Starting phenix.real_space_refine on Wed Feb 12 09:24:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cmi_30407/02_2025/7cmi_30407.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cmi_30407/02_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_30407/02_2025/7cmi_30407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cmi_30407/02_2025/7cmi_30407.map" model { file = "/net/cci-nas-00/data/ceres_data/7cmi_30407/02_2025/7cmi_30407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cmi_30407/02_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-5592/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: 4.98, per 1000 atoms: 0.68 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: 1.95 Conformation dependent library (CDL) restraints added in 1.1 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: 0.66 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: 1.99 Time building geometry restraints manager: 2.20 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: 0.710 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: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.300 Find NCS groups from input model: 0.120 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:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.780 ------------------------------------------------------------------------------- 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 : 0.771 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: 0.7299 time to fit residues: 204.7696 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 : 0.901 ------------------------------------------------------------------------------- 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 = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.087011 restraints weight = 12668.244| |-----------------------------------------------------------------------------| 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 : 0.783 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: 0.7118 (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: 0.7116 time to fit residues: 142.6201 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 : 0.856 ------------------------------------------------------------------------------- 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: 1.9990 chunk 70 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 53 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 78 optimal weight: 0.0770 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.110858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.087095 restraints weight = 12912.443| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.26 r_work: 0.3057 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4910 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= 0.213 Angle : 0.704 8.593 10225 Z= 0.345 Chirality : 0.045 0.331 1201 Planarity : 0.005 0.064 1258 Dihedral : 11.474 78.836 1244 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.72 % Favored : 93.17 % Rotamer: Outliers : 6.16 % Allowed : 19.53 % 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: 483 sheet: 0.40 (0.62), residues: 58 loop : -2.67 (0.27), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 124 HIS 0.002 0.001 HIS B 358 PHE 0.019 0.002 PHE B 433 TYR 0.036 0.002 TYR B 253 ARG 0.004 0.000 ARG A 212 *********************** 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 192 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 145 time to evaluate : 0.810 Fit side-chains REVERT: A 269 GLN cc_start: 0.7611 (tm-30) cc_final: 0.7382 (tp40) REVERT: B 171 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8552 (tm) REVERT: B 185 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7670 (ptm160) REVERT: B 294 GLN cc_start: 0.8452 (tp40) cc_final: 0.8147 (tp-100) REVERT: B 314 MET cc_start: 0.7066 (ptt) cc_final: 0.6568 (pmm) REVERT: B 327 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.8092 (t80) REVERT: B 347 GLU cc_start: 0.8469 (tp30) cc_final: 0.7994 (tt0) REVERT: B 426 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7931 (t80) outliers start: 47 outliers final: 8 residues processed: 173 average time/residue: 0.7421 time to fit residues: 139.9040 Evaluate side-chains 131 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 295 LEU 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 171 LEU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 465 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 64 optimal weight: 0.0010 chunk 70 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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** 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 = 0.3553 r_free = 0.3553 target = 