Starting phenix.real_space_refine on Wed Mar 12 09:24:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cmi_30407/03_2025/7cmi_30407.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cmi_30407/03_2025/7cmi_30407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cmi_30407/03_2025/7cmi_30407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cmi_30407/03_2025/7cmi_30407.map" model { file = "/net/cci-nas-00/data/ceres_data/7cmi_30407/03_2025/7cmi_30407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cmi_30407/03_2025/7cmi_30407.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 2 5.49 5 S 27 5.16 5 C 4814 2.51 5 N 1176 2.21 5 O 1334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7353 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3650 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain: "B" Number of atoms: 3480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3480 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 25, 'TRANS': 432} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 102 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2, 'water': 6} Link IDs: {None: 7} Time building chain proxies: 4.81, per 1000 atoms: 0.65 Number of scatterers: 7353 At special positions: 0 Unit cell: (82.612, 86.96, 125.005, 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 27 16.00 P 2 15.00 O 1334 8.00 N 1176 7.00 C 4814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 154 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 1.0 seconds 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1700 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 3 sheets defined 55.4% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 167 through 175 removed outlier: 4.142A pdb=" N LYS A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.879A pdb=" N THR A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 208 removed outlier: 3.781A pdb=" N LEU A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.521A pdb=" N GLN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 240 removed outlier: 3.599A pdb=" N GLY A 240 " --> pdb=" O HIS A 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 237 through 240' Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 248 through 255 Processing helix chain 'A' and resid 287 through 301 removed outlier: 3.793A pdb=" N SER A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 342 removed outlier: 3.564A pdb=" N ALA A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 372 removed outlier: 4.269A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 391 removed outlier: 3.598A pdb=" N ILE A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 427 removed outlier: 4.013A pdb=" N THR A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 459 removed outlier: 3.506A pdb=" N MET A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 519 through 532 removed outlier: 4.514A pdb=" N GLN A 530 " --> pdb=" O ARG A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'B' and resid 42 through 54 removed outlier: 3.858A pdb=" N GLY B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 70 removed outlier: 3.671A pdb=" N ASN B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 100 removed outlier: 3.629A pdb=" N ALA B 75 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 96 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.634A pdb=" N TYR B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 111 " --> pdb=" O TYR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 129 removed outlier: 3.802A pdb=" N PHE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 147 removed outlier: 3.671A pdb=" N ILE B 138 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 178 removed outlier: 3.636A pdb=" N ARG B 162 " --> pdb=" O GLU B 158 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 186 removed outlier: 3.733A pdb=" N ALA B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 210 removed outlier: 3.545A pdb=" N GLY B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 194 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 207 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 208 " --> pdb=" O MET B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 242 removed outlier: 3.524A pdb=" N ALA B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 removed outlier: 4.099A pdb=" N GLU B 257 " --> pdb=" O VAL B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 289 removed outlier: 3.631A pdb=" N ILE B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE B 270 " --> pdb=" O PRO B 266 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 271 " --> pdb=" O ARG B 267 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 273 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Proline residue: B 274 - end of helix removed outlier: 3.562A pdb=" N TYR