Starting phenix.real_space_refine on Wed Mar 4 04:30:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ovb_13083/03_2026/7ovb_13083.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ovb_13083/03_2026/7ovb_13083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ovb_13083/03_2026/7ovb_13083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ovb_13083/03_2026/7ovb_13083.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ovb_13083/03_2026/7ovb_13083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ovb_13083/03_2026/7ovb_13083.map" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 48 5.16 5 C 6889 2.51 5 N 1870 2.21 5 O 2046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10854 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3665 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 453} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2085 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 241} Chain: "C" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1615 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 197} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2284 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 275} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1204 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 5, 'TRANS': 182} Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 8, 'ARG:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 5, 'GLN:plan1': 4, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6091 SG CYS C 46 68.490 32.143 59.833 1.00 53.64 S ATOM 6117 SG CYS C 49 71.848 32.551 59.854 1.00 45.97 S ATOM 6346 SG CYS C 78 70.020 35.728 59.140 1.00 54.09 S ATOM 6369 SG CYS C 81 70.418 33.055 56.514 1.00 52.98 S Time building chain proxies: 2.44, per 1000 atoms: 0.22 Number of scatterers: 10854 At special positions: 0 Unit cell: (142.8, 111.3, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 48 16.00 O 2046 8.00 N 1870 7.00 C 6889 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: 0.90 Conformation dependent library (CDL) restraints added in 500.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 49 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 78 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 46 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 81 " Number of angles added : 6 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2646 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 4 sheets defined 57.1% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 121 through 127 removed outlier: 3.810A pdb=" N THR A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.543A pdb=" N SER A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.674A pdb=" N ARG A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 218 through 228 removed outlier: 3.816A pdb=" N VAL A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 228 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 262 removed outlier: 3.670A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 removed outlier: 4.169A pdb=" N ASP A 276 " --> pdb=" O ASN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 285 Processing helix chain 'A' and resid 303 through 316 removed outlier: 4.259A pdb=" N THR A 307 " --> pdb=" O PRO A 303 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Proline residue: A 309 - end of helix removed outlier: 3.608A pdb=" N LEU A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 353 removed outlier: 4.272A pdb=" N GLN A 328 " --> pdb=" O LYS A 324 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N SER A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLN A 335 " --> pdb=" O GLN A 331 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLN A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 373 Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 395 through 405 removed outlier: 4.053A pdb=" N VAL A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 458 removed outlier: 3.735A pdb=" N SER A 457 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 476 removed outlier: 4.371A pdb=" N SER A 476 " --> pdb=" O PHE A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 487 Processing helix chain 'A' and resid 594 through 615 removed outlier: 3.572A pdb=" N MET A 599 " --> pdb=" O ASP A 595 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS A 600 " --> pdb=" O ASP A 596 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 606 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 615 " --> pdb=" O ILE A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 removed outlier: 3.955A pdb=" N ALA A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 658 Processing helix chain 'B' and resid 126 through 134 removed outlier: 3.515A pdb=" N ARG B 131 " --> pdb=" O MET B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 141 through 146 removed outlier: 3.518A pdb=" N VAL B 145 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 141 through 146' Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 196 through 208 removed outlier: 3.842A pdb=" N ARG B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 207 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 