Starting phenix.real_space_refine on Tue Jul 29 01:14:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ovb_13083/07_2025/7ovb_13083.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ovb_13083/07_2025/7ovb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ovb_13083/07_2025/7ovb_13083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ovb_13083/07_2025/7ovb_13083.map" model { file = "/net/cci-nas-00/data/ceres_data/7ovb_13083/07_2025/7ovb_13083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ovb_13083/07_2025/7ovb_13083.cif" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, '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: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2} 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: 6.78, per 1000 atoms: 0.62 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: 2.94 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.41 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: 3.09 Time building geometry restraints manager: 3.41 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.070 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: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.590 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.230 ------------------------------------------------------------------------------- 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 : 22.05 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.045 0.004 TRP C 19 HIS 0.006 0.002 HIS A 128 PHE 0.055 0.004 PHE E 62 TYR 0.030 0.004 TYR A 433 ARG 0.011 0.001 ARG B 296 Details of bonding type rmsd hydrogen bonds : bond 0.27848 ( 450) hydrogen bonds : angle 10.96097 ( 1305) metal coordination : bond 0.03318 ( 4) metal coordination : angle 7.63022 ( 6) covalent geometry : bond 0.01301 (11041) covalent geometry : angle 1.12884 (14921) *********************** 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 : 4.000 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: 0.2684 time to fit residues: 40.6044 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 : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN D 54 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.104521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.084020 restraints weight = 27665.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.086072 restraints weight = 17179.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.087445 restraints weight = 12544.896| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11045 Z= 0.162 Angle : 0.685 13.745 14927 Z= 0.358 Chirality : 0.043 0.176 1685 Planarity : 0.005 0.054 1936 Dihedral : 5.727 24.148 1513 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.21), residues: 1389 helix: -1.45 (0.18), residues: 741 sheet: -1.87 (0.57), residues: 72 loop : -2.64 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 317 HIS 0.015 0.002 HIS D 180 PHE 0.039 0.002 PHE E 62 TYR 0.024 0.002 TYR A 313 ARG 0.005 0.001 ARG B 296 Details of bonding type rmsd hydrogen bonds : bond 0.05715 ( 450) hydrogen bonds : angle 5.93756 ( 1305) metal coordination : bond 0.00746 ( 4) metal coordination : angle 3.32809 ( 6) covalent geometry : bond 0.00365 (11041) covalent geometry : angle 0.68166 (14921) *********************** 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 105 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 1.257 Fit side-chains REVERT: A 258 MET cc_start: 0.7923 (tpt) cc_final: 0.7570 (tmm) REVERT: B 248 ASP cc_start: 0.6715 (m-30) cc_final: 0.6471 (m-30) REVERT: B 375 MET cc_start: 0.8429 (tpt) cc_final: 0.7977 (tpp) REVERT: C 79 CYS cc_start: 0.8383 (t) cc_final: 0.8120 (t) REVERT: C 208 ASP cc_start: 0.5582 (t0) cc_final: 0.5327 (p0) REVERT: E 53 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7533 (mt) REVERT: E 95 HIS cc_start: 0.8081 (m90) cc_final: 0.7777 (m90) outliers start: 2 outliers final: 0 residues processed: 105 average time/residue: 0.2345 time to fit residues: 38.2283 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 : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 53 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 27 optimal weight: 0.0980 chunk 87 optimal weight: 0.9980 chunk 132 optimal weight: 30.0000 chunk 56 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** A 269 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.106477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.085958 restraints weight = 27771.