Starting phenix.real_space_refine on Thu Feb 13 16:39:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yj1_33868/02_2025/7yj1_33868.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yj1_33868/02_2025/7yj1_33868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yj1_33868/02_2025/7yj1_33868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yj1_33868/02_2025/7yj1_33868.map" model { file = "/net/cci-nas-00/data/ceres_data/7yj1_33868/02_2025/7yj1_33868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yj1_33868/02_2025/7yj1_33868.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 50 5.16 5 C 5889 2.51 5 N 1545 2.21 5 O 1655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9140 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3962 Classifications: {'peptide': 502} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 483} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1165 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "C" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 411 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "A" Number of atoms: 3285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3285 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.45, per 1000 atoms: 0.60 Number of scatterers: 9140 At special positions: 0 Unit cell: (92.88, 83.16, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 P 1 15.00 O 1655 8.00 N 1545 7.00 C 5889 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.2 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 48.0% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'B' and resid 67 through 95 removed outlier: 3.592A pdb=" N THR B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 76 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TRP B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 removed outlier: 4.029A pdb=" N LYS B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 177 through 181 removed outlier: 4.134A pdb=" N PHE B 181 " --> pdb=" O TYR B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 removed outlier: 3.668A pdb=" N ALA B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.769A pdb=" N GLU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.942A pdb=" N ASN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 243 " --> pdb=" O PHE B 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 238 through 243' Processing helix chain 'B' and resid 245 through 249 Processing helix chain 'B' and resid 263 through 274 removed outlier: 3.832A pdb=" N GLY B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 326 through 337 removed outlier: 3.690A pdb=" N LYS B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.867A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 399 removed outlier: 3.573A pdb=" N TYR B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 408 removed outlier: 3.663A pdb=" N VAL B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 427 removed outlier: 3.622A pdb=" N GLN B 418 " --> pdb=" O PRO B 414 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET B 427 " --> pdb=" O MET B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 455 removed outlier: 3.718A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 489 removed outlier: 3.728A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'E' and resid 11 through 20 removed outlier: 3.949A pdb=" N GLN E 15 " --> pdb=" O VAL E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 38 removed outlier: 3.709A pdb=" N LEU E 25 " --> pdb=" O PRO E 21 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 27 " --> pdb=" O TYR E 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 39 removed outlier: 3.622A pdb=" N ILE D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 66 Processing helix chain 'D' and resid 88 through 93 Processing helix chain 'D' and resid 96 through 116 removed outlier: 3.664A pdb=" N THR D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) Proline residue: D 106 - end of helix removed outlier: 3.512A pdb=" N TYR D 110 " --> pdb=" O PRO D 106 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 134 removed outlier: 3.598A pdb=" N SER D 133 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 143 Proline residue: D 140 - end of helix removed outlier: 3.831A pdb=" N HIS D 143 " --> pdb=" O PRO D 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.537A pdb=" N TRP C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE C 16 " --> pdb=" O GLN C 12 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 55 removed outlier: 3.790A pdb=" N VAL C 36 " --> pdb=" O TRP C 32 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE C 37 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE C 44 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR C 51 " --> pdb=" O MET C 47 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.632A pdb=" N GLU A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TRP