208 " --> pdb=" O PHE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 234 removed outlier: 3.878A pdb=" N VAL B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 234 " --> pdb=" O MET B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 252 removed outlier: 3.755A pdb=" N ALA B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 246 " --> pdb=" O ASN B 242 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 271 through 279 Processing helix chain 'B' and resid 283 through 296 removed outlier: 3.626A pdb=" N LEU B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 294 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.823A pdb=" N PHE B 306 " --> pdb=" O SER B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 4.106A pdb=" N VAL B 312 " --> pdb=" O TRP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 321 removed outlier: 3.594A pdb=" N ASN B 321 " --> pdb=" O TRP B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 346 Processing helix chain 'B' and resid 356 through 364 removed outlier: 3.504A pdb=" N LEU B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 Processing helix chain 'C' and resid 17 through 28 removed outlier: 4.267A pdb=" N LEU C 21 " --> pdb=" O GLY C 17 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 27 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.573A pdb=" N TYR C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU C 35 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 86 Processing helix chain 'C' and resid 108 through 118 removed outlier: 3.951A pdb=" N LEU C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 141 removed outlier: 3.514A pdb=" N GLN C 133 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 138 " --> pdb=" O ASN C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.810A pdb=" N PHE C 150 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 166 removed outlier: 3.602A pdb=" N GLN C 162 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET C 164 " --> pdb=" O PHE C 160 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 187 through 190 removed outlier: 3.758A pdb=" N LYS C 190 " --> pdb=" O SER C 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 190' Processing helix chain 'C' and resid 191 through 196 removed outlier: 3.546A pdb=" N GLU C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 207 removed outlier: 3.530A pdb=" N GLU C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 30 removed outlier: 3.842A pdb=" N LEU D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 Processing helix chain 'D' and resid 50 through 87 removed outlier: 4.235A pdb=" N ILE D 55 " --> pdb=" O HIS D 51 " (cutoff:3.500A) Proline residue: D 56 - end of helix removed outlier: 3.549A pdb=" N ASN D 59 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR D 72 " --> pdb=" O GLN D 68 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER D 86 " --> pdb=" O ASP D 82 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY D 87 " --> pdb=" O TYR D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 160 removed outlier: 4.359A pdb=" N THR D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG D 101 " --> pdb=" O GLY D 97 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU D 102 " --> pdb=" O ALA D 98 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N SER D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU D 107 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP D 116 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP D 142 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN D 160 " --> pdb=" O SER D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 181 removed outlier: 3.680A pdb=" N LYS D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 203 removed outlier: 3.597A pdb=" N GLN D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 217 removed outlier: 3.501A pdb=" N LEU D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 265 removed outlier: 3.973A pdb=" N LEU D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN D 230 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 235 " --> pdb=" O THR D 231 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE D 236 " --> pdb=" O LYS D 232 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS D 242 " --> pdb=" O ASP D 238 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL D 257 " --> pdb=" O GLN D 253 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE D 262 " --> pdb=" O ILE D 258 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 274 through 282 removed outlier: 3.640A pdb=" N ILE D 280 " --> pdb=" O ALA D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 286 removed outlier: 3.744A pdb=" N TYR D 286 " --> pdb=" O GLU D 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 283 through 286' Processing helix chain 'E' and resid 8 through 18 Processing helix chain 'E' and resid 22 through 39 Processing helix chain 'E' and resid 43 through 64 Processing helix chain 'E' and resid 69 through 73 Processing helix chain 'E' and resid 79 through 96 removed outlier: 3.556A pdb=" N THR E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 142 Processing