Starting phenix.real_space_refine on Fri Jul 25 13:33:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cmi_30407/07_2025/7cmi_30407.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cmi_30407/07_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_30407/07_2025/7cmi_30407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cmi_30407/07_2025/7cmi_30407.map" model { file = "/net/cci-nas-00/data/ceres_data/7cmi_30407/07_2025/7cmi_30407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cmi_30407/07_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.23, per 1000 atoms: 0.71 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: 2.26 Conformation dependent library (CDL) restraints added in 940.7 milliseconds 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: 0.77 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: 2.07 Time building geometry restraints manager: 2.61 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: 0.910 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.830 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.530 ------------------------------------------------------------------------------- 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 7530 Z= 0.321 Angle : 1.028 13.260 10251 Z= 0.552 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 4) link_NAG-ASN : angle 4.39518 ( 12) link_BETA1-4 : bond 0.01223 ( 4) link_BETA1-4 : angle 3.25152 ( 12) hydrogen bonds : bond 0.34454 ( 292) hydrogen bonds : angle 10.33981 ( 852) SS BOND : bond 0.00165 ( 1) SS BOND : angle 1.79920 ( 2) covalent geometry : bond 0.00635 ( 7521) covalent geometry : angle 1.01217 (10225) *********************** 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 : 0.722 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: 0.7048 time to fit residues: 197.6864 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 : 0.776 ------------------------------------------------------------------------------- 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 7530 Z= 0.177 Angle : 0.836 10.940 10251 Z= 0.408 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 4) link_NAG-ASN : angle 3.00595 ( 12) link_BETA1-4 : bond 0.00393 ( 4) link_BETA1-4 : angle 1.92752 ( 12) hydrogen bonds : bond 0.05444 ( 292) hydrogen bonds : angle 4.97001 ( 852) SS BOND : bond 0.00500 ( 1) SS BOND : angle 2.85978 ( 2) covalent geometry : bond 0.00389 ( 7521) covalent geometry : angle 0.82740 (10225) *********************** 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 : 1.093 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: 0.7541 time to fit residues: 151.9892 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 : 0.810 ------------------------------------------------------------------------------- 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 7530 Z= 0.167 Angle : 0.737 8.540 10251 Z= 0.360 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00627 ( 4) link_NAG-ASN : angle 2.92407 ( 12) link_BETA1-4 : bond 0.00574 ( 4) link_BETA1-4 : angle 2.21676 ( 12) hydrogen bonds : bond 0.05440 ( 292) hydrogen bonds : angle 4.39572 ( 852) SS BOND : bond 0.00329 ( 1) SS BOND : angle 2.30211 ( 2) covalent geometry : bond 0.00375 ( 7521) covalent geometry : angle 0.72659 (10225) *********************** 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 : 0.815 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: 0.7859 time to fit residues: 142.6683 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 : 0.793 ------------------------------------------------------------------------------- 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: 0.2980 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: 0.5380 ------------------------------------------------------------------------------- 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 B 331 ASN B 406 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.110495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.086469 restraints weight = 13030.498| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.31 r_work: 0.3048 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.6151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7530 Z= 0.130 Angle : 0.700 8.746 10251 Z= 0.333 Chirality : 0.045 0.308 1201 