B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 288 " --> pdb=" O ASN B 284 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 301 through 309 removed outlier: 3.645A pdb=" N LYS B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 336 removed outlier: 3.701A pdb=" N ILE B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET B 318 " --> pdb=" O MET B 314 " (cutoff:3.500A) Proline residue: B 319 - end of helix removed outlier: 3.535A pdb=" N GLY B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR B 336 " --> pdb=" O GLY B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 removed outlier: 3.532A pdb=" N ARG B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 378 removed outlier: 3.533A pdb=" N PHE B 370 " --> pdb=" O PRO B 366 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 371 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 412 removed outlier: 3.953A pdb=" N ILE B 394 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR B 402 " --> pdb=" O PHE B 398 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 403 " --> pdb=" O TYR B 399 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG B 410 " --> pdb=" O GLN B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 445 removed outlier: 3.798A pdb=" N ILE B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR B 430 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 467 removed outlier: 3.692A pdb=" N ILE B 451 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 453 " --> pdb=" O CYS B 449 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 455 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET B 456 " --> pdb=" O GLY B 452 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 460 " --> pdb=" O MET B 456 " (cutoff:3.500A) Proline residue: B 461 - end of helix removed outlier: 3.729A pdb=" N PHE B 464 " --> pdb=" O VAL B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 491 removed outlier: 3.524A pdb=" N ASP B 478 " --> pdb=" O LYS B 474 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N PHE B 479 " --> pdb=" O CYS B 475 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE B 480 " --> pdb=" O PHE B 476 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 402 removed outlier: 3.552A pdb=" N LEU A 400 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N PHE A 346 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N GLY A 380 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL A 348 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY A 345 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 307 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 347 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP A 308 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 226 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 541 through 545 removed outlier: 4.624A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLY A 622 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER A 599 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU A 624 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 357 through 358 292 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1834 1.33 - 1.45: 1445 1.45 - 1.57: 4199 1.57 - 1.69: 2 1.69 - 1.81: 41 Bond restraints: 7521 Sorted by residual: bond pdb=" C31 3PH B 602 " pdb=" O31 3PH B 602 " ideal model delta sigma weight residual 1.325 1.454 -0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C31 3PH B 603 " pdb=" O31 3PH B 603 " ideal model delta sigma weight residual 1.325 1.449 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C21 3PH B 603 " pdb=" O21 3PH B 603 " ideal model delta sigma weight residual 1.328 1.451 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" C21 3PH B 602 " pdb=" O21 3PH B 602 " ideal model delta sigma weight residual 1.328 1.449 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" O11 3PH B 603 " pdb=" P 3PH B 603 " ideal model delta sigma weight residual 1.703 1.607 0.096 2.00e-02 2.50e+03 2.31e+01 ... (remaining 7516 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 9953 2.65 - 5.30: 224 5.30 - 7.96: 38 7.96 - 10.61: 8 10.61 - 13.26: 2 Bond angle restraints: 10225 Sorted by residual: angle pdb=" C LEU B 265 " pdb=" N PRO B 266 " pdb=" CA PRO B 266 " ideal model delta sigma weight residual 119.64 114.12 5.52 1.01e+00 9.80e-01 2.98e+01 angle pdb=" N TYR B 385 " pdb=" CA TYR B 385 " pdb=" C TYR B 385 " ideal model delta sigma weight residual 113.50 107.10 6.40 1.23e+00 6.61e-01 2.70e+01 angle pdb=" N GLY B 115 " pdb=" CA GLY B 115 " pdb=" C GLY B 115 " ideal model delta sigma weight residual 112.49 118.69 -6.20 1.21e+00 6.83e-01 2.63e+01 angle pdb=" N THR B 386 " pdb=" CA THR B 386 " pdb=" C THR B 386 " ideal model delta sigma weight residual 112.23 105.86 6.37 1.26e+00 6.30e-01 2.55e+01 angle pdb=" N SER B 179 " pdb=" CA SER B 179 " pdb=" C SER B 179 " ideal model delta sigma weight residual 111.02 117.09 -6.07 1.25e+00 6.40e-01 2.36e+01 ... (remaining 10220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.27: 4152 22.27 - 44.54: 313 44.54 - 66.80: 54 66.80 - 89.07: 9 89.07 - 111.34: 8 Dihedral angle restraints: 4536 sinusoidal: 1884 harmonic: 2652 Sorted by residual: dihedral pdb=" CA SER B 178 " pdb=" C SER B 178 " pdb=" N SER B 179 " pdb=" CA SER B 179 " ideal model delta harmonic sigma weight residual 180.00 151.28 28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA SER A 176 " pdb=" C SER A 176 " pdb=" N PRO A 177 " pdb=" CA PRO A 177 " ideal model delta harmonic sigma weight residual 180.00 154.21 25.79 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA PHE B 114 " pdb=" C PHE B 114 " pdb=" N GLY B 115 " pdb=" CA GLY B 115 " ideal model delta harmonic sigma weight residual -180.00 -156.10 -23.90 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 4533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1178 0.134 - 0.269: 20 0.269 - 0.403: 2 0.403 - 0.538: 0 0.538 - 0.672: 1 Chirality restraints: 1201 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 366 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CB VAL B 493 " pdb=" CA VAL B 493 " pdb=" CG1 VAL B 493 " pdb=" CG2 VAL B 493 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 425 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 1198 not shown) Planarity restraints: 1262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 228 " -0.056 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO B 229 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 618 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO A 619 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 619 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 619 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 131 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO B 132 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " -0.030 5.00e-02 4.00e+02 ... (remaining 1259 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 35 2.50 - 3.10: 4426 3.10 - 3.70: 10892 3.70 - 4.30: 15771 4.30 - 4.90: 25638 Nonbonded interactions: 56762 Sorted by model distance: nonbonded pdb=" O THR B 381 " pdb=" O SER B 382 " model vdw 1.904 3.040 nonbonded pdb=" OG1 THR B 381 " pdb=" N SER B 382 " model vdw 2.246 3.120 nonbonded pdb=" O PHE B 243 " pdb=" CB LEU B 601 " model vdw 2.248 3.440 nonbonded pdb=" O LEU B 379 " pdb=" N THR B 381 " model vdw 2.258 3.120 nonbonded pdb=" OH TYR B 396 " pdb=" O HOH B 701 " model vdw 2.262 3.040 ... (remaining 56757 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.200 Find NCS groups from input model: 0.110 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:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 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 0.129 7521 Z= 0.389 Angle : 1.012 13.260 10225 Z= 0.549 Chirality : 0.055 0.672 1201 Planarity : 0.006 0.083 1258 Dihedral : 16.611 111.339 2833 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 1.41 % Allowed : 7.15 % Favored : 91.44 % Rotamer: Outliers : 1.44 % Allowed : 6.95 % Favored : 91.61 % 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: -5.99 (0.17), residues: 923 helix: -4.51 (0.10), residues: 471 sheet: -1.07 (0.58), residues: 72 loop : -3.68 (0.22), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 124 HIS 0.006 0.001 HIS B 358 PHE 0.023 0.002 PHE B 335 TYR 0.016 0.002 TYR A 313 ARG 0.003 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 253 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 500 ILE cc_start: 0.6211 (mt) cc_final: 0.5999 (mt) REVERT: B 99 THR cc_start: 0.6872 (m) cc_final: 0.6403 (m) outliers start: 11 outliers final: 4 residues processed: 258 average time/residue: 0.6949 time to fit residues: 195.6712 Evaluate side-chains 148 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.0370 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 275 GLN A 296 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 561 ASN B 134 ASN B 264 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.110570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.087008 restraints weight = 12668.224| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.21 r_work: 0.3047 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7521 Z= 0.248 Angle : 0.827 10.940 10225 Z= 0.407 Chirality : 0.048 0.293 1201 Planarity : 0.006 0.063 1258 Dihedral : 13.374 91.711 1249 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.26 % Favored : 92.63 % Rotamer: Outliers : 4.59 % Allowed : 19.00 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.84 (0.22), residues: 923 helix: -2.46 (0.19), residues: 464 sheet: -0.40 (0.61), residues: 67 loop : -2.96 