helix chain 'E' and resid 170 through 183 Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 120 removed outlier: 6.333A pdb=" N PHE A 120 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE A 107 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 110 " --> pdb=" O ARG A 570 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 558 " --> pdb=" O ALA A 569 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS A 492 " --> pdb=" O HIS A 559 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 490 " --> pdb=" O PHE A 561 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU A 130 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR A 433 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ILE A 463 " --> pdb=" O TYR A 433 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS A 435 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ALA A 465 " --> pdb=" O CYS A 435 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 437 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE A 158 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR A 159 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU A 186 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LEU A 380 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE A 188 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 289 Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 61 removed outlier: 3.676A pdb=" N ASP C 58 " --> pdb=" O ALA C 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 99 through 101 450 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2323 1.32 - 1.45: 2424 1.45 - 1.57: 6214 1.57 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 11041 Sorted by residual: bond pdb=" CA ASP B 236 " pdb=" CB ASP B 236 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.32e-02 5.74e+03 1.07e+01 bond pdb=" CA SER E 79 " pdb=" CB SER E 79 " ideal model delta sigma weight residual 1.526 1.485 0.041 1.26e-02 6.30e+03 1.04e+01 bond pdb=" C PRO E 77 " pdb=" O PRO E 77 " ideal model delta sigma weight residual 1.233 1.200 0.033 1.23e-02 6.61e+03 7.28e+00 bond pdb=" CB TRP E 71 " pdb=" CG TRP E 71 " ideal model delta sigma weight residual 1.498 1.418 0.080 3.10e-02 1.04e+03 6.73e+00 bond pdb=" N SER E 79 " pdb=" CA SER E 79 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.24e-02 6.50e+03 6.48e+00 ... (remaining 11036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 14171 2.32 - 4.63: 650 4.63 - 6.95: 81 6.95 - 9.27: 11 9.27 - 11.59: 8 Bond angle restraints: 14921 Sorted by residual: angle pdb=" N PRO E 77 " pdb=" CA PRO E 77 " pdb=" C PRO E 77 " ideal model delta sigma weight residual 111.03 100.29 10.74 1.54e+00 4.22e-01 4.87e+01 angle pdb=" C LEU D 85 " pdb=" N SER D 86 " pdb=" CA SER D 86 " ideal model delta sigma weight residual 122.56 115.64 6.92 1.50e+00 4.44e-01 2.13e+01 angle pdb=" C PHE A 108 " pdb=" N GLY A 109 " pdb=" CA GLY A 109 " ideal model delta sigma weight residual 120.56 114.22 6.34 1.42e+00 4.96e-01 1.99e+01 angle pdb=" C LYS E 52 " pdb=" N ILE E 53 " pdb=" CA ILE E 53 " ideal model delta sigma weight residual 120.64 113.86 6.78 1.64e+00 3.72e-01 1.71e+01 angle pdb=" N ILE D 179 " pdb=" CA ILE D 179 " pdb=" C ILE D 179 " ideal model delta sigma weight residual 113.42 108.76 4.66 1.17e+00 7.31e-01 1.58e+01 ... (remaining 14916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 6012 17.78 - 35.57: 615 35.57 - 53.35: 75 53.35 - 71.13: 17 71.13 - 88.92: 21 Dihedral angle restraints: 6740 sinusoidal: 2652 harmonic: 4088 Sorted by residual: dihedral pdb=" CA GLU D 235 " pdb=" C GLU D 235 " pdb=" N PHE D 236 " pdb=" CA PHE D 236 " ideal model delta harmonic sigma weight residual 180.00 -150.15 -29.85 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA GLN D 253 " pdb=" C GLN D 253 " pdb=" N PHE D 254 " pdb=" CA PHE D 254 " ideal model delta harmonic sigma weight residual 180.00 153.08 26.92 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA GLU A 591 " pdb=" C GLU A 591 " pdb=" N PRO A 592 " pdb=" CA PRO A 592 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 6737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1273 0.067 - 0.134: 372 0.134 - 0.201: 35 0.201 - 0.268: 3 0.268 - 0.335: 2 Chirality restraints: 1685 Sorted by residual: chirality pdb=" CA THR E 78 " pdb=" N THR E 78 " pdb=" C THR E 78 " pdb=" CB THR E 78 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CB ILE D 31 " pdb=" CA ILE D 31 " pdb=" CG1 ILE D 31 " pdb=" CG2 ILE D 31 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ARG E 76 " pdb=" N ARG E 76 " pdb=" C ARG E 76 " pdb=" CB ARG E 76 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1682 not shown) Planarity restraints: 1936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 75 " -0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C GLU E 75 " 0.061 2.00e-02 2.50e+03 pdb=" O GLU E 75 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG E 76 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 62 " -0.033 2.00e-02 2.50e+03 2.51e-02 1.10e+01 pdb=" CG PHE E 62 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE E 62 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE E 