Planarity : 0.004 0.066 1258 Dihedral : 10.225 64.052 1242 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.04 % Favored : 92.85 % Rotamer: Outliers : 5.24 % Allowed : 22.54 % Favored : 72.21 % 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: -1.75 (0.27), residues: 923 helix: -0.42 (0.23), residues: 489 sheet: 0.57 (0.66), residues: 53 loop : -2.39 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 124 HIS 0.001 0.000 HIS A 266 PHE 0.017 0.001 PHE A 337 TYR 0.024 0.002 TYR B 253 ARG 0.003 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 4) link_NAG-ASN : angle 2.99860 ( 12) link_BETA1-4 : bond 0.00488 ( 4) link_BETA1-4 : angle 2.12771 ( 12) hydrogen bonds : bond 0.03877 ( 292) hydrogen bonds : angle 4.20612 ( 852) SS BOND : bond 0.01191 ( 1) SS BOND : angle 2.94886 ( 2) covalent geometry : bond 0.00293 ( 7521) covalent geometry : angle 0.68869 (10225) *********************** 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 159 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 0.804 Fit side-chains REVERT: A 269 GLN cc_start: 0.8115 (tp40) cc_final: 0.7653 (tp40) REVERT: A 611 GLU cc_start: 0.7698 (pm20) cc_final: 0.7220 (pp20) REVERT: B 52 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8538 (t160) REVERT: B 53 ILE cc_start: 0.7715 (mm) cc_final: 0.7380 (mt) REVERT: B 95 GLU cc_start: 0.8928 (tp30) cc_final: 0.8695 (tp30) REVERT: B 162 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7915 (mtt180) REVERT: B 171 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8927 (tm) REVERT: B 181 ARG cc_start: 0.8369 (mtp180) cc_final: 0.8167 (mtp180) REVERT: B 314 MET cc_start: 0.7508 (ptt) cc_final: 0.7267 (pmm) REVERT: B 327 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.8342 (t80) REVERT: B 347 GLU cc_start: 0.8593 (tp30) cc_final: 0.8369 (mm-30) REVERT: B 426 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8241 (t80) REVERT: B 432 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8626 (mm) REVERT: B 456 MET cc_start: 0.8914 (ttp) cc_final: 0.8630 (ttt) outliers start: 40 outliers final: 14 residues processed: 147 average time/residue: 0.7860 time to fit residues: 125.4228 Evaluate side-chains 121 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 293 SER Chi-restraints excluded: chain A residue 435 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 A residue 629 TYR Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 171 LEU 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 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: 4.9990 chunk 68 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.109389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.085202 restraints weight = 12972.813| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.29 r_work: 0.3010 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.6667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7530 Z= 0.126 Angle : 0.679 8.934 10251 Z= 0.322 Chirality : 0.044 0.309 1201 Planarity : 0.004 0.067 1258 Dihedral : 9.532 59.469 1242 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.48 % Favored : 92.42 % Rotamer: Outliers : 4.98 % Allowed : 23.72 % Favored : 71.30 % 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: -1.30 (0.27), residues: 923 helix: -0.01 (0.24), residues: 487 sheet: 0.54 (0.65), residues: 53 loop : -2.22 (0.30), 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 0.022 0.001 PHE B 250 TYR 0.024 0.002 TYR A 469 ARG 0.004 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 4) link_NAG-ASN : angle 2.98316 ( 12) link_BETA1-4 : bond 0.00570 ( 4) link_BETA1-4 : angle 2.28831 ( 12) hydrogen bonds : bond 0.03889 ( 292) hydrogen bonds : angle 4.12705 ( 852) SS BOND : bond 0.00363 ( 1) SS BOND : angle 2.59529 ( 2) covalent geometry : bond 0.00284 ( 7521) covalent geometry : angle 0.66679 (10225) *********************** 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 142 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 104 time to evaluate : 0.781 Fit side-chains REVERT: A 269 GLN cc_start: 0.7928 (tp40) cc_final: 0.7399 (tp40) REVERT: A 398 ASP cc_start: 0.6234 (t0) cc_final: 0.5981 (t0) REVERT: A 451 LEU cc_start: 0.8864 (tt) cc_final: 0.8599 (tp) REVERT: A 611 GLU cc_start: 0.7793 (pm20) cc_final: 