fit residues: 44.3532 Evaluate side-chains 97 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 66 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 96 optimal weight: 30.0000 chunk 62 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 65 optimal weight: 30.0000 chunk 135 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 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** ** C 88 GLN ** 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 = 0.2832 r_free = 0.2832 target = 0.035993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.026752 restraints weight = 102175.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.027568 restraints weight = 65980.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.028152 restraints weight = 48026.601| |-----------------------------------------------------------------------------| r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3613 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= 0.172 Angle : 0.714 8.880 16190 Z= 0.357 Chirality : 0.046 0.218 1876 Planarity : 0.004 0.060 2067 Dihedral : 7.773 82.390 1727 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.22), residues: 1519 helix: -0.49 (0.20), residues: 642 sheet: -2.37 (0.30), residues: 253 loop : -2.18 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 358 HIS 0.008 0.002 HIS B 194 PHE 0.030 0.002 PHE E 183 TYR 0.014 0.002 TYR C 86 ARG 0.005 0.000 ARG C 74 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 379) hydrogen bonds : angle 5.29555 ( 1086) covalent geometry : bond 0.00368 (11901) covalent geometry : angle 0.71394 (16190) *********************** 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 129 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.431 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: 0.8918 (m-10) cc_final: 0.8623 (m-10) REVERT: A 209 MET cc_start: 0.9243 (mmm) cc_final: 0.8705 (mmm) REVERT: A 231 MET cc_start: 0.8343 (mpp) cc_final: 0.8007 (mpp) REVERT: A 391 ASN cc_start: 0.9720 (t0) cc_final: 0.9406 (t0) REVERT: A 395 ILE cc_start: 0.9357 (mm) cc_final: 0.9137 (mm) REVERT: A 396 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8662 (mm-30) REVERT: B 34 LEU cc_start: 0.9745 (mp) cc_final: 0.9467 (mp) REVERT: B 46 MET cc_start: 0.9291 (mmp) cc_final: 0.9055 (mmm) REVERT: B 127 LYS cc_start: 0.9462 (ptmm) cc_final: 0.8895 (pttm) REVERT: B 133 MET cc_start: 0.9596 (mtm) cc_final: 0.9316 (mtp) REVERT: B 143 LEU cc_start: 0.9749 (mt) cc_final: 0.9500 (mt) REVERT: B 295 MET cc_start: 0.9127 (mmm) cc_final: 0.8830 (mmp) REVERT: C 37 HIS cc_start: 0.9320 (m90) cc_final: 0.9008 (m90) REVERT: C 46 MET cc_start: 0.9592 (mmp) cc_final: 0.9347 (mmm) REVERT: C 133 MET cc_start: 0.9632 (mtp) cc_final: 0.9229 (mtp) REVERT: D 66 MET cc_start: 0.9512 (tpp) cc_final: 0.9149 (tpp) REVERT: D 101 LEU cc_start: 0.9355 (mt) cc_final: 0.9129 (mt) REVERT: D 189 PHE cc_start: 0.9303 (t80) cc_final: 0.8929 (t80) REVERT: E 66 MET cc_start: 0.9243 (tpp) cc_final: 0.8735 (tpp) REVERT: E 72 LEU cc_start: 0.9646 (mm) cc_final: 0.9342 (tt) REVERT: E 76 ASP cc_start: 0.8860 (p0) cc_final: 0.8423 (p0) REVERT: E 170 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8721 (tm-30) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2395 time to fit residues: 45.3390 Evaluate side-chains 101 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 101 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 146 optimal weight: 0.4980 chunk 55 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 362 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** ** C 88 GLN ** 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 = 0.2845 r_free = 0.2845 target = 0.036346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.026959 restraints weight = 100631.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.027810 restraints weight = 65588.