62 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE E 62 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 62 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 62 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 19 " -0.007 2.00e-02 2.50e+03 1.79e-02 7.99e+00 pdb=" CG TRP C 19 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 19 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP C 19 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP C 19 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 19 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 19 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 19 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 19 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 19 " -0.001 2.00e-02 2.50e+03 ... (remaining 1933 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 140 2.55 - 3.14: 9749 3.14 - 3.72: 16082 3.72 - 4.31: 22737 4.31 - 4.90: 36136 Nonbonded interactions: 84844 Sorted by model distance: nonbonded pdb=" O ALA A 150 " pdb=" OG SER A 155 " model vdw 1.960 3.040 nonbonded pdb=" O MET A 175 " pdb=" OG SER A 178 " model vdw 2.038 3.040 nonbonded pdb=" NH2 ARG D 101 " pdb=" OE2 GLU D 102 " model vdw 2.062 3.120 nonbonded pdb=" OH TYR B 283 " pdb=" O LEU B 350 " model vdw 2.070 3.040 nonbonded pdb=" OG SER A 387 " pdb=" OD1 ASP A 389 " model vdw 2.076 3.040 ... (remaining 84839 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.010 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 0.013 0.080 11045 Z= 0.568 Angle : 1.139 14.262 14927 Z= 0.632 Chirality : 0.059 0.335 1685 Planarity : 0.006 0.066 1936 Dihedral : 15.016 88.916 4094 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 0.09 % Allowed : 0.44 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.16 (0.20), residues: 1389 helix: -2.73 (0.16), residues: 711 sheet: -2.05 (0.58), residues: 71 loop : -2.76 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 296 TYR 0.030 0.004 TYR A 433 PHE 0.055 0.004 PHE E 62 TRP 0.045 0.004 TRP C 19 HIS 0.006 0.002 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.01301 (11041) covalent geometry : angle 1.12884 (14921) hydrogen bonds : bond 0.27848 ( 450) hydrogen bonds : angle 10.96097 ( 1305) metal coordination : bond 0.03318 ( 4) metal coordination : angle 7.63022 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.264 Fit side-chains REVERT: A 169 TYR cc_start: 0.8411 (t80) cc_final: 0.8191 (t80) REVERT: A 258 MET cc_start: 0.8032 (tpt) cc_final: 0.7796 (tmm) REVERT: E 29 MET cc_start: 0.7698 (tmm) cc_final: 0.7017 (tmm) outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.0912 time to fit residues: 13.3959 Evaluate side-chains 81 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 374 GLN D 54 GLN ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.104992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.083909 restraints weight = 27702.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.086222 restraints weight = 16161.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.087744 restraints weight = 11380.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.088743 restraints weight = 9046.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.089417 restraints weight = 7782.352| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11045 Z= 0.166 Angle : 0.682 13.762 14927 Z= 0.356 Chirality : 0.043 0.204 1685 Planarity : 0.005 0.055 1936 Dihedral : 5.654 23.994 1513 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.18 % Allowed : 7.62 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.21), residues: 1389 helix: -1.41 (0.18), residues: 746 sheet: -1.87 (0.58), residues: 72 loop : -2.67 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 279 TYR 0.026 0.002 TYR A 313 PHE 0.039 0.002 PHE E 62 TRP 0.015 0.002 TRP C 19 HIS 0.012 0.002 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00356 (11041) covalent geometry : angle 0.67864 (14921) hydrogen bonds : bond 0.05537 ( 450) hydrogen bonds : angle 5.84529 ( 1305) metal coordination : bond 0.00710 ( 4) metal coordination : angle 3.19506 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.420 Fit side-chains REVERT: A 258 MET cc_start: 0.7942 (tpt) cc_final: 0.7583 (tmm) REVERT: A 313 TYR cc_start: 0.6551 (t80) cc_final: 0.6342 (t80) REVERT: B 248 ASP cc_start: 0.6670 (m-30) cc_final: 0.6434 (m-30) REVERT: B 353 MET cc_start: 0.6879 (mtp) cc_final: 0.6655 (mtp) REVERT: B 375 MET cc_start: 0.8393 (tpt) cc_final: 0.7954 (tpp) REVERT: C 79 CYS cc_start: 0.8450 (t) cc_final: 0.8155 (t) REVERT: C 208 ASP cc_start: 0.5557 (t0) cc_final: 0.5298 (p0) REVERT: E 95 HIS cc_start: 0.8020 (m90) cc_final: 0.7703 (m90) outliers start: 2 outliers final: 1 residues processed: 108 average time/residue: 0.0898 time to fit residues: 14.8897 Evaluate side-chains 92 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 135 optimal weight: 50.0000 chunk 107 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 134 optimal weight: 30.0000 chunk 76 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.103879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.082903 restraints weight = 28531.