0.7337 (pp20) REVERT: B 52 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8526 (t160) REVERT: B 95 GLU cc_start: 0.8950 (tp30) cc_final: 0.8674 (tp30) REVERT: B 162 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7967 (mtt180) REVERT: B 314 MET cc_start: 0.7558 (ptt) cc_final: 0.6990 (pmm) REVERT: B 327 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8524 (t80) REVERT: B 396 TYR cc_start: 0.8788 (m-80) cc_final: 0.8560 (m-80) REVERT: B 426 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8334 (t80) REVERT: B 432 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8651 (mm) REVERT: B 456 MET cc_start: 0.8929 (ttp) cc_final: 0.8647 (ttt) outliers start: 38 outliers final: 11 residues processed: 132 average time/residue: 0.8720 time to fit residues: 124.2010 Evaluate side-chains 116 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 444 SER 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 98 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 186 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 386 THR Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 432 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 53 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 73 optimal weight: 0.0170 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.109603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.085431 restraints weight = 12896.492| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.27 r_work: 0.3021 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.7513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7530 Z= 0.138 Angle : 0.703 9.999 10251 Z= 0.333 Chirality : 0.045 0.307 1201 Planarity : 0.004 0.066 1258 Dihedral : 8.732 59.864 1242 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.72 % Favored : 93.17 % Rotamer: Outliers : 5.24 % Allowed : 23.59 % Favored : 71.17 % 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: -0.86 (0.28), residues: 923 helix: 0.42 (0.24), residues: 487 sheet: 0.55 (0.68), residues: 51 loop : -2.06 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 124 HIS 0.005 0.001 HIS B 349 PHE 0.024 0.001 PHE B 250 TYR 0.018 0.001 TYR A 554 ARG 0.003 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 4) link_NAG-ASN : angle 3.05388 ( 12) link_BETA1-4 : bond 0.00621 ( 4) link_BETA1-4 : angle 2.50458 ( 12) hydrogen bonds : bond 0.03689 ( 292) hydrogen bonds : angle 4.08553 ( 852) SS BOND : bond 0.00325 ( 1) SS BOND : angle 2.47245 ( 2) covalent geometry : bond 0.00308 ( 7521) covalent geometry : angle 0.69000 (10225) *********************** 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 156 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.742 Fit side-chains REVERT: A 165 LEU cc_start: 0.5631 (pt) cc_final: 0.4808 (pp) REVERT: A 269 GLN cc_start: 0.8002 (tp40) cc_final: 0.7545 (tp40) REVERT: A 344 ASP cc_start: 0.7804 (t0) cc_final: 0.7592 (t0) REVERT: A 398 ASP cc_start: 0.6648 (t0) cc_final: 0.6411 (t0) REVERT: A 611 GLU cc_start: 0.7764 (pm20) cc_final: 0.7367 (pp20) REVERT: B 52 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8601 (t160) REVERT: B 95 GLU cc_start: 0.8944 (tp30) cc_final: 0.8526 (tp30) REVERT: B 162 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7918 (mtt180) REVERT: B 185 ARG cc_start: 0.8783 (mmm160) cc_final: 0.8057 (ptt180) REVERT: B 314 MET cc_start: 0.7534 (ptt) cc_final: 0.7065 (pmm) REVERT: B 327 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8497 (t80) REVERT: B 347 GLU cc_start: 0.8276 (tt0) cc_final: 0.7996 (tp30) REVERT: B 396 TYR cc_start: 0.8914 (m-80) cc_final: 0.8678 (m-80) REVERT: B 426 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8542 (t80) REVERT: B 456 MET cc_start: 0.8963 (ttp) cc_final: 0.8552 (ttt) REVERT: B 469 TRP cc_start: 0.7277 (t-100) cc_final: 0.7071 (t60) outliers start: 40 outliers final: 12 residues processed: 142 average time/residue: 0.8374 time to fit residues: 128.5024 Evaluate side-chains 113 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 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 98 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 162 ARG 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 386 THR 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: 0.7980 chunk 66 