Starting phenix.real_space_refine on Fri Sep 11 04:36:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cmi_30407/09_2026/7cmi_30407.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cmi_30407/09_2026/7cmi_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7cmi_30407/09_2026/7cmi_30407.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cmi_30407/09_2026/7cmi_30407.cif" model { file = "/net/cci-nas-00/data/ceres_data/7cmi_30407/09_2026/7cmi_30407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cmi_30407/09_2026/7cmi_30407.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cmi_30407/09_2026/7cmi_30407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cmi_30407/09_2026/7cmi_30407.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'GLU:plan': 4, 'TYR:plan': 1, 'PHE:plan': 3, 'TRP:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1} 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 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 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 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 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: 1.64, per 1000 atoms: 0.22 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: 0.65 Conformation dependent library (CDL) restraints added in 396.0 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: 0.19 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: 1.06 Time building geometry restraints manager: 0.88 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 - 17.59: 3856 17.59 - 35.18: 378 35.18 - 52.76: 97 52.76 - 70.35: 15 70.35 - 87.94: 4 Dihedral angle restraints: 4350 sinusoidal: 1698 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 4347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1178 0.134 - 0.269: 20 0.269 - 0.403: 2 0.403 - 0.538: 0 0.538 - 0.672: 1 Chirality restraints: 1201 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 366 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CB VAL B 493 " pdb=" CA VAL B 493 " pdb=" CG1 VAL B 493 " pdb=" CG2 VAL B 493 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 425 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 1198 not shown) Planarity restraints: 1262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 228 " -0.056 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO B 229 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 618 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO A 619 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 619 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 619 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 131 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO B 132 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " -0.030 5.00e-02 4.00e+02 ... (remaining 1259 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 35 2.50 - 3.10: 4426 3.10 - 3.70: 10892 3.70 - 4.30: 15771 4.30 - 4.90: 25638 Nonbonded interactions: 56762 Sorted by model distance: nonbonded pdb=" O THR B 381 " pdb=" O SER B 382 " model vdw 1.904 3.040 nonbonded pdb=" OG1 THR B 381 " pdb=" N SER B 382 " model vdw 2.246 3.120 nonbonded pdb=" O PHE B 243 " pdb=" CB LEU B 601 " model vdw 2.248 3.440 nonbonded pdb=" O LEU B 379 " pdb=" N THR B 381 " model vdw 2.258 3.120 nonbonded pdb=" OH TYR B 396 " pdb=" O HOH B 701 " model vdw 2.262 3.040 ... (remaining 56757 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.910 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 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 : 15.070 87.937 2647 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG A 349 TYR 0.016 0.002 TYR A 313 PHE 0.023 0.002 PHE B 335 TRP 0.021 0.002 TRP B 124 HIS 0.006 0.001 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.32 ( 7521) covalent geometry : angle 1.01217 / 0.55 (10225) SS BOND : bond 0.00165 / 0.09 ( 1) SS BOND : angle 1.79920 / 0.82 ( 2) hydrogen bonds : bond 0.34454 / 22.73 ( 292) hydrogen bonds : angle 10.33981 / 7.23 ( 852) link_BETA1-4 : bond 0.01223 / 0.58 ( 4) link_BETA1-4 : angle 3.25152 / 1.93 ( 12) link_NAG-ASN : bond 0.00364 / 0.17 ( 4) link_NAG-ASN : angle 4.39518 / 2.27 ( 12) *********************** 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 : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 500 ILE cc_start: 0.6211 (mt) cc_final: 0.6000 (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: 0.3357 time to fit residues: 94.5034 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 : 0.245 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.0870 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.109766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.086036 