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.084921 restraints weight = 17931.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.086266 restraints weight = 13226.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.087145 restraints weight = 10821.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.087663 restraints weight = 9493.461| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11045 Z= 0.206 Angle : 0.641 10.166 14927 Z= 0.332 Chirality : 0.043 0.147 1685 Planarity : 0.004 0.048 1936 Dihedral : 5.333 23.218 1513 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.89 % Allowed : 11.96 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.22), residues: 1389 helix: -0.96 (0.19), residues: 754 sheet: -1.45 (0.57), residues: 83 loop : -2.62 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 291 TYR 0.028 0.002 TYR A 169 PHE 0.035 0.002 PHE E 62 TRP 0.006 0.001 TRP B 212 HIS 0.022 0.002 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00490 (11041) covalent geometry : angle 0.63657 (14921) hydrogen bonds : bond 0.04774 ( 450) hydrogen bonds : angle 5.36660 ( 1305) metal coordination : bond 0.01092 ( 4) metal coordination : angle 3.77990 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.405 Fit side-chains REVERT: A 175 MET cc_start: 0.8344 (ttp) cc_final: 0.8120 (ttt) REVERT: A 258 MET cc_start: 0.7909 (tpt) cc_final: 0.7647 (mmm) REVERT: B 248 ASP cc_start: 0.6691 (m-30) cc_final: 0.6473 (m-30) REVERT: C 79 CYS cc_start: 0.8462 (t) cc_final: 0.8210 (t) REVERT: D 215 ILE cc_start: 0.8130 (pt) cc_final: 0.7904 (pt) REVERT: E 63 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7124 (ttpt) REVERT: E 86 GLU cc_start: 0.6520 (mm-30) cc_final: 0.5694 (tm-30) outliers start: 10 outliers final: 5 residues processed: 102 average time/residue: 0.0815 time to fit residues: 12.6538 Evaluate side-chains 93 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 63 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 95 optimal weight: 0.0270 chunk 118 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.106560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.085395 restraints weight = 27836.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.087796 restraints weight = 15951.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.089381 restraints weight = 11096.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.090277 restraints weight = 8759.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.090987 restraints weight = 7601.373| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11045 Z= 0.122 Angle : 0.550 9.015 14927 Z= 0.287 Chirality : 0.040 0.166 1685 Planarity : 0.004 0.044 1936 Dihedral : 4.813 22.043 1513 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.97 % Allowed : 14.17 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.22), residues: 1389 helix: -0.61 (0.19), residues: 741 sheet: -1.17 (0.59), residues: 83 loop : -2.34 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 291 TYR 0.020 0.001 TYR A 169 PHE 0.026 0.001 PHE E 62 TRP 0.018 0.001 TRP B 212 HIS 0.020 0.002 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00278 (11041) covalent geometry : angle 0.54771 (14921) hydrogen bonds : bond 0.04038 ( 450) hydrogen bonds : angle 4.87838 ( 1305) metal coordination : bond 0.00292 ( 4) metal coordination : angle 2.77185 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 313 TYR cc_start: 0.6844 (t80) cc_final: 0.6625 (t80) REVERT: C 19 TRP cc_start: 0.8728 (t-100) cc_final: 0.8164 (t60) REVERT: C 79 CYS cc_start: 0.8431 (t) cc_final: 0.8176 (t) REVERT: D 215 ILE cc_start: 0.8126 (pt) cc_final: 0.7922 (pt) REVERT: E 29 MET cc_start: 0.7541 (tmm) cc_final: 0.6920 (tmm) REVERT: E 62 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7366 (m-80) REVERT: E 86 GLU cc_start: 0.6647 (mm-30) cc_final: 0.6292 (tp30) outliers start: 11 outliers final: 3 residues processed: 105 average time/residue: 0.0780 time to fit residues: 12.6594 Evaluate side-chains 90 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain E residue 62 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 107 optimal weight: 0.1980 chunk 81 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN D 155 ASN ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 GLN E 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.105205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.084154 restraints weight = 27447.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.086461 restraints weight = 15785.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.088005 restraints weight = 11049.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.088988 restraints weight = 8762.