optimal weight: 0.2980 chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.106691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.082909 restraints weight = 12915.484| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.23 r_work: 0.2965 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.7972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7530 Z= 0.129 Angle : 0.712 9.185 10251 Z= 0.339 Chirality : 0.045 0.299 1201 Planarity : 0.004 0.061 1258 Dihedral : 8.357 58.469 1242 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.93 % Favored : 92.96 % Rotamer: Outliers : 3.93 % Allowed : 25.95 % 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: -0.67 (0.28), residues: 923 helix: 0.60 (0.24), residues: 486 sheet: 0.58 (0.67), residues: 51 loop : -1.98 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 124 HIS 0.003 0.001 HIS B 349 PHE 0.019 0.001 PHE B 250 TYR 0.018 0.002 TYR A 469 ARG 0.005 0.000 ARG B 122 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 4) link_NAG-ASN : angle 3.20563 ( 12) link_BETA1-4 : bond 0.00710 ( 4) link_BETA1-4 : angle 2.30666 ( 12) hydrogen bonds : bond 0.03619 ( 292) hydrogen bonds : angle 4.06311 ( 852) SS BOND : bond 0.00348 ( 1) SS BOND : angle 2.32420 ( 2) covalent geometry : bond 0.00291 ( 7521) covalent geometry : angle 0.69919 (10225) *********************** 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 129 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.882 Fit side-chains REVERT: A 269 GLN cc_start: 0.8158 (tp40) cc_final: 0.7799 (tp40) REVERT: A 292 ASP cc_start: 0.9085 (t0) cc_final: 0.8647 (m-30) REVERT: A 611 GLU cc_start: 0.7752 (pm20) cc_final: 0.7471 (pp20) REVERT: B 52 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8532 (t160) REVERT: B 95 GLU cc_start: 0.8940 (tp30) cc_final: 0.8519 (tp30) REVERT: B 162 ARG cc_start: 0.8461 (mtm-85) cc_final: 0.8162 (mtt180) REVERT: B 185 ARG cc_start: 0.8790 (mmm160) cc_final: 0.8110 (ptt180) REVERT: B 314 MET cc_start: 0.7491 (ptt) cc_final: 0.7213 (pmm) REVERT: B 327 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8457 (t80) REVERT: B 426 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8586 (t80) REVERT: B 456 MET cc_start: 0.8949 (ttp) cc_final: 0.8535 (ttt) outliers start: 30 outliers final: 15 residues processed: 120 average time/residue: 1.2975 time to fit residues: 166.4777 Evaluate side-chains 108 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 1.984 ------------------------------------------------------------------------------- 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 446 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 579 LEU 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 99 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 209 ILE 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 350 LEU 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: 2.9990 chunk 70 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 0.0970 chunk 86 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.107516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.083340 restraints weight = 13023.137| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.27 r_work: 0.2971 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.8157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7530 Z= 0.122 Angle : 0.702 9.143 10251 Z= 0.336 Chirality : 0.044 0.299 1201 Planarity : 0.004 0.057 1258 Dihedral : 8.092 57.935 1242 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.72 % Favored : 93.17 % Rotamer: Outliers : 4.19 % Allowed : 25.95 % Favored : 69.86 % 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: 0.82 (0.25), residues: 486 sheet: 0.56 (0.68), residues: 51 loop : -1.98 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 124 HIS 0.004 0.001 HIS B 471 PHE 0.016 0.001 PHE B 250 TYR 0.016 0.001 TYR B 253 ARG 0.007 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 4) link_NAG-ASN : angle 3.04950 ( 12) link_BETA1-4 : bond 0.00551 ( 4) link_BETA1-4 : angle 2.35681 ( 12) hydrogen bonds : bond 0.03459 ( 292) hydrogen bonds : angle 4.01117 ( 852) SS BOND : bond 0.00324 ( 1) SS BOND : angle 2.27711 ( 2) covalent geometry : bond 0.00274 ( 7521) covalent geometry : angle 0.68997 (10225) *********************** 