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 124 HIS 0.002 0.001 HIS B 349 PHE 0.028 0.002 PHE B 250 TYR 0.016 0.002 TYR B 93 ARG 0.008 0.001 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.787 Fit side-chains REVERT: A 360 PHE cc_start: 0.8048 (m-80) cc_final: 0.7738 (m-80) REVERT: B 171 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8192 (tm) REVERT: B 314 MET cc_start: 0.7119 (ptt) cc_final: 0.6674 (pmm) REVERT: B 347 GLU cc_start: 0.8495 (tp30) cc_final: 0.8182 (tp30) outliers start: 35 outliers final: 11 residues processed: 183 average time/residue: 0.6715 time to fit residues: 134.8828 Evaluate side-chains 142 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 465 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 ASN B 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.110221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.086397 restraints weight = 12983.818| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.26 r_work: 0.3050 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7521 Z= 0.237 Angle : 0.727 8.540 10225 Z= 0.357 Chirality : 0.046 0.332 1201 Planarity : 0.005 0.065 1258 Dihedral : 11.399 77.953 1244 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.93 % Favored : 92.96 % Rotamer: Outliers : 6.55 % Allowed : 19.13 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.46 (0.25), residues: 923 helix: -1.07 (0.22), residues: 484 sheet: 0.43 (0.63), residues: 58 loop : -2.68 (0.27), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 124 HIS 0.003 0.001 HIS B 349 PHE 0.020 0.002 PHE B 433 TYR 0.036 0.002 TYR B 253 ARG 0.004 0.001 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 138 time to evaluate : 0.841 Fit side-chains REVERT: B 95 GLU cc_start: 0.8722 (tp30) cc_final: 0.8504 (tp30) REVERT: B 171 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8676 (tm) REVERT: B 254 VAL cc_start: 0.7921 (OUTLIER) cc_final: 0.7627 (m) REVERT: B 294 GLN cc_start: 0.8460 (tp40) cc_final: 0.8163 (tp-100) REVERT: B 314 MET cc_start: 0.6957 (ptt) cc_final: 0.6641 (pmm) REVERT: B 327 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.8181 (t80) REVERT: B 347 GLU cc_start: 0.8448 (tp30) cc_final: 0.8222 (tp30) REVERT: B 426 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.7959 (t80) outliers start: 50 outliers final: 10 residues processed: 167 average time/residue: 0.8339 time to fit residues: 150.8468 Evaluate side-chains 125 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 426 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 64 optimal weight: 0.0980 chunk 70 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN A 580 GLN B 331 ASN B 406 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.110139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.086081 restraints weight = 13059.947| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.32 r_work: 0.3042 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.6432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7521 Z= 0.204 Angle : 0.707 8.904 10225 Z= 0.339 Chirality : 0.046 0.307 1201 Planarity : 0.004 0.066 1258 Dihedral : 10.061 61.357 1242 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.93 % Favored : 92.96 % Rotamer: Outliers : 6.42 % Allowed : 20.97 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.69 (0.27), residues: 923 helix: -0.38 (0.23), residues: 489 sheet: 0.57 (0.66), residues: 53 loop : -2.36 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 124 HIS 0.002 0.001 HIS A 266 PHE 0.013 0.001 PHE A 337 TYR 0.024 0.002 TYR A 629 ARG 0.005 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 116 time to evaluate : 0.764 Fit side-chains REVERT: A 269 GLN cc_start: 0.8200 (tp40) cc_final: 0.7746 (tp40) REVERT: A 611 GLU cc_start: 0.7759 (pm20) cc_final: 0.7289 (pp20) REVERT: B 52 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8539 (t160) REVERT: B 95 GLU cc_start: 0.8951 (tp30) cc_final: 0.8693 (tp30) REVERT: B 162 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7974 (mtt180) REVERT: B 314 MET cc_start: 0.7543 (ptt) cc_final: 0.7294 (pmm) REVERT: B 327 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8463 (t80) REVERT: B 396 TYR cc_start: 0.8772 (m-80) cc_final: 0.8565 (m-80) REVERT: B 426 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8306 (t80) REVERT: B 432 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8668 (mm) REVERT: B 440 PHE cc_start: 0.8477 (m-80) cc_final: 0.8207 (m-10) REVERT: B 456 MET cc_start: 0.8936 (ttp) cc_final: 0.8615 (ttt) outliers start: 49 outliers final: 13 residues processed: 151 average time/residue: 0.7631 time to fit residues: 125.1936 Evaluate side-chains 127 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 432 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 21 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 