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.089551 restraints weight = 7539.598| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11045 Z= 0.169 Angle : 0.580 8.560 14927 Z= 0.298 Chirality : 0.042 0.223 1685 Planarity : 0.004 0.041 1936 Dihedral : 4.755 21.655 1513 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.59 % Allowed : 15.50 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.22), residues: 1389 helix: -0.45 (0.19), residues: 741 sheet: -1.06 (0.58), residues: 83 loop : -2.31 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 296 TYR 0.022 0.002 TYR A 169 PHE 0.030 0.001 PHE E 62 TRP 0.009 0.001 TRP B 212 HIS 0.004 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00402 (11041) covalent geometry : angle 0.57633 (14921) hydrogen bonds : bond 0.03968 ( 450) hydrogen bonds : angle 4.81427 ( 1305) metal coordination : bond 0.00803 ( 4) metal coordination : angle 3.28114 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 291 ARG cc_start: 0.6629 (mtm180) cc_final: 0.5710 (mtm180) REVERT: A 341 MET cc_start: 0.6440 (ppp) cc_final: 0.5672 (ppp) REVERT: B 319 MET cc_start: 0.8684 (tpp) cc_final: 0.8446 (tpp) REVERT: C 19 TRP cc_start: 0.8803 (t-100) cc_final: 0.8234 (t60) REVERT: D 155 ASN cc_start: 0.7370 (OUTLIER) cc_final: 0.7033 (m-40) REVERT: E 29 MET cc_start: 0.7675 (tmm) cc_final: 0.7025 (tmm) REVERT: E 62 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7282 (m-80) REVERT: E 86 GLU cc_start: 0.6707 (mm-30) cc_final: 0.5792 (tm-30) outliers start: 18 outliers final: 10 residues processed: 104 average time/residue: 0.0898 time to fit residues: 13.7680 Evaluate side-chains 96 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain E residue 63 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 78 optimal weight: 0.3980 chunk 117 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 18 optimal weight: 0.0670 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN ** D 218 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 = 0.3820 r_free = 0.3820 target = 0.107610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.086537 restraints weight = 27222.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.089001 restraints weight = 15311.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.090602 restraints weight = 10547.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.091638 restraints weight = 8274.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.092306 restraints weight = 7072.580| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11045 Z= 0.110 Angle : 0.533 8.045 14927 Z= 0.273 Chirality : 0.040 0.160 1685 Planarity : 0.003 0.039 1936 Dihedral : 4.457 20.628 1513 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.42 % Allowed : 16.74 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.22), residues: 1389 helix: -0.26 (0.19), residues: 749 sheet: -1.00 (0.58), residues: 81 loop : -2.22 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 291 TYR 0.042 0.001 TYR A 313 PHE 0.029 0.001 PHE E 62 TRP 0.012 0.001 TRP B 212 HIS 0.004 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00249 (11041) covalent geometry : angle 0.53024 (14921) hydrogen bonds : bond 0.03642 ( 450) hydrogen bonds : angle 4.55677 ( 1305) metal coordination : bond 0.00194 ( 4) metal coordination : angle 2.92399 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.431 Fit side-chains REVERT: A 149 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8753 (t0) REVERT: A 179 MET cc_start: 0.8197 (mmm) cc_final: 0.7953 (tpp) REVERT: A 214 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6842 (pp30) REVERT: A 291 ARG cc_start: 0.6617 (mtm180) cc_final: 0.5721 (mtm180) REVERT: A 341 MET cc_start: 0.6402 (ppp) cc_final: 0.5638 (ppp) REVERT: B 182 LEU cc_start: 0.7929 (mm) cc_final: 0.7188 (tt) REVERT: C 19 TRP cc_start: 0.8783 (t-100) cc_final: 0.8326 (t60) REVERT: C 35 GLU cc_start: 0.6331 (tt0) cc_final: 0.6056 (tt0) REVERT: E 29 MET cc_start: 0.7585 (tmm) cc_final: 0.6942 (tmm) REVERT: E 62 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7387 (m-80) REVERT: E 86 GLU cc_start: 0.6538 (mm-30) cc_final: 0.6230 (tp30) outliers start: 16 outliers final: 6 residues processed: 110 average time/residue: 0.0949 time to fit residues: 15.4105 Evaluate side-chains 94 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain E residue 62 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 107 optimal weight: 0.0980 chunk 41 optimal weight: 0.8980 chunk 127 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN B 221 GLN ** D 218 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 = 0.3815 r_free = 0.3815 target = 0.107416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.086444 restraints weight = 27593.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.088722 restraints weight = 16298.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.090235 restraints weight = 11570.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.091216 restraints weight = 9249.