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.088064 restraints weight = 16942.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.089468 restraints weight = 12255.969| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2335 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= 0.129 Angle : 0.573 9.113 14927 Z= 0.298 Chirality : 0.041 0.149 1685 Planarity : 0.004 0.051 1936 Dihedral : 4.961 22.393 1513 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.71 % Allowed : 11.69 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.22), residues: 1389 helix: -0.82 (0.19), residues: 743 sheet: -1.45 (0.57), residues: 83 loop : -2.46 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 119 HIS 0.019 0.002 HIS D 180 PHE 0.033 0.001 PHE E 62 TYR 0.038 0.002 TYR A 313 ARG 0.006 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.04315 ( 450) hydrogen bonds : angle 5.06191 ( 1305) metal coordination : bond 0.00463 ( 4) metal coordination : angle 2.87669 ( 6) covalent geometry : bond 0.00296 (11041) covalent geometry : angle 0.56980 (14921) *********************** 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 111 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 2.246 Fit side-chains revert: symmetry clash REVERT: C 79 CYS cc_start: 0.8408 (t) cc_final: 0.8125 (t) REVERT: D 215 ILE cc_start: 0.8099 (pt) cc_final: 0.7878 (pt) REVERT: E 12 LEU cc_start: 0.8352 (tp) cc_final: 0.8116 (tp) REVERT: E 29 MET cc_start: 0.7476 (tmm) cc_final: 0.6930 (tmm) REVERT: E 86 GLU cc_start: 0.6341 (mm-30) cc_final: 0.5955 (tp30) outliers start: 8 outliers final: 2 residues processed: 110 average time/residue: 0.2777 time to fit residues: 47.0134 Evaluate side-chains 91 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 327 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 58 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 ASN B 221 GLN 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** E 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.104225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.083252 restraints weight = 28328.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.085298 restraints weight = 17771.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.086584 restraints weight = 13061.086| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11045 Z= 0.215 Angle : 0.632 9.238 14927 Z= 0.324 Chirality : 0.044 0.318 1685 Planarity : 0.004 0.042 1936 Dihedral : 5.026 22.449 1513 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.42 % Allowed : 14.08 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.22), residues: 1389 helix: -0.66 (0.19), residues: 741 sheet: -1.22 (0.58), residues: 83 loop : -2.45 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 212 HIS 0.005 0.001 HIS A 128 PHE 0.030 0.002 PHE E 62 TYR 0.020 0.002 TYR A 159 ARG 0.006 0.001 ARG B 296 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 450) hydrogen bonds : angle 5.04407 ( 1305) metal coordination : bond 0.01108 ( 4) metal coordination : angle 3.81576 ( 6) covalent geometry : bond 0.00512 (11041) covalent geometry : angle 0.62766 (14921) *********************** 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 107 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 1.335 Fit side-chains REVERT: A 240 TRP cc_start: 0.4877 (m-10) cc_final: 0.3542 (p90) REVERT: A 313 TYR cc_start: 0.6841 (t80) cc_final: 0.6588 (t80) REVERT: A 341 MET cc_start: 0.6419 (ppp) cc_final: 0.5688 (ppp) REVERT: C 79 CYS cc_start: 0.8389 (t) cc_final: 0.8151 (t) REVERT: D 215 ILE cc_start: 0.8204 (pt) cc_final: 0.8000 (pt) REVERT: E 29 MET cc_start: 0.7659 (tmm) cc_final: 0.7023 (tmm) REVERT: E 62 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: E 86 GLU cc_start: 0.6696 (mm-30) cc_final: 0.5772 (tm-30) outliers start: 16 outliers final: 9 residues processed: 101 average time/residue: 0.2108 time to fit residues: 32.4490 Evaluate side-chains 97 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER 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 221 GLN Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain E residue 63 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 118 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 131 optimal weight: 0.0870 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.106796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.085827 restraints weight = 27079.