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 130 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.9040 (mtm) cc_final: 0.8791 (mtm) REVERT: A 269 GLN cc_start: 0.8224 (tp40) cc_final: 0.7894 (tp40) REVERT: A 292 ASP cc_start: 0.9100 (t0) cc_final: 0.8685 (m-30) REVERT: A 325 ASP cc_start: 0.9003 (m-30) cc_final: 0.8440 (p0) REVERT: A 366 ASN cc_start: 0.6480 (t0) cc_final: 0.6180 (t0) REVERT: A 572 ASP cc_start: 0.8656 (m-30) cc_final: 0.8304 (p0) REVERT: B 52 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8500 (t160) REVERT: B 95 GLU cc_start: 0.8919 (tp30) cc_final: 0.8503 (tp30) REVERT: B 162 ARG cc_start: 0.8448 (mtm-85) cc_final: 0.8182 (mtt180) REVERT: B 185 ARG cc_start: 0.8774 (mmm160) cc_final: 0.8094 (ptt180) REVERT: B 327 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8473 (t80) REVERT: B 426 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8630 (t80) REVERT: B 456 MET cc_start: 0.8941 (ttp) cc_final: 0.8574 (ttt) outliers start: 32 outliers final: 18 residues processed: 119 average time/residue: 0.8804 time to fit residues: 112.8730 Evaluate side-chains 108 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 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 98 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 125 ILE 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 327 PHE Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 487 SER 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: 0.8980 chunk 6 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** A 580 GLN B 406 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.104552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.080512 restraints weight = 13102.987| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.25 r_work: 0.2922 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.8714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7530 Z= 0.151 Angle : 0.764 12.629 10251 Z= 0.366 Chirality : 0.046 0.301 1201 Planarity : 0.004 0.057 1258 Dihedral : 7.949 57.612 1242 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.93 % Favored : 92.96 % Rotamer: Outliers : 4.46 % Allowed : 26.74 % Favored : 68.81 % 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: -0.41 (0.28), residues: 923 helix: 0.85 (0.24), residues: 490 sheet: 0.59 (0.68), residues: 51 loop : -1.94 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 469 HIS 0.005 0.001 HIS B 471 PHE 0.015 0.001 PHE B 250 TYR 0.014 0.002 TYR B 253 ARG 0.007 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 4) link_NAG-ASN : angle 3.08513 ( 12) link_BETA1-4 : bond 0.00466 ( 4) link_BETA1-4 : angle 2.31366 ( 12) hydrogen bonds : bond 0.03909 ( 292) hydrogen bonds : angle 4.05780 ( 852) SS BOND : bond 0.00401 ( 1) SS BOND : angle 2.25067 ( 2) covalent geometry : bond 0.00351 ( 7521) covalent geometry : angle 0.75253 (10225) *********************** 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 129 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 0.838 Fit side-chains REVERT: A 269 GLN cc_start: 0.8411 (tp40) cc_final: 0.8197 (tp40) REVERT: A 292 ASP cc_start: 0.9114 (t0) cc_final: 0.8695 (m-30) REVERT: A 325 ASP cc_start: 0.9041 (m-30) cc_final: 0.8382 (p0) REVERT: A 366 ASN cc_start: 0.6720 (t0) cc_final: 0.6439 (t0) REVERT: B 52 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8444 (t160) REVERT: B 95 GLU cc_start: 0.8888 (tp30) cc_final: 0.8398 (tp30) REVERT: B 162 ARG cc_start: 0.8545 (mtm-85) cc_final: 0.8240 (mtt180) REVERT: B 185 ARG cc_start: 0.8787 (mmm160) cc_final: 0.8088 (ptt180) REVERT: B 260 ASP cc_start: 0.8826 (t0) cc_final: 0.8486 (p0) REVERT: B 340 LEU cc_start: 0.9249 (tt) cc_final: 0.9038 (tp) REVERT: B 426 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8805 (t80) REVERT: B 436 PHE cc_start: 0.8101 (m-10) cc_final: 0.7827 (t80) REVERT: B 456 MET cc_start: 0.8984 (ttp) cc_final: 0.8640 (ttt) REVERT: B 469 TRP cc_start: 0.7381 (OUTLIER) cc_final: 0.7125 (t60) outliers start: 34 outliers final: 15 residues processed: 117 average time/residue: 1.0845 time to fit residues: 137.1515 Evaluate side-chains 104 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 445 PHE Chi-restraints excluded: chain A residue 446 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 