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.091764 restraints weight = 7989.719| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11045 Z= 0.118 Angle : 0.534 7.240 14927 Z= 0.273 Chirality : 0.040 0.149 1685 Planarity : 0.003 0.038 1936 Dihedral : 4.347 20.046 1513 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.77 % Allowed : 16.83 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.23), residues: 1389 helix: -0.04 (0.19), residues: 748 sheet: -0.86 (0.59), residues: 81 loop : -2.07 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 296 TYR 0.018 0.001 TYR A 313 PHE 0.029 0.001 PHE E 62 TRP 0.013 0.001 TRP A 119 HIS 0.004 0.001 HIS B 281 Details of bonding type rmsd covalent geometry : bond 0.00279 (11041) covalent geometry : angle 0.53159 (14921) hydrogen bonds : bond 0.03509 ( 450) hydrogen bonds : angle 4.47274 ( 1305) metal coordination : bond 0.00383 ( 4) metal coordination : angle 2.75664 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.414 Fit side-chains REVERT: A 149 ASN cc_start: 0.9326 (OUTLIER) cc_final: 0.8967 (t0) REVERT: A 214 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6908 (pp30) REVERT: A 291 ARG cc_start: 0.6536 (mtm180) cc_final: 0.5597 (mtm180) REVERT: A 313 TYR cc_start: 0.6887 (t80) cc_final: 0.6393 (t80) REVERT: A 341 MET cc_start: 0.6492 (ppp) cc_final: 0.5718 (ppp) REVERT: B 182 LEU cc_start: 0.7900 (mm) cc_final: 0.7169 (tt) REVERT: C 35 GLU cc_start: 0.6280 (tt0) cc_final: 0.6058 (tt0) REVERT: E 29 MET cc_start: 0.7676 (tmm) cc_final: 0.7038 (tmm) REVERT: E 62 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7389 (m-80) REVERT: E 86 GLU cc_start: 0.6586 (mm-30) cc_final: 0.6234 (tp30) outliers start: 20 outliers final: 11 residues processed: 108 average time/residue: 0.0804 time to fit residues: 13.5484 Evaluate side-chains 101 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain E residue 62 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 90 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN C 124 ASN ** D 218 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 = 0.3813 r_free = 0.3813 target = 0.107376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.086314 restraints weight = 28179.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.088577 restraints weight = 16640.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.090088 restraints weight = 11844.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.091019 restraints weight = 9480.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.091665 restraints weight = 8243.855| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11045 Z= 0.115 Angle : 0.528 7.360 14927 Z= 0.273 Chirality : 0.040 0.230 1685 Planarity : 0.003 0.038 1936 Dihedral : 4.262 19.695 1513 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.51 % Allowed : 17.63 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.23), residues: 1389 helix: 0.16 (0.20), residues: 741 sheet: -0.64 (0.59), residues: 83 loop : -1.92 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 296 TYR 0.016 0.001 TYR A 313 PHE 0.029 0.001 PHE E 62 TRP 0.009 0.001 TRP A 119 HIS 0.004 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00269 (11041) covalent geometry : angle 0.52528 (14921) hydrogen bonds : bond 0.03455 ( 450) hydrogen bonds : angle 4.37484 ( 1305) metal coordination : bond 0.00443 ( 4) metal coordination : angle 2.81505 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.425 Fit side-chains REVERT: A 149 ASN cc_start: 0.9234 (OUTLIER) cc_final: 0.8785 (t0) REVERT: A 214 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6985 (pp30) REVERT: A 313 TYR cc_start: 0.6890 (t80) cc_final: 0.6386 (t80) REVERT: A 341 MET cc_start: 0.6387 (ppp) cc_final: 0.5634 (ppp) REVERT: B 182 LEU cc_start: 0.7846 (mm) cc_final: 0.7121 (tt) REVERT: B 319 MET cc_start: 0.8634 (tpp) cc_final: 0.8143 (tpp) REVERT: C 35 GLU cc_start: 0.6236 (tt0) cc_final: 0.6008 (tt0) REVERT: E 29 MET cc_start: 0.7692 (tmm) cc_final: 0.7118 (tmm) REVERT: E 62 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7388 (m-80) REVERT: E 86 GLU cc_start: 0.6574 (mm-30) cc_final: 0.6248 (tp30) outliers start: 17 outliers final: 12 residues processed: 103 average time/residue: 0.0779 time to fit residues: 12.5043 Evaluate side-chains 100 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain E residue 62 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 86 optimal weight: 0.0170 overall best weight: 1.1420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN C 124 ASN ** D 218 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 = 0.3810 r_free = 0.3810 target = 0.107183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.086422 restraints weight = 28202.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.088498 restraints weight = 17228.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.089920 restraints weight = 12575.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.090770 restraints weight = 10196.