A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 129 removed outlier: 4.077A pdb=" N SER A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 157 removed outlier: 3.729A pdb=" N ALA A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.783A pdb=" N ALA A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.712A pdb=" N TYR A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 213 through 230 removed outlier: 3.564A pdb=" N LEU A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 268 removed outlier: 4.064A pdb=" N LYS A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.723A pdb=" N ILE A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.670A pdb=" N ASP A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 330 removed outlier: 3.564A pdb=" N LEU A 330 " --> pdb=" O HIS A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 327 through 330' Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 359 removed outlier: 3.509A pdb=" N GLU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 377 removed outlier: 3.684A pdb=" N VAL A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N HIS A 374 " --> pdb=" O CYS A 370 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 420 removed outlier: 3.956A pdb=" N ASP A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 467 removed outlier: 3.641A pdb=" N LYS A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 48 removed outlier: 3.646A pdb=" N HIS B 47 " --> pdb=" O TYR B 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 62 removed outlier: 3.617A pdb=" N ALA B 62 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.102A pdb=" N VAL B 146 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY B 169 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 148 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASN B 165 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N GLN B 152 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR B 163 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 231 through 234 removed outlier: 6.625A pdb=" N LEU B 341 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N MET B 374 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU B 343 " --> pdb=" O MET B 374 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N THR B 376 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP B 259 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N GLU B 315 " --> pdb=" O ASP B 259 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE B 256 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N PHE B 280 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER B 258 " --> pdb=" O PHE B 280 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 317 through 318 removed outlier: 3.567A pdb=" N SER B 323 " --> pdb=" O TYR B 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 471 through 472 removed outlier: 3.807A pdb=" N ARG B 507 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.359A pdb=" N ALA A 425 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 160 through 164 Processing sheet with id=AA9, first strand: chain 'A' and resid 205 through 209 removed outlier: 6.146A pdb=" N VAL A 185 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N PHE A 209 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL A 187 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 188 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 383 through 386 removed outlier: 3.509A pdb=" N LYS A 384 " --> pdb=" O GLN A 397 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 386 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 948 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2924 1.34 - 1.46: 1484 1.46 - 1.57: 4850 1.57 - 1.69: 1 1.69 - 1.81: 83 Bond restraints: 9342 Sorted by residual: bond pdb=" C2 PLP B 601 " pdb=" C3 PLP B 601 " ideal model delta sigma weight residual 1.390 1.484 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C4 PLP B 601 " pdb=" C5 PLP B 601 " ideal model delta sigma weight residual 1.390 1.483 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C3 PLP B 601 " pdb=" C4 PLP B 601 " ideal model delta sigma weight residual 1.390 1.480 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" CA ASN A 107 " pdb=" CB ASN A 107 " ideal model delta sigma weight residual 1.525 1.555 -0.030 1.47e-02 4.63e+03 4.12e+00 bond pdb=" C ILE D 136 " pdb=" O ILE D 136 " ideal model delta sigma weight residual 1.242 1.226 0.016 8.60e-03 1.35e+04 3.29e+00 ... (remaining 9337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 12154 1.94 - 3.88: 433 3.88 - 5.82: 51 5.82 - 7.76: 7 7.76 - 9.70: 2 Bond angle restraints: 12647 Sorted by residual: angle pdb=" N PRO A 78 " pdb=" CA PRO A 78 " pdb=" CB PRO A 78 " ideal model delta sigma weight residual 103.33 110.23 -6.90 1.10e+00 8.26e-01 3.93e+01 angle pdb=" CA ILE D 136 " pdb=" C ILE D 136 " pdb=" N PRO D 137 " ideal model delta sigma weight residual 120.83 117.08 