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.028407 restraints weight = 47240.201| |-----------------------------------------------------------------------------| r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3714 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= 0.148 Angle : 0.706 9.454 16190 Z= 0.349 Chirality : 0.045 0.249 1876 Planarity : 0.004 0.060 2067 Dihedral : 7.615 82.655 1727 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.22), residues: 1519 helix: -0.44 (0.21), residues: 644 sheet: -2.33 (0.30), residues: 253 loop : -2.16 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 20 HIS 0.009 0.001 HIS B 194 PHE 0.030 0.002 PHE E 183 TYR 0.013 0.001 TYR A 351 ARG 0.005 0.000 ARG C 74 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 379) hydrogen bonds : angle 5.20977 ( 1086) covalent geometry : bond 0.00322 (11901) covalent geometry : angle 0.70623 (16190) ********************** 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 : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.8884 (m-10) cc_final: 0.8595 (m-10) REVERT: A 209 MET cc_start: 0.9215 (mmm) cc_final: 0.8678 (mmm) REVERT: A 231 MET cc_start: 0.8355 (mpp) cc_final: 0.8011 (mpp) REVERT: A 391 ASN cc_start: 0.9621 (t0) cc_final: 0.9413 (t0) REVERT: A 396 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8653 (mm-30) REVERT: B 46 MET cc_start: 0.9270 (mmp) cc_final: 0.9043 (mmm) REVERT: B 127 LYS cc_start: 0.9441 (ptmm) cc_final: 0.8887 (pttm) REVERT: B 133 MET cc_start: 0.9667 (mtm) cc_final: 0.9221 (mtp) REVERT: B 143 LEU cc_start: 0.9738 (mt) cc_final: 0.9518 (mt) REVERT: B 295 MET cc_start: 0.9150 (mmm) cc_final: 0.8854 (mmp) REVERT: C 37 HIS cc_start: 0.9323 (m90) cc_final: 0.9018 (m90) REVERT: C 46 MET cc_start: 0.9580 (mmp) cc_final: 0.9329 (mmm) REVERT: C 133 MET cc_start: 0.9628 (mtp) cc_final: 0.9252 (mtp) REVERT: D 66 MET cc_start: 0.9519 (tpp) cc_final: 0.9159 (tpp) REVERT: D 101 LEU cc_start: 0.9373 (mt) cc_final: 0.9125 (mt) REVERT: D 189 PHE cc_start: 0.9306 (t80) cc_final: 0.8935 (t80) REVERT: D 219 ASP cc_start: 0.9507 (p0) cc_final: 0.8434 (p0) REVERT: D 221 TYR cc_start: 0.8858 (t80) cc_final: 0.8485 (t80) REVERT: D 222 ARG cc_start: 0.9527 (mtm-85) cc_final: 0.8760 (mtm-85) REVERT: E 66 MET cc_start: 0.9260 (tpp) cc_final: 0.8841 (tpp) REVERT: E 76 ASP cc_start: 0.8958 (p0) cc_final: 0.8508 (p0) REVERT: E 170 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8753 (tm-30) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2320 time to fit residues: 44.0007 Evaluate side-chains 103 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.658 ------------------------------------------------------------------------------- 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: 0.7980 chunk 28 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 146 optimal weight: 0.0770 chunk 52 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 overall best weight: 2.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.036589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.027236 restraints weight = 100657.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.028078 restraints weight = 64900.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.028690 restraints weight = 47037.371| |-----------------------------------------------------------------------------| r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11901 Z= 0.144 Angle : 0.700 9.434 16190 Z= 0.345 Chirality : 0.045 0.223 1876 Planarity : 0.004 0.059 2067 Dihedral : 7.530 82.564 1727 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.22), residues: 1519 helix: -0.42 (0.21), residues: 644 sheet: -2.35 (0.30), residues: 253 loop : -2.16 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 352 HIS 0.008 0.001 HIS B 194 PHE 0.029 0.002 PHE E 183 TYR 0.024 0.002 TYR A 351 ARG 0.005 0.000 ARG C 74 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 379) hydrogen bonds : angle 5.16094 ( 1086) covalent geometry : bond 0.00315 (11901) covalent geometry : angle 0.70049 (16190) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3562.66 seconds wall clock time: 65 minutes 50.53 seconds (3950.53 seconds total)