0.111271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.087189 restraints weight = 12985.524| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.30 r_work: 0.3065 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5921 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= 0.186 Angle : 0.693 8.535 10225 Z= 0.330 Chirality : 0.045 0.300 1201 Planarity : 0.004 0.066 1258 Dihedral : 10.135 62.626 1242 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.39 % Favored : 93.50 % Rotamer: Outliers : 5.77 % Allowed : 22.28 % Favored : 71.95 % 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: -1.73 (0.26), residues: 923 helix: -0.39 (0.23), residues: 488 sheet: 0.52 (0.66), residues: 53 loop : -2.41 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 124 HIS 0.001 0.000 HIS B 471 PHE 0.015 0.001 PHE A 337 TYR 0.026 0.002 TYR B 253 ARG 0.004 0.000 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 162 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 118 time to evaluate : 0.838 Fit side-chains REVERT: A 269 GLN cc_start: 0.7454 (tm-30) cc_final: 0.7080 (tp40) REVERT: A 611 GLU cc_start: 0.7699 (pm20) cc_final: 0.7329 (pp20) REVERT: B 52 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8494 (t160) REVERT: B 53 ILE cc_start: 0.7501 (mm) cc_final: 0.7147 (mt) REVERT: B 95 GLU cc_start: 0.8779 (tp30) cc_final: 0.8575 (tp30) REVERT: B 162 ARG cc_start: 0.8242 (mtm-85) cc_final: 0.7911 (mtt180) REVERT: B 171 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8755 (tm) REVERT: B 294 GLN cc_start: 0.8450 (tp40) cc_final: 0.8108 (tp-100) REVERT: B 314 MET cc_start: 0.7503 (ptt) cc_final: 0.7060 (pmm) REVERT: B 327 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8256 (t80) REVERT: B 361 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7430 (pmt170) REVERT: B 426 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8175 (t80) REVERT: B 440 PHE cc_start: 0.8401 (m-80) cc_final: 0.8121 (m-10) REVERT: B 456 MET cc_start: 0.8881 (ttp) cc_final: 0.8590 (ttt) outliers start: 44 outliers final: 12 residues processed: 147 average time/residue: 0.8375 time to fit residues: 133.3206 Evaluate side-chains 125 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 435 SER Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 98 VAL 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 259 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 304 VAL 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 361 ARG Chi-restraints excluded: chain B residue 426 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 21 optimal weight: 0.8980 chunk 68 optimal weight: 0.0050 chunk 32 optimal weight: 0.0030 chunk 61 optimal weight: 4.9990 chunk 47 optimal weight: 0.2980 chunk 53 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 overall best weight: 0.4404 ------------------------------------------------------------------------------- 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 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 = 0.3551 r_free = 0.3551 target = 0.111210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.087042 restraints weight = 12905.512| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.30 r_work: 0.3064 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.6312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7521 Z= 0.160 Angle : 0.658 9.043 10225 Z= 0.312 Chirality : 0.044 0.307 1201 Planarity : 0.004 0.066 1258 Dihedral : 9.418 59.795 1242 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.72 % Favored : 93.17 % Rotamer: Outliers : 4.59 % Allowed : 23.46 % Favored : 71.95 % 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: -1.29 (0.27), residues: 923 helix: 0.02 (0.24), residues: 487 sheet: 0.65 (0.65), residues: 53 loop : -2.25 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 124 HIS 0.002 0.001 HIS B 358 PHE 0.024 0.001 PHE B 250 TYR 0.025 0.002 TYR A 469 ARG 0.006 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 148 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.842 Fit side-chains REVERT: A 611 GLU cc_start: 0.7894 (pm20) cc_final: 0.7367 (pp20) REVERT: B 52 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8532 (t160) REVERT: B 53 ILE cc_start: 0.7644 (mm) cc_final: 0.7310 (mt) REVERT: B 95 GLU cc_start: 0.8761 (tp30) cc_final: 0.8459 (tp30) REVERT: B 294 GLN cc_start: 0.8458 (tp40) cc_final: 0.8105 (tp-100) REVERT: B 314 MET cc_start: 0.7475 (ptt) cc_final: 0.6976 (pmm) REVERT: B 327 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.8343 (t80) REVERT: B 426 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8279 (t80) REVERT: B 440 PHE cc_start: 0.8429 (m-80) cc_final: 0.8112 (m-10) REVERT: B 456 MET cc_start: 0.8889 (ttp) cc_final: 