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.088143 restraints weight = 15496.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.089702 restraints weight = 10834.685| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2699 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= 0.117 Angle : 0.539 8.360 14927 Z= 0.278 Chirality : 0.040 0.196 1685 Planarity : 0.004 0.040 1936 Dihedral : 4.611 21.374 1513 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.24 % Allowed : 15.68 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.23), residues: 1389 helix: -0.35 (0.19), residues: 737 sheet: -1.08 (0.59), residues: 83 loop : -2.25 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 212 HIS 0.005 0.001 HIS B 281 PHE 0.030 0.001 PHE E 62 TYR 0.012 0.001 TYR A 313 ARG 0.006 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 450) hydrogen bonds : angle 4.66256 ( 1305) metal coordination : bond 0.00303 ( 4) metal coordination : angle 2.72662 ( 6) covalent geometry : bond 0.00273 (11041) covalent geometry : angle 0.53644 (14921) *********************** 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 112 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 1.562 Fit side-chains REVERT: A 149 ASN cc_start: 0.9303 (OUTLIER) cc_final: 0.8936 (t0) REVERT: A 291 ARG cc_start: 0.6711 (mtm180) cc_final: 0.5746 (mtm180) REVERT: A 341 MET cc_start: 0.6486 (ppp) cc_final: 0.5746 (ppp) REVERT: C 19 TRP cc_start: 0.8768 (t-100) cc_final: 0.8260 (t60) REVERT: C 35 GLU cc_start: 0.6463 (tt0) cc_final: 0.6229 (tt0) REVERT: C 79 CYS cc_start: 0.8393 (t) cc_final: 0.8015 (t) REVERT: E 29 MET cc_start: 0.7642 (tmm) cc_final: 0.6962 (tmm) REVERT: E 62 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7430 (m-80) REVERT: E 86 GLU cc_start: 0.6687 (mm-30) cc_final: 0.6267 (tp30) outliers start: 14 outliers final: 5 residues processed: 109 average time/residue: 0.2543 time to fit residues: 43.5856 Evaluate side-chains 97 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN 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 D residue 195 LEU Chi-restraints excluded: chain E residue 62 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 130 optimal weight: 30.0000 chunk 89 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 134 optimal weight: 40.0000 chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.103193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.082200 restraints weight = 28698.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.084209 restraints weight = 17968.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.085578 restraints weight = 13224.471| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11045 Z= 0.258 Angle : 0.659 8.188 14927 Z= 0.337 Chirality : 0.045 0.189 1685 Planarity : 0.004 0.038 1936 Dihedral : 4.969 21.966 1513 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.95 % Allowed : 17.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.22), residues: 1389 helix: -0.44 (0.19), residues: 740 sheet: -1.05 (0.58), residues: 83 loop : -2.33 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 212 HIS 0.005 0.001 HIS A 128 PHE 0.032 0.002 PHE E 62 TYR 0.048 0.002 TYR A 313 ARG 0.005 0.001 ARG B 296 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 450) hydrogen bonds : angle 4.94607 ( 1305) metal coordination : bond 0.01361 ( 4) metal coordination : angle 4.03253 ( 6) covalent geometry : bond 0.00609 (11041) covalent geometry : angle 0.65381 (14921) *********************** 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 114 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 2.054 Fit side-chains revert: symmetry clash REVERT: A 149 ASN cc_start: 0.9497 (OUTLIER) cc_final: 0.9111 (t160) REVERT: A 214 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.6887 (pp30) REVERT: A 240 TRP cc_start: 0.4550 (m-10) cc_final: 0.3654 (p90) REVERT: A 341 MET cc_start: 0.6428 (ppp) cc_final: 0.5715 (ppp) REVERT: C 19 TRP cc_start: 0.8817 (t-100) cc_final: 0.8242 (t60) REVERT: C 79 CYS cc_start: 0.8361 (t) cc_final: 0.8133 (t) REVERT: E 29 MET cc_start: 0.7782 (tmm) cc_final: 0.7107 (tmm) REVERT: E 62 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: E 86 GLU cc_start: 0.6601 (mm-30) cc_final: 0.5717 (tm-30) outliers start: 22 outliers final: 15 residues processed: 106 average time/residue: 0.3067 time to fit residues: 48.8503 Evaluate side-chains 105 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER 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 211 TYR 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 112 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 53 ILE 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 62 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 52 optimal weight: 0.0270 chunk 21 optimal weight: 0.2980 chunk 119 optimal weight: 0.