restraints weight = 12901.384| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.25 r_work: 0.3041 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7530 Z= 0.174 Angle : 0.806 10.270 10251 Z= 0.397 Chirality : 0.046 0.282 1201 Planarity : 0.006 0.070 1258 Dihedral : 9.865 59.548 1063 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.72 % Favored : 93.17 % Rotamer: Outliers : 4.33 % Allowed : 19.00 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.95 (0.22), residues: 923 helix: -2.51 (0.19), residues: 470 sheet: -0.37 (0.62), residues: 67 loop : -3.09 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 346 TYR 0.016 0.002 TYR B 93 PHE 0.026 0.002 PHE B 250 TRP 0.016 0.002 TRP A 338 HIS 0.002 0.001 HIS A 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 7521) covalent geometry : angle 0.79698 / 0.40 (10225) SS BOND : bond 0.00430 / 0.23 ( 1) SS BOND : angle 2.85206 / 1.45 ( 2) hydrogen bonds : bond 0.05984 / 3.96 ( 292) hydrogen bonds : angle 4.98171 / 3.48 ( 852) link_BETA1-4 : bond 0.00634 / 0.32 ( 4) link_BETA1-4 : angle 1.78596 / 1.09 ( 12) link_NAG-ASN : bond 0.00421 / 0.21 ( 4) link_NAG-ASN : angle 3.07951 / 1.67 ( 12) *********************** 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: 33 poor density : 161 time to evaluate : 0.350 Fit side-chains REVERT: A 360 PHE cc_start: 0.8009 (m-80) cc_final: 0.7704 (m-80) REVERT: B 262 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.7961 (m-80) REVERT: B 314 MET cc_start: 0.7176 (ptt) cc_final: 0.6696 (pmm) REVERT: B 347 GLU cc_start: 0.8422 (tp30) cc_final: 0.8106 (tp30) REVERT: B 380 VAL cc_start: 0.6167 (m) cc_final: 0.5765 (p) outliers start: 33 outliers final: 9 residues processed: 183 average time/residue: 0.3286 time to fit residues: 65.8840 Evaluate side-chains 139 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 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 61 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 62 optimal weight: 0.0030 chunk 7 optimal weight: 4.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.110750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.086926 restraints weight = 12880.679| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.27 r_work: 0.3045 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7530 Z= 0.158 Angle : 0.717 8.941 10251 Z= 0.353 Chirality : 0.045 0.287 1201 Planarity : 0.005 0.068 1258 Dihedral : 8.822 57.913 1058 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.83 % Favored : 93.07 % Rotamer: Outliers : 6.16 % Allowed : 19.92 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.25), residues: 923 helix: -1.21 (0.22), residues: 483 sheet: 0.35 (0.63), residues: 58 loop : -2.69 (0.27), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 212 TYR 0.037 0.002 TYR B 253 PHE 0.021 0.002 PHE A 337 TRP 0.019 0.002 TRP B 124 HIS 0.003 0.001 HIS A 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 7521) covalent geometry : angle 0.70768 / 0.35 (10225) SS BOND : bond 0.00369 / 0.19 ( 1) SS BOND : angle 2.44869 / 1.17 ( 2) hydrogen bonds : bond 0.05085 / 3.32 ( 292) hydrogen bonds : angle 4.41994 / 3.13 ( 852) link_BETA1-4 : bond 0.00438 / 0.19 ( 4) link_BETA1-4 : angle 1.89887 / 1.16 ( 12) link_NAG-ASN : bond 0.00534 / 0.26 ( 4) link_NAG-ASN : angle 2.71185 / 1.50 ( 12) *********************** 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 190 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 0.284 Fit side-chains REVERT: A 391 SER cc_start: 0.8368 (m) cc_final: 0.7931 (p) REVERT: B 185 ARG cc_start: 0.8544 (mmm160) cc_final: 0.7680 (ptm160) REVERT: B 294 GLN cc_start: 0.8546 (tp40) cc_final: 0.8221 (tp-100) REVERT: B 314 MET cc_start: 0.7095 (ptt) cc_final: 0.6581 (pmm) REVERT: B 327 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.8099 (t80) REVERT: B 347 GLU cc_start: 0.8469 (tp30) cc_final: 0.7996 (tt0) REVERT: B 384 MET cc_start: 0.8051 (mmm) cc_final: 0.7021 (tmm) REVERT: B 426 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7933 (t80) outliers start: 47 outliers final: 13 residues processed: 171 average time/residue: 0.3455 time to fit residues: 64.4954 Evaluate side-chains 132 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 444 SER Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 304 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 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 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.0170 chunk 71 optimal weight: 7.9990 chunk 23 optimal weight: 0.0170 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3567 r_free = 0.3567 target = 0.112242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.088457 restraints weight = 12995.677| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.29 r_work: 0.3084 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5580 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= 0.120 Angle : 0.672 8.744 10251 Z= 0.321 Chirality : 0.044 0.276 1201 Planarity : 0.004 0.065 1258 Dihedral : 8.254 59.831 1056 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.39 % Favored : 93.50 % Rotamer: Outliers : 5.11 % Allowed : 22.