32 optimal weight: 0.0670 chunk 61 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.108511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.084332 restraints weight = 13006.286| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.28 r_work: 0.3008 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.6994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7521 Z= 0.187 Angle : 0.667 7.836 10225 Z= 0.319 Chirality : 0.044 0.312 1201 Planarity : 0.004 0.067 1258 Dihedral : 9.340 59.652 1242 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.15 % Favored : 92.74 % Rotamer: Outliers : 4.98 % Allowed : 23.85 % Favored : 71.17 % 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: -1.22 (0.27), residues: 923 helix: 0.06 (0.24), residues: 487 sheet: 0.58 (0.65), residues: 53 loop : -2.18 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 124 HIS 0.002 0.000 HIS B 358 PHE 0.025 0.001 PHE B 250 TYR 0.020 0.002 TYR A 554 ARG 0.003 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 0.768 Fit side-chains REVERT: A 269 GLN cc_start: 0.8014 (tp40) cc_final: 0.7449 (tp40) REVERT: A 398 ASP cc_start: 0.6371 (t0) cc_final: 0.6134 (t0) REVERT: A 451 LEU cc_start: 0.9009 (tt) cc_final: 0.8757 (tp) REVERT: A 611 GLU cc_start: 0.7794 (pm20) cc_final: 0.7362 (pp20) REVERT: B 52 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8554 (t160) REVERT: B 95 GLU cc_start: 0.8923 (tp30) cc_final: 0.8591 (tp30) REVERT: B 162 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7942 (mtt180) REVERT: B 185 ARG cc_start: 0.8792 (mmm160) cc_final: 0.7968 (ptt180) REVERT: B 203 ILE cc_start: 0.8833 (pt) cc_final: 0.8620 (mp) REVERT: B 314 MET cc_start: 0.7582 (ptt) cc_final: 0.7009 (pmm) REVERT: B 327 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8561 (t80) REVERT: B 383 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7426 (p0) REVERT: B 396 TYR cc_start: 0.8816 (m-80) cc_final: 0.8541 (m-80) REVERT: B 426 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8364 (t80) REVERT: B 432 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8673 (mm) REVERT: B 456 MET cc_start: 0.8939 (ttp) cc_final: 0.8608 (ttt) outliers start: 38 outliers final: 13 residues processed: 132 average time/residue: 0.8375 time to fit residues: 119.3722 Evaluate side-chains 118 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 487 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 53 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.106048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.081603 restraints weight = 12942.887| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.25 r_work: 0.2932 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.8375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7521 Z= 0.242 Angle : 0.730 11.015 10225 Z= 0.351 Chirality : 0.046 0.316 1201 Planarity : 0.004 0.066 1258 Dihedral : 8.725 59.359 1242 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.04 % Favored : 92.85 % Rotamer: Outliers : 5.11 % Allowed : 23.85 % Favored : 71.04 % 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: -0.92 (0.28), residues: 923 helix: 0.33 (0.24), residues: 488 sheet: 0.51 (0.68), residues: 51 loop : -2.02 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 469 HIS 0.002 0.001 HIS B 471 PHE 0.019 0.002 PHE B 250 TYR 0.019 0.002 TYR A 469 ARG 0.003 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 292 ASP cc_start: 0.9144 (t0) cc_final: 0.8707 (m-30) REVERT: A 471 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8664 (m-30) REVERT: A 611 GLU cc_start: 0.7985 (pm20) cc_final: 0.7675 (pp20) REVERT: B 52 ASN cc_start: 0.8962 (OUTLIER) cc_final: 0.8700 (t160) REVERT: B 95 GLU cc_start: 0.8916 (tp30) cc_final: 0.8469 (tp30) REVERT: B 162 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8106 (mtt180) REVERT: B 185 ARG cc_start: 0.8786 (mmm160) cc_final: 0.8072 (ptt180) REVERT: B 260 ASP cc_start: 0.8732 (t0) cc_final: 0.8292 (p0) REVERT: B 346 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.8020 (ttm-80) REVERT: B 356 MET cc_start: 0.8108 (mtt) cc_final: 0.7806 (mtt) REVERT: B 426 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8823 (t80) REVERT: B 456 MET cc_start: 0.9024 (ttp) cc_final: 0.8679 (ttt) REVERT: B 469 TRP cc_start: 0.7282 (t-100) cc_final: 0.7033 (t60) outliers start: 39 outliers final: 13 residues processed: 136 average time/residue: 1.5044 time to fit residues: 220.3224 Evaluate side-chains 98 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 487 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 51 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 83 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.104825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.080906 restraints weight = 