0.8589 (ttt) outliers start: 35 outliers final: 12 residues processed: 139 average time/residue: 0.8064 time to fit residues: 121.6998 Evaluate side-chains 114 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 435 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 164 LEU 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 386 THR Chi-restraints excluded: chain B residue 426 PHE 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: 0.2980 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 73 optimal weight: 0.0060 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.110854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.086429 restraints weight = 12858.227| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.32 r_work: 0.3044 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.6827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7521 Z= 0.168 Angle : 0.663 9.074 10225 Z= 0.320 Chirality : 0.044 0.306 1201 Planarity : 0.004 0.064 1258 Dihedral : 8.947 59.295 1242 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.39 % Favored : 93.50 % Rotamer: Outliers : 5.37 % Allowed : 23.20 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.27), residues: 923 helix: 0.34 (0.24), residues: 487 sheet: 0.16 (0.65), residues: 56 loop : -2.19 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 124 HIS 0.002 0.001 HIS B 358 PHE 0.026 0.001 PHE B 250 TYR 0.018 0.001 TYR B 253 ARG 0.005 0.000 ARG B 346 *********************** 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 149 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 0.804 Fit side-chains REVERT: A 269 GLN cc_start: 0.7709 (tp40) cc_final: 0.7288 (tp40) REVERT: A 451 LEU cc_start: 0.8815 (tt) cc_final: 0.8514 (tp) REVERT: A 611 GLU cc_start: 0.7931 (pm20) cc_final: 0.7429 (pp20) REVERT: B 52 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8499 (t160) REVERT: B 95 GLU cc_start: 0.8826 (tp30) cc_final: 0.8508 (tp30) REVERT: B 162 ARG cc_start: 0.8208 (mtt180) cc_final: 0.8001 (mtt180) REVERT: B 164 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8912 (tp) REVERT: B 314 MET cc_start: 0.7626 (ptt) cc_final: 0.7075 (pmm) REVERT: B 327 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8456 (t80) REVERT: B 396 TYR cc_start: 0.8807 (m-80) cc_final: 0.8569 (m-80) REVERT: B 426 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8400 (t80) REVERT: B 440 PHE cc_start: 0.8500 (m-80) cc_final: 0.8203 (m-10) REVERT: B 456 MET cc_start: 0.8931 (ttp) cc_final: 0.8575 (ttt) outliers start: 41 outliers final: 14 residues processed: 136 average time/residue: 0.8759 time to fit residues: 128.2888 Evaluate side-chains 119 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 471 ASP 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 76 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 209 ILE 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 386 THR Chi-restraints excluded: chain B residue 426 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 83 optimal weight: 0.0980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 240 GLN B 488 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.107212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.082837 restraints weight = 12595.571| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.13 r_work: 0.2977 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.8026 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= 0.243 Angle : 0.741 10.273 10225 Z= 0.359 Chirality : 0.047 0.319 1201 Planarity : 0.004 0.060 1258 Dihedral : 8.552 59.501 1242 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.15 % Favored : 92.74 % Rotamer: Outliers : 4.59 % Allowed : 23.59 % Favored : 71.82 % 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: -0.83 (0.28), residues: 923 helix: 0.40 (0.24), residues: 492 sheet: 0.58 (0.66), residues: 51 loop : -2.01 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 558 HIS 0.003 0.001 HIS B 349 PHE 0.018 0.001 PHE B 250 TYR 0.027 0.002 TYR A 469 ARG 0.004 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 140 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.851 Fit side-chains REVERT: A 471 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8517 (m-30) REVERT: B 52 ASN cc_start: 0.8870 (OUTLIER) cc_final: 0.8624 (t160) REVERT: B 95 GLU cc_start: 0.8735 (tp30) cc_final: 0.8382 (tp30) REVERT: B 162 ARG cc_start: 0.8435 (mtt180) cc_final: 0.8231 (mtt180) REVERT: B 185 ARG cc_start: 0.8746 (mmm160) cc_final: 0.8145 (ptt180) REVERT: B 327 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8617 (t80) REVERT: B 356 MET cc_start: 0.8027 (mtt) cc_final: 0.7573 (mtt) REVERT: B 426 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8733 (t80) REVERT: B 456 MET cc_start: 0.9015 (ttp) cc_final: 0.8594 (ttt) outliers start: 35 outliers final: 13 residues processed: 132 average time/residue: 0.8736 time to fit residues: 124.4955 Evaluate side-chains 104 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 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 76 LEU Chi-restraints excluded: chain B residue 91 LEU 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 327 PHE Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 426 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 80 optimal weight: 0.4980 chunk 70 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 79 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.0010 chunk 86 optimal weight: 5.9990 overall best weight: 0.4544 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.107164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.083310 restraints weight = 13084.669| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.26 r_work: 0.2973 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.8308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7521 Z= 0.178 Angle : 0.716 9.024 10225 Z= 0.344 Chirality : 0.045 0.300 1201 Planarity : 0.004 0.057 1258 Dihedral : 8.189 57.810 1242 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.15 % Favored : 92.74 % Rotamer: Outliers : 3.15 % Allowed : 26.74 % Favored : 70.12 % 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: -0.61 (0.28), residues: 923 helix: 0.71 (0.24), residues: 488 sheet: 0.13 (0.64), residues: 56 loop : -2.02 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 124 HIS 0.002 0.001 HIS B 471 PHE 0.016 0.001 PHE B 250 TYR 0.016 0.001 TYR B 253 ARG 0.009 0.001 ARG B 346 *********************** 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 126 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 1.048 Fit side-chains REVERT: A 167 LYS cc_start: 0.7914 (tmmt) cc_final: 0.7667 (pptt) REVERT: A 269 GLN cc_start: 0.8195 (tp40) cc_final: 0.7899 (tp40) REVERT: A 292 ASP cc_start: 0.9113 (t0) cc_final: 0.8668 (m-30) REVERT: A 325 ASP cc_start: 0.9019 (m-30) cc_final: 0.8351 (p0) REVERT: A 366 ASN cc_start: 0.6392 (t0) cc_final: 0.6056 (t0) REVERT: A 471 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8477 (m-30) REVERT: B 52 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.8511 (t160) REVERT: B 95 GLU cc_start: 0.8788 (tp30) cc_final: 0.8311 (tp30) REVERT: B 162 ARG cc_start: 0.8384 (mtt180) cc_final: 0.8153 (mtt180) REVERT: B 185 ARG cc_start: 0.8765 (mmm160) cc_final: 0.8098 (ptt180) REVERT: B 327 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8566 (t80) REVERT: B 356 MET cc_start: 0.8112 (mtt) cc_final: 0.7682 (mtt) REVERT: B 426 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8724 (t80) REVERT: B 456 MET cc_start: 0.8956 (ttp) cc_final: 0.8578 (ttt) outliers start: 24 outliers final: 12 residues processed: 120 average time/residue: 0.8991 time to fit residues: 116.2568 Evaluate side-chains 105 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 471 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 98 VAL 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 327 PHE Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 426 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 0.0020 chunk 80 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 46 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 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 = 0.3470 r_free = 0.3470 target = 0.106437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.082643 restraints weight = 13066.334| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.25 r_work: 0.2955 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.8531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7521 Z= 0.194 Angle : 0.715 9.438 10225 Z= 0.346 Chirality : 0.045 0.302 1201 Planarity : 0.004 0.057 1258 Dihedral : 7.987 57.706 1242 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.15 % Favored : 92.74 % Rotamer: Outliers : 3.15 % Allowed : 26.21 % Favored : 70.64 % 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: -0.48 (0.28), residues: 923 helix: 0.83 (0.25), residues: 489 sheet: 0.56 (0.67), residues: 51 loop : -2.03 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 469 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 0.009 0.000 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 118 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.862 Fit side-chains REVERT: A 292 ASP cc_start: 0.9127 (t0) cc_final: 0.8690 (m-30) REVERT: A 325 ASP cc_start: 0.9058 (m-30) cc_final: 0.8407 (p0) REVERT: A 366 ASN cc_start: 0.6523 (t0) cc_final: 0.6238 (t0) REVERT: A 471 