3.75 6.10e-01 2.69e+00 3.79e+01 angle pdb=" N ILE B 503 " pdb=" CA ILE B 503 " pdb=" C ILE B 503 " ideal model delta sigma weight residual 110.23 116.24 -6.01 1.04e+00 9.25e-01 3.34e+01 angle pdb=" N GLY B 497 " pdb=" CA GLY B 497 " pdb=" C GLY B 497 " ideal model delta sigma weight residual 112.55 119.97 -7.42 1.44e+00 4.82e-01 2.65e+01 angle pdb=" N TYR E 44 " pdb=" CA TYR E 44 " pdb=" C TYR E 44 " ideal model delta sigma weight residual 110.80 120.50 -9.70 2.13e+00 2.20e-01 2.07e+01 ... (remaining 12642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4815 17.95 - 35.89: 522 35.89 - 53.84: 173 53.84 - 71.78: 53 71.78 - 89.73: 16 Dihedral angle restraints: 5579 sinusoidal: 2237 harmonic: 3342 Sorted by residual: dihedral pdb=" CA PRO B 142 " pdb=" C PRO B 142 " pdb=" N GLY B 143 " pdb=" CA GLY B 143 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA TYR B 461 " pdb=" C TYR B 461 " pdb=" N GLY B 462 " pdb=" CA GLY B 462 " ideal model delta harmonic sigma weight residual 180.00 160.21 19.79 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA LEU B 473 " pdb=" C LEU B 473 " pdb=" N TYR B 474 " pdb=" CA TYR B 474 " ideal model delta harmonic sigma weight residual -180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 5576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1106 0.057 - 0.114: 260 0.114 - 0.171: 43 0.171 - 0.228: 1 0.228 - 0.285: 3 Chirality restraints: 1413 Sorted by residual: chirality pdb=" CA TYR E 44 " pdb=" N TYR E 44 " pdb=" C TYR E 44 " pdb=" CB TYR E 44 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA GLU A 400 " pdb=" N GLU A 400 " pdb=" C GLU A 400 " pdb=" CB GLU A 400 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO A 78 " pdb=" N PRO A 78 " pdb=" C PRO A 78 " pdb=" CB PRO A 78 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1410 not shown) Planarity restraints: 1605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 42 " 0.012 2.00e-02 2.50e+03 1.61e-02 4.52e+00 pdb=" CG PHE D 42 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE D 42 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE D 42 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE D 42 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 42 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 42 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 135 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C PRO A 135 " 0.030 2.00e-02 2.50e+03 pdb=" O PRO A 135 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A 136 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 501 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO B 502 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.024 5.00e-02 4.00e+02 ... (remaining 1602 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 2 2.17 - 2.85: 3237 2.85 - 3.53: 11282 3.53 - 4.22: 19969 4.22 - 4.90: 36184 Nonbonded interactions: 70674 Sorted by model distance: nonbonded pdb=" OG SER A 381 " pdb=" OE1 GLN A 469 " model vdw 1.486 3.040 nonbonded pdb=" OH TYR A 128 " pdb=" OD1 ASP A 143 " model vdw 2.143 3.040 nonbonded pdb=" O ARG B 399 " pdb=" OH TYR A 82 " model vdw 2.190 3.040 nonbonded pdb=" OD2 ASP D 76 " pdb=" NH1 ARG A 181 " model vdw 2.214 3.120 nonbonded pdb=" OD1 ASN B 245 " pdb=" OG SER B 402 " model vdw 2.219 3.040 ... (remaining 70669 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=0.80 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.170 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 9342 Z= 0.368 Angle : 0.838 9.697 12647 Z= 0.547 Chirality : 0.051 0.285 1413 Planarity : 0.004 0.043 1605 Dihedral : 18.001 89.730 3441 Min Nonbonded Distance : 1.486 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.43 % Favored : 91.87 % Rotamer: Outliers : 9.53 % Allowed : 5.64 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.24), residues: 1144 helix: -1.36 (0.23), residues: 504 sheet: -1.93 (0.51), residues: 109 loop : -2.61 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.004 0.001 HIS A 327 PHE 0.037 0.002 PHE D 42 TYR 0.025 0.002 TYR B 461 ARG 0.002 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 113 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8797 (mttt) REVERT: B 109 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8048 (mtmm) REVERT: B 136 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8932 (mtt180) REVERT: B 196 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8782 (tp) REVERT: B 197 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7680 (tp30) REVERT: B 288 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8645 (tp) REVERT: B 429 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.7072 (tt0) REVERT: B 471 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8418 (tp) REVERT: B 475 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.7656 (mmt) REVERT: B 505 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7356 (mt-10) REVERT: B 538 