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.107062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.085636 restraints weight = 28137.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.088026 restraints weight = 16281.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.089565 restraints weight = 11405.930| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11045 Z= 0.113 Angle : 0.549 7.836 14927 Z= 0.281 Chirality : 0.040 0.175 1685 Planarity : 0.003 0.038 1936 Dihedral : 4.537 20.949 1513 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.23), residues: 1389 helix: -0.15 (0.20), residues: 739 sheet: -0.96 (0.59), residues: 83 loop : -2.05 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 212 HIS 0.004 0.001 HIS A 559 PHE 0.028 0.001 PHE E 62 TYR 0.018 0.001 TYR A 313 ARG 0.008 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 450) hydrogen bonds : angle 4.53760 ( 1305) metal coordination : bond 0.00232 ( 4) metal coordination : angle 2.69318 ( 6) covalent geometry : bond 0.00262 (11041) covalent geometry : angle 0.54680 (14921) *********************** 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 114 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 1.687 Fit side-chains revert: symmetry clash REVERT: A 125 MET cc_start: 0.6673 (tpt) cc_final: 0.6374 (tpt) REVERT: A 149 ASN cc_start: 0.9261 (OUTLIER) cc_final: 0.8915 (t0) REVERT: A 179 MET cc_start: 0.8239 (mmm) cc_final: 0.7943 (tpp) REVERT: A 214 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6774 (pp30) REVERT: A 313 TYR cc_start: 0.6827 (t80) cc_final: 0.6385 (t80) REVERT: A 341 MET cc_start: 0.6378 (ppp) cc_final: 0.5680 (ppp) REVERT: B 182 LEU cc_start: 0.7994 (mm) cc_final: 0.7175 (tt) REVERT: C 19 TRP cc_start: 0.8779 (t-100) cc_final: 0.8393 (t60) REVERT: C 35 GLU cc_start: 0.6487 (tt0) cc_final: 0.6217 (tt0) REVERT: C 79 CYS cc_start: 0.8400 (t) cc_final: 0.8125 (t) REVERT: E 62 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: E 86 GLU cc_start: 0.6512 (mm-30) cc_final: 0.6186 (tp30) outliers start: 15 outliers final: 11 residues processed: 111 average time/residue: 0.3918 time to fit residues: 65.2582 Evaluate side-chains 105 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 1.741 ------------------------------------------------------------------------------- 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 211 TYR Chi-restraints excluded: chain B residue 287 VAL 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 32 ARG 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 129 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN B 221 GLN ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3785 r_free = 0.3785 target = 0.105707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.084974 restraints weight = 28255.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.087028 restraints weight = 17294.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.088418 restraints weight = 12619.891| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11045 Z= 0.147 Angle : 0.561 8.404 14927 Z= 0.286 Chirality : 0.041 0.150 1685 Planarity : 0.003 0.038 1936 Dihedral : 4.493 20.925 1513 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.86 % Allowed : 18.07 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.23), residues: 1389 helix: -0.04 (0.20), residues: 739 sheet: -0.83 (0.60), residues: 83 loop : -2.03 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 119 HIS 0.004 0.001 HIS B 281 PHE 0.030 0.001 PHE E 62 TYR 0.018 0.001 TYR A 313 ARG 0.006 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 450) hydrogen bonds : angle 4.54195 ( 1305) metal coordination : bond 0.00581 ( 4) metal coordination : angle 