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.26), residues: 923 helix: -0.43 (0.23), residues: 485 sheet: 0.41 (0.66), residues: 53 loop : -2.35 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.024 0.001 TYR B 253 PHE 0.013 0.001 PHE A 337 TRP 0.015 0.001 TRP B 124 HIS 0.001 0.000 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 7521) covalent geometry : angle 0.66336 / 0.32 (10225) SS BOND : bond 0.00285 / 0.15 ( 1) SS BOND : angle 2.12638 / 1.04 ( 2) hydrogen bonds : bond 0.03730 / 2.42 ( 292) hydrogen bonds : angle 4.22445 / 3.00 ( 852) link_BETA1-4 : bond 0.00556 / 0.25 ( 4) link_BETA1-4 : angle 1.61348 / 0.97 ( 12) link_NAG-ASN : bond 0.00319 / 0.16 ( 4) link_NAG-ASN : angle 2.66383 / 1.45 ( 12) *********************** 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 156 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.297 Fit side-chains REVERT: B 52 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8403 (t160) REVERT: B 171 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8628 (tm) REVERT: B 294 GLN cc_start: 0.8449 (tp40) cc_final: 0.8097 (tp-100) REVERT: B 314 MET cc_start: 0.7253 (ptt) cc_final: 0.6867 (pmm) REVERT: B 327 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.8051 (t80) REVERT: B 361 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7454 (pmt170) REVERT: B 426 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8138 (t80) REVERT: B 456 MET cc_start: 0.8832 (ttp) cc_final: 0.8551 (ttt) outliers start: 39 outliers final: 8 residues processed: 143 average time/residue: 0.3786 time to fit residues: 58.8381 Evaluate side-chains 119 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 259 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 48 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 1 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 84 optimal weight: 0.1980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.111518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.087551 restraints weight = 13002.196| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.30 r_work: 0.3067 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.6299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 7530 Z= 0.124 Angle : 0.661 7.993 10251 Z= 0.318 Chirality : 0.043 0.275 1201 Planarity : 0.004 0.063 1258 Dihedral : 7.582 59.202 1056 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.04 % Favored : 92.85 % Rotamer: Outliers : 5.50 % Allowed : 23.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.27), residues: 923 helix: 0.05 (0.24), residues: 484 sheet: 0.59 (0.64), residues: 53 loop : -2.26 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 346 TYR 0.026 0.002 TYR A 469 PHE 0.013 0.001 PHE B 433 TRP 0.014 0.001 TRP B 124 HIS 0.002 0.001 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 7521) covalent geometry : angle 0.65145 / 0.32 (10225) SS BOND : bond 0.00261 / 0.14 ( 1) SS BOND : angle 2.56619 / 1.25 ( 2) hydrogen bonds : bond 0.03845 / 2.49 ( 292) hydrogen bonds : angle 4.11326 / 2.93 ( 852) link_BETA1-4 : bond 0.00483 / 0.22 ( 4) link_BETA1-4 : angle 1.78073 / 1.09 ( 12) link_NAG-ASN : bond 0.00368 / 0.18 ( 4) link_NAG-ASN : angle 2.61040 / 1.45 ( 12) *********************** 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 163 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 0.215 Fit side-chains REVERT: A 611 GLU cc_start: 0.7843 (pm20) cc_final: 0.7298 (pp20) REVERT: B 52 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8504 (t160) REVERT: B 53 ILE cc_start: 0.7660 (mm) cc_final: 0.7325 (mt) REVERT: B 162 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.8025 (mtt180) REVERT: B 171 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8949 (tm) REVERT: B 294 GLN cc_start: 0.8369 (tp40) cc_final: 0.8038 (tp-100) REVERT: B 314 MET cc_start: 0.7474 (ptt) cc_final: 0.6954 (pmm) REVERT: B 327 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.8172 (t80) REVERT: B 346 ARG cc_start: 0.8069 (ttm-80) cc_final: 0.7820 (ttm-80) REVERT: B 361 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7577 (pmt170) REVERT: B 426 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8163 (t80) REVERT: B 440 PHE cc_start: 