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8864 (mttp) REVERT: E 38 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8479 (pt) REVERT: D 118 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8057 (mtpt) REVERT: D 124 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7911 (t80) REVERT: A 58 GLU cc_start: 0.7939 (tp30) cc_final: 0.7275 (tp30) REVERT: A 77 HIS cc_start: 0.5934 (OUTLIER) cc_final: 0.4069 (t-90) REVERT: A 136 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8440 (ttt180) REVERT: A 234 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8238 (tttt) outliers start: 93 outliers final: 49 residues processed: 190 average time/residue: 0.2695 time to fit residues: 66.7170 Evaluate side-chains 165 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 99 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 134 TRP Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 467 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 ASN D 121 GLN A 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.103629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.081607 restraints weight = 13293.473| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.98 r_work: 0.2697 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9342 Z= 0.386 Angle : 0.668 6.699 12647 Z= 0.352 Chirality : 0.047 0.247 1413 Planarity : 0.005 0.044 1605 Dihedral : 12.254 82.443 1439 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.24 % Favored : 94.67 % Rotamer: Outliers : 4.82 % Allowed : 12.81 % Favored : 82.38 % 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: -2.23 (0.24), residues: 1144 helix: -0.58 (0.24), residues: 500 sheet: -1.59 (0.47), residues: 121 loop : -2.35 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 94 HIS 0.007 0.001 HIS B 47 PHE 0.019 0.002 PHE B 449 TYR 0.024 0.002 TYR E 44 ARG 0.003 0.000 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 108 time to evaluate : 1.071 Fit side-chains REVERT: B 46 HIS cc_start: 0.7375 (t-90) cc_final: 0.6505 (t-90) REVERT: B 289 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.8048 (tp30) REVERT: B 292 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8354 (mp) REVERT: B 429 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6978 (tt0) REVERT: B 473 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8950 (pp) REVERT: B 505 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7822 (mt-10) REVERT: A 58 GLU cc_start: 0.8471 (tp30) cc_final: 0.7714 (tp30) REVERT: A 77 HIS cc_start: 0.5611 (OUTLIER) cc_final: 0.3720 (t-90) REVERT: A 234 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8117 (tttt) REVERT: A 406 GLU cc_start: 0.7473 (tt0) cc_final: 0.7175 (tt0) outliers start: 47 outliers final: 28 residues processed: 147 average time/residue: 0.2284 time to fit residues: 46.1299 Evaluate side-chains 138 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 103 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 467 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 73 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 94 optimal weight: 0.2980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.104583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.082631 restraints weight = 13420.381| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.00 r_work: 0.2713 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9342 Z= 0.279 Angle : 0.578 6.257 12647 Z= 0.305 Chirality : 0.045 0.217 1413 Planarity : 0.004 0.050 1605 Dihedral : 9.181 75.917 1334 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.79 % Allowed : 14.96 % Favored : 81.25 % 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: -1.82 (0.25), residues: 1144 helix: -0.13 (0.24), residues: 500 sheet: -1.50 (0.46), residues: 121 loop : -2.22 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 94 HIS 0.006 0.001 HIS B 47 PHE 0.014 0.001 PHE D 101 TYR 0.020 0.002 TYR E 44 ARG 0.002 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 1.178 Fit side-chains REVERT: B 46 HIS cc_start: 0.7315 (t-90) cc_final: 0.6498 (t-90) REVERT: B 109 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8371 (mtmm) REVERT: B 198 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8129 (pp20) REVERT: B 289 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.8109 (tp30) REVERT: B 292 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8496 (mp) REVERT: B 345 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8555 (pt0) REVERT: B 374 MET cc_start: 0.8884 (ttt) cc_final: 0.8649 (ttt) REVERT: B 429 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.7101 (tt0) REVERT: B 530 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: A 58 GLU cc_start: 0.8479 (tp30) cc_final: 0.7716 (tp30) REVERT: A 77 HIS cc_start: 0.5461 (OUTLIER) cc_final: 0.3553 (t-90) outliers start: 37 outliers final: 23 residues processed: 133 average time/residue: 0.2522 time to fit residues: 46.4829 