3.03929 ( 6) covalent geometry : bond 0.00351 (11041) covalent geometry : angle 0.55806 (14921) *********************** 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 112 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 2.215 Fit side-chains revert: symmetry clash REVERT: A 125 MET cc_start: 0.6743 (tpt) cc_final: 0.6479 (tpt) REVERT: A 149 ASN cc_start: 0.9309 (OUTLIER) cc_final: 0.8906 (t0) REVERT: A 179 MET cc_start: 0.8369 (mmm) cc_final: 0.8108 (tpp) REVERT: A 214 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.6857 (pp30) REVERT: A 313 TYR cc_start: 0.6927 (t80) cc_final: 0.6469 (t80) REVERT: A 341 MET cc_start: 0.6353 (ppp) cc_final: 0.5670 (ppp) REVERT: B 182 LEU cc_start: 0.8053 (mm) cc_final: 0.7196 (tt) REVERT: C 19 TRP cc_start: 0.8834 (t-100) cc_final: 0.8368 (t60) REVERT: C 35 GLU cc_start: 0.6630 (tt0) cc_final: 0.6330 (tt0) REVERT: C 79 CYS cc_start: 0.8439 (t) cc_final: 0.8129 (t) REVERT: E 29 MET cc_start: 0.7620 (tmm) cc_final: 0.6949 (tmm) REVERT: E 62 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7272 (m-80) REVERT: E 86 GLU cc_start: 0.6562 (mm-30) cc_final: 0.6237 (tp30) outliers start: 21 outliers final: 14 residues processed: 106 average time/residue: 0.2308 time to fit residues: 37.5382 Evaluate side-chains 105 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER 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 211 TYR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain E residue 32 ARG 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 137 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 49 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 80 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN D 155 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 = 0.3820 r_free = 0.3820 target = 0.107831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.086981 restraints weight = 27634.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.089252 restraints weight = 16271.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.090780 restraints weight = 11507.676| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 11045 Z= 0.107 Angle : 0.538 8.064 14927 Z= 0.274 Chirality : 0.040 0.153 1685 Planarity : 0.003 0.046 1936 Dihedral : 4.268 20.109 1513 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.42 % Allowed : 18.69 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.23), residues: 1389 helix: 0.17 (0.20), residues: 741 sheet: -0.57 (0.61), residues: 83 loop : -1.94 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 119 HIS 0.004 0.001 HIS A 559 PHE 0.029 0.001 PHE E 62 TYR 0.015 0.001 TYR A 313 ARG 0.009 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 450) hydrogen bonds : angle 4.33335 ( 1305) metal coordination : bond 0.00143 ( 4) metal coordination : angle 2.62354 ( 6) covalent geometry : bond 0.00250 (11041) covalent geometry : angle 0.53577 (14921) *********************** 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 115 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 1.274 Fit side-chains REVERT: A 149 ASN cc_start: 0.9292 (OUTLIER) cc_final: 0.8928 (t0) REVERT: A 214 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.6971 (pp30) REVERT: A 313 TYR cc_start: 0.6902 (t80) cc_final: 0.6481 (t80) REVERT: A 341 MET cc_start: 0.6320 (ppp) cc_final: 0.5568 (ppp) REVERT: B 182 LEU cc_start: 0.7848 (mm) cc_final: 0.7044 (tt) REVERT: B 319 MET cc_start: 0.8682 (tpp) cc_final: 0.8330 (tpp) REVERT: C 19 TRP cc_start: 0.8760 (t-100) cc_final: 0.8548 (t60) REVERT: C 35 GLU cc_start: 0.6247 (tt0) cc_final: 0.6010 (tt0) REVERT: C 69 ASN cc_start: 0.8477 (p0) cc_final: 0.7867 (p0) REVERT: C 79 CYS cc_start: 0.8320 (t) cc_final: 0.8054 (t) REVERT: D 155 ASN cc_start: 0.7337 (OUTLIER) cc_final: 0.7034 (m-40) REVERT: E 29 MET cc_start: 0.7719 (tmm) cc_final: 0.7231 (tmm) REVERT: E 62 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7310 (m-80) REVERT: E 86 GLU cc_start: 0.6584 (mm-30) cc_final: 0.6233 (tp30) outliers start: 16 outliers final: 10 residues processed: 111 average time/residue: 0.2736 time to fit residues: 45.7914 Evaluate side-chains 105 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 3.273 ------------------------------------------------------------------------------- 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 405 MET Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 184 VAL 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 129 optimal weight: 20.0000 chunk 105 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 chunk 78 optimal weight: 0.0870 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 0.0770 chunk 85 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3824 r_free = 0.3824 target = 0.107987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.087137 restraints weight = 27526.