98 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain B residue 487 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 74 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3451 r_free = 0.3451 target = 0.105018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.081108 restraints weight = 13220.132| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.26 r_work: 0.2931 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.8981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7530 Z= 0.137 Angle : 0.740 10.441 10251 Z= 0.352 Chirality : 0.046 0.299 1201 Planarity : 0.004 0.058 1258 Dihedral : 7.827 57.214 1242 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.04 % Favored : 92.85 % Rotamer: Outliers : 2.75 % Allowed : 28.70 % Favored : 68.55 % 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: -0.33 (0.28), residues: 923 helix: 0.98 (0.25), residues: 489 sheet: 0.64 (0.70), residues: 51 loop : -2.00 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 124 HIS 0.002 0.001 HIS B 358 PHE 0.014 0.001 PHE B 250 TYR 0.015 0.001 TYR A 554 ARG 0.008 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 4) link_NAG-ASN : angle 3.04718 ( 12) link_BETA1-4 : bond 0.00461 ( 4) link_BETA1-4 : angle 2.35209 ( 12) hydrogen bonds : bond 0.03676 ( 292) hydrogen bonds : angle 4.08441 ( 852) SS BOND : bond 0.00344 ( 1) SS BOND : angle 2.20121 ( 2) covalent geometry : bond 0.00319 ( 7521) covalent geometry : angle 0.72820 (10225) ********************** 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 112 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.869 Fit side-chains REVERT: A 292 ASP cc_start: 0.9133 (t0) cc_final: 0.8805 (m-30) REVERT: A 325 ASP cc_start: 0.9081 (m-30) cc_final: 0.8452 (p0) REVERT: A 366 ASN cc_start: 0.6820 (t0) cc_final: 0.6502 (t0) REVERT: B 52 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8513 (t160) REVERT: B 95 GLU cc_start: 0.8889 (tp30) cc_final: 0.8420 (tp30) REVERT: B 162 ARG cc_start: 0.8492 (mtm-85) cc_final: 0.8208 (mtt180) REVERT: B 185 ARG cc_start: 0.8751 (mmm160) cc_final: 0.8053 (ptt180) REVERT: B 426 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8816 (t80) REVERT: B 436 PHE cc_start: 0.8084 (m-10) cc_final: 0.7861 (t80) REVERT: B 456 MET cc_start: 0.8977 (ttp) cc_final: 0.8679 (ttt) REVERT: B 469 TRP cc_start: 0.7177 (OUTLIER) cc_final: 0.6698 (t60) REVERT: B 490 MET cc_start: 0.7864 (ttm) cc_final: 0.7588 (ttm) outliers start: 21 outliers final: 13 residues processed: 105 average time/residue: 0.9842 time to fit residues: 110.9178 Evaluate side-chains 96 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 189 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 B residue 52 ASN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain B residue 487 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 59 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.107550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.082948 restraints weight = 12772.980| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.16 r_work: 0.2982 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.9168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7530 Z= 0.129 Angle : 0.761 11.619 10251 Z= 0.360 Chirality : 0.046 0.301 1201 Planarity : 0.005 0.056 1258 Dihedral : 7.701 56.490 1242 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.04 % Favored : 92.85 % Rotamer: Outliers : 2.88 % Allowed : 28.70 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.29), residues: 923 helix: 1.08 (0.25), residues: 488 sheet: 0.67 (0.70), residues: 51 loop : -1.99 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 124 HIS 0.002 0.000 HIS B 358 PHE 0.013 0.001 PHE B 250 TYR 0.027 0.001 TYR B 253 ARG 0.009 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 4) link_NAG-ASN : angle 2.98222 ( 12) link_BETA1-4 : bond 0.00497 ( 4) link_BETA1-4 : angle 2.28406 ( 12) hydrogen bonds : bond 0.03479 ( 292) hydrogen bonds : angle 4.05216 ( 852) SS BOND : bond 0.00279 ( 1) SS BOND : angle 2.08269 ( 2) covalent geometry : bond 0.00292 ( 7521) covalent geometry : angle 0.75015 (10225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5070.00 seconds wall clock time: 90 minutes 2.69 seconds (5402.69 seconds total)