Evaluate side-chains 132 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 467 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 59 optimal weight: 0.0570 chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 108 optimal weight: 0.0570 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.108053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.086144 restraints weight = 13107.844| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.99 r_work: 0.2778 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9342 Z= 0.147 Angle : 0.497 7.631 12647 Z= 0.260 Chirality : 0.042 0.190 1413 Planarity : 0.004 0.047 1605 Dihedral : 7.631 71.694 1315 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.07 % Allowed : 16.70 % Favored : 80.23 % 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: -1.33 (0.25), residues: 1144 helix: 0.30 (0.25), residues: 512 sheet: -1.26 (0.47), residues: 123 loop : -2.03 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 94 HIS 0.004 0.001 HIS B 47 PHE 0.009 0.001 PHE A 317 TYR 0.020 0.001 TYR E 44 ARG 0.002 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 1.056 Fit side-chains REVERT: B 46 HIS cc_start: 0.7234 (t-90) cc_final: 0.6490 (t-90) REVERT: B 198 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8142 (pp20) REVERT: B 289 GLU cc_start: 0.9199 (OUTLIER) cc_final: 0.8096 (tp30) REVERT: B 505 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8126 (mt-10) REVERT: B 530 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: E 36 ILE cc_start: 0.8499 (mm) cc_final: 0.8277 (tp) REVERT: A 58 GLU cc_start: 0.8515 (tp30) cc_final: 0.7799 (tp30) REVERT: A 77 HIS cc_start: 0.5443 (OUTLIER) cc_final: 0.3490 (t-90) REVERT: A 274 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8453 (tm-30) outliers start: 30 outliers final: 18 residues processed: 131 average time/residue: 0.2510 time to fit residues: 44.6985 Evaluate side-chains 123 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 419 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.106259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.084247 restraints weight = 13245.247| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.99 r_work: 0.2735 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9342 Z= 0.227 Angle : 0.533 10.641 12647 Z= 0.276 Chirality : 0.043 0.189 1413 Planarity : 0.004 0.050 1605 Dihedral : 6.618 69.245 1299 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.18 % Allowed : 17.42 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.26), residues: 1144 helix: 0.59 (0.25), residues: 500 sheet: -1.21 (0.46), residues: 125 loop : -1.92 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 94 HIS 0.005 0.001 HIS B 47 PHE 0.013 0.001 PHE D 101 TYR 0.019 0.001 TYR E 44 ARG 0.001 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 1.063 Fit side-chains REVERT: B 46 HIS cc_start: 0.7147 (t-90) cc_final: 0.6336 (t-90) REVERT: B 198 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8087 (pp20) REVERT: B 289 GLU cc_start: 0.9270 (OUTLIER) cc_final: 0.8092 (tp30) REVERT: B 472 MET cc_start: 0.9510 (mmm) cc_final: 0.8859 (mmm) REVERT: B 505 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8115 (mt-10) REVERT: B 530 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: E 36 ILE cc_start: 0.8373 (mm) cc_final: 0.8151 (tp) REVERT: A 58 GLU cc_start: 0.8477 (tp30) cc_final: 0.7749 (tp30) REVERT: A 59 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8232 (mm-30) REVERT: A 77 HIS cc_start: 0.5383 (OUTLIER) cc_final: 0.3474 (t-90) REVERT: A 274 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8385 (tm-30) outliers start: 31 outliers final: 20 residues processed: 130 average time/residue: 0.2523 time to fit residues: 44.4119 Evaluate side-chains 126 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 419 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.105261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.083229 restraints weight = 13187.984| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.99 r_work: 0.2721 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9342 Z= 0.268 Angle : 0.550 8.700 12647 Z= 0.286 Chirality : 0.044 0.186 1413 Planarity : 0.004 0.051 1605 Dihedral : 6.478 66.834 1297 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.69 % Allowed : 17.21 % Favored : 79.10 % 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: -0.95 (0.26), residues: 1144 helix: 0.68 (0.25), residues: 500 sheet: -1.16 (0.47), residues: 125 loop : -1.83 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 94 HIS 0.005 0.001 HIS B 47 PHE 0.014 0.001 PHE D 101 TYR 0.018 0.001 TYR E 44 ARG 0.001 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.849 Fit side-chains REVERT: B 46 HIS cc_start: 0.7190 (t-90) cc_final: 0.6358 (t-90) REVERT: B 198 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8139 (pp20) REVERT: B 289 