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.089416 restraints weight = 16108.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.090885 restraints weight = 11396.298| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11045 Z= 0.112 Angle : 0.545 7.930 14927 Z= 0.281 Chirality : 0.041 0.236 1685 Planarity : 0.003 0.042 1936 Dihedral : 4.193 19.690 1513 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.33 % Allowed : 18.95 % Favored : 79.72 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.23), residues: 1389 helix: 0.29 (0.20), residues: 737 sheet: -0.50 (0.60), residues: 88 loop : -1.82 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 308 HIS 0.004 0.001 HIS A 559 PHE 0.029 0.001 PHE E 62 TYR 0.026 0.001 TYR A 169 ARG 0.012 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 450) hydrogen bonds : angle 4.29874 ( 1305) metal coordination : bond 0.00176 ( 4) metal coordination : angle 2.63448 ( 6) covalent geometry : bond 0.00259 (11041) covalent geometry : angle 0.54241 (14921) ********************** 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 109 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 1.409 Fit side-chains REVERT: A 149 ASN cc_start: 0.9206 (OUTLIER) cc_final: 0.8820 (t0) REVERT: A 214 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6904 (pp30) REVERT: A 313 TYR cc_start: 0.6909 (t80) cc_final: 0.6501 (t80) REVERT: A 341 MET cc_start: 0.6220 (ppp) cc_final: 0.5476 (ppp) REVERT: A 440 TYR cc_start: 0.6905 (t80) cc_final: 0.6663 (t80) REVERT: B 182 LEU cc_start: 0.7892 (mm) cc_final: 0.7059 (tt) REVERT: C 19 TRP cc_start: 0.8802 (t-100) cc_final: 0.8535 (t60) REVERT: C 35 GLU cc_start: 0.6436 (tt0) cc_final: 0.6180 (tt0) REVERT: C 69 ASN cc_start: 0.8488 (p0) cc_final: 0.7854 (p0) REVERT: C 79 CYS cc_start: 0.8387 (t) cc_final: 0.8098 (t) REVERT: E 29 MET cc_start: 0.7658 (tmm) cc_final: 0.7034 (tmm) REVERT: E 62 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7257 (m-80) REVERT: E 86 GLU cc_start: 0.6539 (mm-30) cc_final: 0.6203 (tp30) outliers start: 15 outliers final: 9 residues processed: 105 average time/residue: 0.1976 time to fit residues: 32.0691 Evaluate side-chains 102 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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 316 THR Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain B residue 287 VAL 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 39 optimal weight: 0.0970 chunk 86 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN C 124 ASN ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3769 r_free = 0.3769 target = 0.104713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.083732 restraints weight = 28304.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.085787 restraints weight = 17623.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.087152 restraints weight = 12960.205| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11045 Z= 0.217 Angle : 0.632 7.985 14927 Z= 0.323 Chirality : 0.044 0.278 1685 Planarity : 0.004 0.039 1936 Dihedral : 4.493 20.737 1513 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.06 % Allowed : 19.31 % Favored : 79.63 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.23), residues: 1389 helix: 0.14 (0.19), residues: 741 sheet: -0.63 (0.60), residues: 88 loop : -1.98 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 308 HIS 0.005 0.001 HIS D 51 PHE 0.031 0.002 PHE E 62 TYR 0.032 0.002 TYR A 169 ARG 0.011 0.001 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 450) hydrogen bonds : angle 4.54630 ( 1305) metal coordination : bond 0.01039 ( 4) metal coordination : angle 3.51106 ( 6) covalent geometry : bond 0.00513 (11041) covalent geometry : angle 0.62779 (14921) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4112.69 seconds wall clock time: 79 minutes 34.28 seconds (4774.28 seconds total)