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8497 (m-30) REVERT: B 52 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8566 (t160) REVERT: B 95 GLU cc_start: 0.8797 (tp30) cc_final: 0.8296 (tp30) REVERT: B 162 ARG cc_start: 0.8410 (mtt180) cc_final: 0.8179 (mtt180) REVERT: B 185 ARG cc_start: 0.8782 (mmm160) cc_final: 0.8036 (ptt180) REVERT: B 347 GLU cc_start: 0.8401 (tt0) cc_final: 0.8126 (tp30) REVERT: B 356 MET cc_start: 0.8099 (mtt) cc_final: 0.7650 (mtt) REVERT: B 426 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8745 (t80) REVERT: B 436 PHE cc_start: 0.8011 (m-10) cc_final: 0.7673 (t80) REVERT: B 456 MET cc_start: 0.8959 (ttp) cc_final: 0.8606 (ttt) REVERT: B 469 TRP cc_start: 0.7622 (OUTLIER) cc_final: 0.7335 (t60) outliers start: 24 outliers final: 13 residues processed: 112 average time/residue: 0.9558 time to fit residues: 115.0725 Evaluate side-chains 104 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 471 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 579 LEU 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 260 ASP Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 469 TRP 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: 1.9990 chunk 67 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.106748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.082897 restraints weight = 13163.476| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.26 r_work: 0.2962 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.8683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7521 Z= 0.187 Angle : 0.723 11.245 10225 Z= 0.347 Chirality : 0.045 0.303 1201 Planarity : 0.005 0.064 1258 Dihedral : 7.872 57.307 1242 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.26 % Favored : 92.63 % Rotamer: Outliers : 1.97 % Allowed : 27.79 % Favored : 70.25 % 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: -0.39 (0.28), residues: 923 helix: 0.95 (0.25), residues: 489 sheet: 0.01 (0.64), residues: 56 loop : -1.98 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 469 HIS 0.001 0.000 HIS B 358 PHE 0.015 0.001 PHE B 250 TYR 0.016 0.001 TYR B 253 ARG 0.009 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 104 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.814 Fit side-chains REVERT: A 292 ASP cc_start: 0.9109 (t0) cc_final: 0.8675 (m-30) REVERT: A 325 ASP cc_start: 0.9038 (m-30) cc_final: 0.8362 (p0) REVERT: A 366 ASN cc_start: 0.6559 (t0) cc_final: 0.6256 (t0) REVERT: A 471 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8518 (m-30) REVERT: A 583 ASP cc_start: 0.8543 (m-30) cc_final: 0.7752 (p0) REVERT: B 52 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8535 (t160) REVERT: B 95 GLU cc_start: 0.8792 (tp30) cc_final: 0.8291 (tp30) REVERT: B 185 ARG cc_start: 0.8727 (mmm160) cc_final: 0.8012 (ptt180) REVERT: B 347 GLU cc_start: 0.8380 (tt0) cc_final: 0.8086 (tp30) REVERT: B 356 MET cc_start: 0.8110 (mtt) cc_final: 0.7675 (mtt) REVERT: B 426 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8724 (t80) REVERT: B 436 PHE cc_start: 0.8102 (m-10) cc_final: 0.7747 (t80) REVERT: B 456 MET cc_start: 0.8930 (ttp) cc_final: 0.8616 (ttt) REVERT: B 469 TRP cc_start: 0.7378 (t60) cc_final: 0.6867 (t60) outliers start: 15 outliers final: 10 residues processed: 102 average time/residue: 0.9887 time to fit residues: 108.0274 Evaluate side-chains 96 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 471 ASP 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 98 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 426 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 59 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 0.0870 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.107694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.083255 restraints weight = 12809.679| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.18 r_work: 0.2983 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.8995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7521 Z= 0.190 Angle : 0.710 9.017 10225 Z= 0.344 Chirality : 0.045 0.303 1201 Planarity : 0.004 0.056 1258 Dihedral : 7.715 56.569 1242 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.26 % Favored : 92.63 % Rotamer: Outliers : 2.49 % Allowed : 27.39 % Favored : 70.12 % 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: -0.28 (0.28), residues: 923 helix: 1.02 (0.25), residues: 490 sheet: 0.62 (0.69), residues: 51 loop : -1.97 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 124 HIS 0.001 0.000 HIS B 358 PHE 0.014 0.001 PHE B 250 TYR 0.016 0.001 TYR B 253 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: 4432.15 seconds wall clock time: 79 minutes 4.46 seconds (4744.46 seconds total)