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.8115 (tp30) REVERT: B 292 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8531 (mp) REVERT: B 472 MET cc_start: 0.9512 (mmm) cc_final: 0.8911 (mmm) REVERT: B 530 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8051 (mt-10) REVERT: E 36 ILE cc_start: 0.8426 (mm) cc_final: 0.8200 (tp) REVERT: A 58 GLU cc_start: 0.8517 (tp30) cc_final: 0.7771 (tp30) REVERT: A 59 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8231 (mm-30) REVERT: A 77 HIS cc_start: 0.5442 (OUTLIER) cc_final: 0.3496 (t-90) REVERT: A 274 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8417 (tm-30) outliers start: 36 outliers final: 25 residues processed: 129 average time/residue: 0.2411 time to fit residues: 42.2997 Evaluate side-chains 129 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 419 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.091954 restraints weight = 13022.304| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.91 r_work: 0.2725 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9342 Z= 0.263 Angle : 0.555 7.981 12647 Z= 0.290 Chirality : 0.044 0.182 1413 Planarity : 0.004 0.051 1605 Dihedral : 6.387 64.571 1297 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.00 % Allowed : 17.21 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.85 (0.26), residues: 1144 helix: 0.78 (0.25), residues: 500 sheet: -1.14 (0.46), residues: 123 loop : -1.79 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 94 HIS 0.005 0.001 HIS B 47 PHE 0.013 0.001 PHE D 101 TYR 0.019 0.001 TYR E 44 ARG 0.002 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 101 time to evaluate : 1.008 Fit side-chains REVERT: B 46 HIS cc_start: 0.7204 (t-90) cc_final: 0.6317 (t-90) REVERT: B 198 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8133 (pp20) REVERT: B 289 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8109 (tp30) REVERT: B 292 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8520 (mp) REVERT: B 418 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.7344 (tt0) REVERT: B 472 MET cc_start: 0.9503 (mmm) cc_final: 0.8928 (mmm) REVERT: B 530 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: E 36 ILE cc_start: 0.8451 (mm) cc_final: 0.8217 (tp) REVERT: D 121 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7156 (mp10) REVERT: A 58 GLU cc_start: 0.8516 (tp30) cc_final: 0.7777 (tp30) REVERT: A 59 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8209 (mm-30) REVERT: A 77 HIS cc_start: 0.5544 (OUTLIER) cc_final: 0.3499 (t-90) REVERT: A 274 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8416 (tm-30) outliers start: 39 outliers final: 27 residues processed: 131 average time/residue: 0.2519 time to fit residues: 44.9802 Evaluate side-chains 132 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 134 TRP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 419 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 37 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.107362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.085413 restraints weight = 13385.977| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.99 r_work: 0.2753 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9342 Z= 0.178 Angle : 0.512 7.365 12647 Z= 0.269 Chirality : 0.043 0.219 1413 Planarity : 0.004 0.049 1605 Dihedral : 6.080 60.190 1297 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.07 % Allowed : 18.14 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.62 (0.26), residues: 1144 helix: 0.93 (0.25), residues: 508 sheet: -0.97 (0.47), residues: 125 loop : -1.67 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 94 HIS 0.004 0.001 HIS B 47 PHE 0.010 0.001 PHE A 209 TYR 0.019 0.001 TYR E 44 ARG 0.002 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.991 Fit side-chains REVERT: B 46 HIS cc_start: 0.7178 (t-90) cc_final: 0.6291 (t-90) REVERT: B 92 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.6371 (ptm160) REVERT: B 198 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8152 (pp20) REVERT: B 472 MET cc_start: 0.9465 (mmm) cc_final: 0.8880 (mmm) REVERT: B 505 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8088 (mt-10) REVERT: B 530 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7999 (mt-10) REVERT: E 36 ILE cc_start: 0.8465 (mm) cc_final: 0.8241 (tp) REVERT: A 58 GLU cc_start: 0.8514 (tp30) cc_final: 0.7813 (tp30) REVERT: A 59 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8215 (mm-30) REVERT: A 77 HIS cc_start: 0.5537 (OUTLIER) cc_final: 0.3478 (t-90) REVERT: A 214 MET cc_start: 0.8799 (mmm) cc_final: 0.8509 (mmp) REVERT: A 274 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8473 (tm-30) outliers start: 30 outliers final: 21 residues processed: 132 average time/residue: 0.2452 time to fit residues: 44.0347 Evaluate side-chains 127 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 HIS E 24 HIS C 38 ASN A 428 