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.091207 restraints weight = 8953.766| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11045 Z= 0.140 Angle : 0.560 8.949 14927 Z= 0.288 Chirality : 0.041 0.191 1685 Planarity : 0.004 0.050 1936 Dihedral : 4.289 19.672 1513 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.59 % Allowed : 17.89 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.23), residues: 1389 helix: 0.19 (0.20), residues: 736 sheet: -0.58 (0.60), residues: 83 loop : -1.90 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 291 TYR 0.015 0.001 TYR A 313 PHE 0.029 0.001 PHE E 62 TRP 0.007 0.001 TRP A 119 HIS 0.005 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00333 (11041) covalent geometry : angle 0.55687 (14921) hydrogen bonds : bond 0.03509 ( 450) hydrogen bonds : angle 4.40660 ( 1305) metal coordination : bond 0.00587 ( 4) metal coordination : angle 2.87540 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 149 ASN cc_start: 0.9348 (OUTLIER) cc_final: 0.8929 (t0) REVERT: A 214 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.6992 (pp30) REVERT: A 313 TYR cc_start: 0.6954 (t80) cc_final: 0.6544 (t80) REVERT: A 341 MET cc_start: 0.6358 (ppp) cc_final: 0.5617 (ppp) REVERT: C 35 GLU cc_start: 0.6291 (tt0) cc_final: 0.6049 (tt0) REVERT: E 29 MET cc_start: 0.7708 (tmm) cc_final: 0.7063 (tmm) REVERT: E 62 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7282 (m-80) REVERT: E 86 GLU cc_start: 0.6574 (mm-30) cc_final: 0.6245 (tp30) outliers start: 18 outliers final: 13 residues processed: 100 average time/residue: 0.0787 time to fit residues: 12.2709 Evaluate side-chains 101 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain E residue 62 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 134 optimal weight: 40.0000 chunk 23 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN C 124 ASN ** D 218 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 = 0.3821 r_free = 0.3821 target = 0.107706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.086520 restraints weight = 27497.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.088904 restraints weight = 15745.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.090464 restraints weight = 10982.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.091487 restraints weight = 8712.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.092069 restraints weight = 7485.041| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11045 Z= 0.117 Angle : 0.535 7.469 14927 Z= 0.277 Chirality : 0.041 0.216 1685 Planarity : 0.003 0.041 1936 Dihedral : 4.208 19.392 1513 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.51 % Allowed : 17.63 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.23), residues: 1389 helix: 0.29 (0.20), residues: 741 sheet: -0.59 (0.58), residues: 88 loop : -1.89 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 291 TYR 0.015 0.001 TYR A 169 PHE 0.028 0.001 PHE E 62 TRP 0.026 0.001 TRP B 308 HIS 0.004 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00274 (11041) covalent geometry : angle 0.53232 (14921) hydrogen bonds : bond 0.03442 ( 450) hydrogen bonds : angle 4.33529 ( 1305) metal coordination : bond 0.00355 ( 4) metal coordination : angle 2.69926 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.309 Fit side-chains REVERT: A 149 ASN cc_start: 0.9248 (OUTLIER) cc_final: 0.8803 (t0) REVERT: A 214 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.6973 (pp30) REVERT: A 313 TYR cc_start: 0.6944 (t80) cc_final: 0.6545 (t80) REVERT: A 341 MET cc_start: 0.6312 (ppp) cc_final: 0.5587 (ppp) REVERT: A 440 TYR cc_start: 0.6929 (t80) cc_final: 0.6610 (t80) REVERT: B 319 MET cc_start: 0.8637 (tpp) cc_final: 0.8259 (tpp) REVERT: C 35 GLU cc_start: 0.6409 (tt0) cc_final: 0.6171 (tt0) REVERT: E 29 MET cc_start: 0.7688 (tmm) cc_final: 0.7119 (tmm) REVERT: E 62 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7231 (m-80) REVERT: E 86 GLU cc_start: 0.6581 (mm-30) cc_final: 0.6260 (tp30) outliers start: 17 outliers final: 12 residues processed: 104 average time/residue: 0.0839 time to fit residues: 13.4159 Evaluate side-chains 104 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain E residue 62 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 58 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN C 124 ASN ** D 218 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 = 0.3756 r_free = 0.3756 target = 0.103845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.082686 restraints weight = 28701.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.084691 restraints weight = 17999.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.086043 restraints weight = 13275.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.086803 restraints weight = 10880.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.087451 restraints weight = 9608.116| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11045 Z= 0.262 Angle : 0.671 7.050 14927 Z= 0.345 Chirality : 0.046 0.258 1685 Planarity : 0.004 0.043 1936 Dihedral : 4.688 20.904 1513 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.33 % Allowed : 18.25 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.23), residues: 1389 helix: -0.01 (0.19), residues: 746 sheet: -0.70 (0.59), residues: 86 loop : -2.00 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 291 TYR 0.023 0.002 TYR A 433 PHE 0.031 0.002 PHE E 62 TRP 0.039 0.002 TRP B 308 HIS 0.007 0.002 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00623 (11041) covalent geometry : angle 0.66699 (14921) hydrogen bonds : bond 0.03954 ( 450) hydrogen bonds : angle 4.69901 ( 1305) metal coordination : bond 0.01388 ( 4) metal coordination : angle 3.88227 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1717.15 seconds wall clock time: 30 minutes 24.77 seconds (1824.77 seconds total)