12844.816| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.19 r_work: 0.2929 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.8623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7521 Z= 0.196 Angle : 0.706 8.999 10225 Z= 0.341 Chirality : 0.045 0.301 1201 Planarity : 0.004 0.066 1258 Dihedral : 8.471 58.892 1242 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.72 % Favored : 93.17 % Rotamer: Outliers : 4.33 % Allowed : 27.00 % Favored : 68.68 % 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: -0.71 (0.28), residues: 923 helix: 0.56 (0.24), residues: 488 sheet: 0.59 (0.68), residues: 51 loop : -2.01 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 124 HIS 0.003 0.000 HIS B 358 PHE 0.015 0.001 PHE B 250 TYR 0.016 0.001 TYR B 253 ARG 0.021 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 ASP cc_start: 0.9144 (t0) cc_final: 0.8547 (m-30) REVERT: A 325 ASP cc_start: 0.9094 (m-30) cc_final: 0.8503 (p0) REVERT: A 366 ASN cc_start: 0.6629 (t0) cc_final: 0.6370 (t0) REVERT: B 52 ASN cc_start: 0.8867 (OUTLIER) cc_final: 0.8570 (t160) REVERT: B 95 GLU cc_start: 0.8843 (tp30) cc_final: 0.8423 (tp30) REVERT: B 162 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8078 (mtt180) REVERT: B 185 ARG cc_start: 0.8752 (mmm160) cc_final: 0.8075 (ptt180) REVERT: B 356 MET cc_start: 0.8218 (mtt) cc_final: 0.7916 (mtt) REVERT: B 426 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8812 (t80) REVERT: B 456 MET cc_start: 0.8981 (ttp) cc_final: 0.8607 (ttt) outliers start: 33 outliers final: 12 residues processed: 117 average time/residue: 1.0439 time to fit residues: 131.3933 Evaluate side-chains 95 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 487 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 80 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 52 optimal weight: 0.0980 chunk 27 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.103554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.079642 restraints weight = 13097.748| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.25 r_work: 0.2906 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.8915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7521 Z= 0.218 Angle : 0.722 10.089 10225 Z= 0.348 Chirality : 0.046 0.304 1201 Planarity : 0.004 0.062 1258 Dihedral : 8.270 58.186 1242 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.15 % Favored : 92.74 % Rotamer: Outliers : 3.67 % Allowed : 27.39 % Favored : 68.94 % 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 (0.28), residues: 923 helix: 0.68 (0.24), residues: 491 sheet: 0.59 (0.69), residues: 51 loop : -2.07 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 124 HIS 0.002 0.001 HIS A 620 PHE 0.015 0.001 PHE B 250 TYR 0.016 0.001 TYR B 253 ARG 0.010 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.7953 (tmmt) cc_final: 0.7579 (pptt) REVERT: A 292 ASP cc_start: 0.9154 (t0) cc_final: 0.8606 (m-30) REVERT: A 325 ASP cc_start: 0.9089 (m-30) cc_final: 0.8523 (p0) REVERT: A 366 ASN cc_start: 0.6840 (t0) cc_final: 0.6562 (t0) REVERT: A 583 ASP cc_start: 0.8618 (m-30) cc_final: 0.7792 (p0) REVERT: B 52 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8546 (t160) REVERT: B 95 GLU cc_start: 0.8844 (tp30) cc_final: 0.8368 (tp30) REVERT: B 162 ARG cc_start: 0.8525 (mtm-85) cc_final: 0.8111 (mtt180) REVERT: B 185 ARG cc_start: 0.8771 (mmm160) cc_final: 0.8112 (ptt180) REVERT: B 314 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.7057 (pmt) REVERT: B 340 LEU cc_start: 0.9254 (tt) cc_final: 0.9043 (tp) REVERT: B 356 MET cc_start: 0.8364 (mtt) cc_final: 0.8054 (mtt) REVERT: B 426 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8871 (t80) REVERT: B 436 PHE cc_start: 0.8085 (m-10) cc_final: 0.7805 (t80) REVERT: B 456 MET cc_start: 0.9007 (ttp) cc_final: 0.8676 (ttt) outliers start: 28 outliers final: 15 residues processed: 108 average time/residue: 1.0378 time to fit residues: 120.5801 Evaluate side-chains 98 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 493 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.100634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.076875 restraints weight = 13170.412| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.19 r_work: 0.2861 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.9535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7521 Z= 0.278 Angle : 0.775 12.788 10225 Z= 0.372 Chirality : 0.048 0.299 1201 Planarity : 0.005 0.058 1258 Dihedral : 8.353 58.143 1242 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.58 % Favored : 92.31 % Rotamer: Outliers : 4.06 % Allowed : 28.18 % Favored : 67.76 % 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: -0.63 (0.28), residues: 923 helix: 0.66 (0.24), residues: 485 sheet: 0.66 (0.70), residues: 51 loop : -2.03 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 