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.104675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.082690 restraints weight = 13244.956| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.98 r_work: 0.2707 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9342 Z= 0.297 Angle : 0.566 7.119 12647 Z= 0.295 Chirality : 0.045 0.213 1413 Planarity : 0.004 0.051 1605 Dihedral : 6.066 58.916 1293 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.59 % Allowed : 17.83 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.65 (0.26), residues: 1144 helix: 0.99 (0.25), residues: 495 sheet: -1.05 (0.46), residues: 123 loop : -1.70 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 94 HIS 0.005 0.001 HIS B 47 PHE 0.014 0.001 PHE D 101 TYR 0.022 0.002 TYR E 44 ARG 0.003 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 1.029 Fit side-chains REVERT: B 46 HIS cc_start: 0.7158 (t-90) cc_final: 0.6232 (t-90) REVERT: B 198 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8129 (pp20) REVERT: B 292 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8491 (mp) REVERT: B 418 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.7476 (tt0) REVERT: B 472 MET cc_start: 0.9520 (mmm) cc_final: 0.8961 (mmm) REVERT: B 530 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: E 36 ILE cc_start: 0.8431 (mm) cc_final: 0.8197 (tp) REVERT: A 58 GLU cc_start: 0.8516 (tp30) cc_final: 0.7772 (tp30) REVERT: A 59 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8202 (mm-30) REVERT: A 77 HIS cc_start: 0.5509 (OUTLIER) cc_final: 0.3476 (t-90) REVERT: A 274 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8419 (tm-30) outliers start: 35 outliers final: 25 residues processed: 125 average time/residue: 0.2527 time to fit residues: 42.5839 Evaluate side-chains 128 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 0.8980 chunk 5 optimal weight: 0.0870 chunk 20 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 HIS A 107 ASN A 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.113921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.092639 restraints weight = 13162.942| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.94 r_work: 0.2794 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9342 Z= 0.164 Angle : 0.508 7.665 12647 Z= 0.266 Chirality : 0.043 0.240 1413 Planarity : 0.004 0.048 1605 Dihedral : 5.769 53.781 1293 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.66 % Allowed : 18.95 % Favored : 78.38 % Cbeta Deviations : 0.09 % 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: -0.41 (0.26), residues: 1144 helix: 1.11 (0.25), residues: 510 sheet: -0.91 (0.47), residues: 125 loop : -1.57 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 94 HIS 0.004 0.000 HIS B 47 PHE 0.010 0.001 PHE A 209 TYR 0.019 0.001 TYR E 44 ARG 0.003 0.000 ARG A 236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 1.047 Fit side-chains REVERT: B 46 HIS cc_start: 0.7243 (t-90) cc_final: 0.6396 (t-90) REVERT: B 92 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.6365 (ptm160) REVERT: B 198 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8196 (pp20) REVERT: B 418 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.7233 (tt0) REVERT: B 472 MET cc_start: 0.9371 (mmm) cc_final: 0.8795 (mmm) REVERT: B 505 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8120 (mt-10) REVERT: B 530 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: E 36 ILE cc_start: 0.8579 (mm) cc_final: 0.8334 (tp) REVERT: A 58 GLU cc_start: 0.8531 (tp30) cc_final: 0.7871 (tp30) REVERT: A 77 HIS cc_start: 0.5685 (OUTLIER) cc_final: 0.3521 (t-90) REVERT: A 274 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8366 (tp30) outliers start: 26 outliers final: 17 residues processed: 122 average time/residue: 0.2383 time to fit residues: 40.0485 Evaluate side-chains 121 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 56 optimal weight: 0.0770 chunk 79 optimal weight: 4.9990 chunk 88 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.108102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.086295 restraints weight = 13212.164| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.98 r_work: 0.2768 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9342 Z= 0.162 Angle : 0.507 7.867 12647 Z= 0.265 Chirality : 0.042 0.198 1413 Planarity : 0.004 0.049 1605 Dihedral : 5.002 50.967 1285 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.46 % Allowed : 19.06 % Favored : 78.48 % 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: -0.24 (0.26), residues: 1144 helix: 1.30 (0.25), residues: 508 sheet: -0.89 (0.47), residues: 125 loop : -1.50 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 94 HIS 0.004 0.000 HIS B 47 PHE 0.023 0.001 PHE B 90 TYR 0.018 0.001 TYR E 44 ARG 0.004 0.000 ARG A 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4645.48 seconds wall clock time: 83 minutes 26.50 seconds (5006.50 seconds total)