319 HIS 0.003 0.001 HIS B 358 PHE 0.013 0.002 PHE B 250 TYR 0.015 0.002 TYR B 262 ARG 0.008 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8170 (tp) REVERT: A 292 ASP cc_start: 0.9134 (t0) cc_final: 0.8633 (m-30) REVERT: A 325 ASP cc_start: 0.9145 (m-30) cc_final: 0.8577 (p0) REVERT: A 366 ASN cc_start: 0.7188 (t0) cc_final: 0.6876 (t0) REVERT: A 583 ASP cc_start: 0.8648 (m-30) cc_final: 0.7918 (p0) REVERT: B 52 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8598 (t160) REVERT: B 95 GLU cc_start: 0.8819 (tp30) cc_final: 0.8336 (tp30) REVERT: B 162 ARG cc_start: 0.8551 (mtm-85) cc_final: 0.8264 (mtt180) REVERT: B 185 ARG cc_start: 0.8848 (mmm160) cc_final: 0.8045 (ptt180) REVERT: B 260 ASP cc_start: 0.8763 (t0) cc_final: 0.8534 (p0) REVERT: B 356 MET cc_start: 0.8608 (mtt) cc_final: 0.8294 (mtt) REVERT: B 441 SER cc_start: 0.9275 (t) cc_final: 0.9064 (m) REVERT: B 443 TRP cc_start: 0.8180 (t-100) cc_final: 0.7754 (t60) REVERT: B 456 MET cc_start: 0.9095 (ttp) cc_final: 0.8779 (ttt) REVERT: B 490 MET cc_start: 0.7965 (ttm) cc_final: 0.7744 (ttm) outliers start: 31 outliers final: 17 residues processed: 107 average time/residue: 1.3531 time to fit residues: 156.6621 Evaluate side-chains 101 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 493 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 74 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 67 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 5 optimal weight: 0.0770 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS B 406 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.104395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.080546 restraints weight = 13151.049| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.23 r_work: 0.2914 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.9632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7521 Z= 0.170 Angle : 0.714 10.103 10225 Z= 0.341 Chirality : 0.044 0.298 1201 Planarity : 0.004 0.058 1258 Dihedral : 8.033 57.156 1242 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.04 % Favored : 92.85 % Rotamer: Outliers : 2.49 % Allowed : 30.28 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.40 (0.28), residues: 923 helix: 0.93 (0.24), residues: 492 sheet: 0.70 (0.71), residues: 51 loop : -2.08 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 124 HIS 0.002 0.001 HIS A 539 PHE 0.016 0.001 PHE B 436 TYR 0.024 0.001 TYR B 253 ARG 0.008 0.000 ARG B 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8119 (tp) REVERT: A 292 ASP cc_start: 0.9088 (t0) cc_final: 0.8736 (m-30) REVERT: A 325 ASP cc_start: 0.9176 (m-30) cc_final: 0.8575 (p0) REVERT: A 366 ASN cc_start: 0.7207 (t0) cc_final: 0.6840 (t0) REVERT: A 583 ASP cc_start: 0.8550 (m-30) cc_final: 0.7856 (p0) REVERT: B 95 GLU cc_start: 0.8723 (tp30) cc_final: 0.8269 (tp30) REVERT: B 162 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.8184 (mtt180) REVERT: B 185 ARG cc_start: 0.8825 (mmm160) cc_final: 0.8035 (ptt180) REVERT: B 356 MET cc_start: 0.8457 (mtt) cc_final: 0.8209 (mtt) REVERT: B 441 SER cc_start: 0.9260 (t) cc_final: 0.9046 (m) REVERT: B 443 TRP cc_start: 0.8133 (t-100) cc_final: 0.7704 (t60) REVERT: B 456 MET cc_start: 0.9013 (ttp) cc_final: 0.8762 (ttt) REVERT: B 469 TRP cc_start: 0.7430 (t-100) cc_final: 0.6695 (t60) REVERT: B 490 MET cc_start: 0.7833 (ttm) cc_final: 0.7608 (ttm) outliers start: 19 outliers final: 12 residues processed: 102 average time/residue: 1.0023 time to fit residues: 109.8682 Evaluate side-chains 91 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 493 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 59 optimal weight: 0.0030 chunk 71 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 52 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.105726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.081318 restraints weight = 12772.727| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.16 r_work: 0.2958 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.9745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7521 Z= 0.180 Angle : 0.744 10.957 10225 Z= 0.354 Chirality : 0.045 0.303 1201 Planarity : 0.004 0.056 1258 Dihedral : 7.828 56.475 1242 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.26 % Favored : 92.63 % Rotamer: Outliers : 2.62 % Allowed : 30.28 % Favored : 67.10 % 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: -0.27 (0.28), residues: 923 helix: 1.06 (0.25), residues: 493 sheet: 0.70 (0.71), residues: 51 loop : -2.04 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 124 HIS 0.002 0.000 HIS B 358 PHE 0.012 0.001 PHE A 291 TYR 0.013 0.001 TYR A 554 ARG 0.008 0.000 ARG B 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4699.53 seconds wall clock time: 84 minutes 21.62 seconds (5061.62 seconds total)