0.8431 (m-80) cc_final: 0.8130 (m-10) REVERT: B 456 MET cc_start: 0.8863 (ttp) cc_final: 0.8585 (ttt) outliers start: 42 outliers final: 13 residues processed: 152 average time/residue: 0.3694 time to fit residues: 61.0549 Evaluate side-chains 122 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 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 162 ARG Chi-restraints excluded: chain B residue 164 LEU 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 349 HIS Chi-restraints excluded: chain B residue 361 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 31 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3542 r_free = 0.3542 target = 0.110437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.086319 restraints weight = 13023.684| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.29 r_work: 0.3048 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.6996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7530 Z= 0.131 Angle : 0.669 9.495 10251 Z= 0.321 Chirality : 0.044 0.269 1201 Planarity : 0.004 0.059 1258 Dihedral : 7.356 58.991 1056 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.61 % Favored : 93.28 % Rotamer: Outliers : 5.50 % Allowed : 23.59 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.27), residues: 923 helix: 0.35 (0.24), residues: 485 sheet: 0.63 (0.65), residues: 53 loop : -2.17 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 346 TYR 0.019 0.001 TYR A 554 PHE 0.024 0.001 PHE B 250 TRP 0.012 0.001 TRP B 124 HIS 0.001 0.001 HIS A 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 7521) covalent geometry : angle 0.66070 / 0.32 (10225) SS BOND : bond 0.00309 / 0.16 ( 1) SS BOND : angle 2.60706 / 1.29 ( 2) hydrogen bonds : bond 0.03718 / 2.39 ( 292) hydrogen bonds : angle 4.04973 / 2.87 ( 852) link_BETA1-4 : bond 0.00674 / 0.31 ( 4) link_BETA1-4 : angle 1.67072 / 1.01 ( 12) link_NAG-ASN : bond 0.00277 / 0.14 ( 4) link_NAG-ASN : angle 2.62243 / 1.44 ( 12) *********************** 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 154 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 112 time to evaluate : 0.290 Fit side-chains REVERT: A 269 GLN cc_start: 0.7829 (tp40) cc_final: 0.7389 (tp40) REVERT: A 471 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8530 (t70) REVERT: A 572 ASP cc_start: 0.8601 (m-30) cc_final: 0.8308 (p0) REVERT: A 611 GLU cc_start: 0.7876 (pm20) cc_final: 0.7459 (pp20) REVERT: B 52 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8466 (t160) REVERT: B 162 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7969 (mtt180) REVERT: B 203 ILE cc_start: 0.8781 (pt) cc_final: 0.8573 (mp) REVERT: B 208 GLN cc_start: 0.7117 (pt0) cc_final: 0.6795 (pt0) REVERT: B 314 MET cc_start: 0.7634 (ptt) cc_final: 0.7176 (pmm) REVERT: B 327 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8394 (t80) REVERT: B 346 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7885 (ttm-80) REVERT: B 383 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7287 (p0) REVERT: B 396 TYR cc_start: 0.8866 (m-80) cc_final: 0.8615 (m-80) REVERT: B 426 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8475 (t80) REVERT: B 440 PHE cc_start: 0.8537 (m-80) cc_final: 0.8224 (m-10) REVERT: B 456 MET cc_start: 0.8939 (ttp) cc_final: 0.8493 (ttt) outliers start: 42 outliers final: 14 residues processed: 140 average time/residue: 0.4115 time to fit residues: 62.2485 Evaluate side-chains 119 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 445 PHE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 510 VAL 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 162 ARG 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 383 ASP 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 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 43 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 72 optimal weight: 0.0670 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 GLN B 349 HIS B 406 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.111065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.086607 restraints weight = 12839.755| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.19 r_work: 0.3048 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.7470 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= 0.122 Angle : 0.678 9.155 10251 Z= 0.326 Chirality : 0.044 0.276 1201 Planarity : 0.004 0.058 1258 Dihedral : 7.143 57.526 1056 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.93 % Favored : 92.96 % Rotamer: Outliers : 4.59 % Allowed : 25.16 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.28), residues: 923 helix: 0.50 (0.24), residues: 486 sheet: 0.63 (0.67), residues: 51 loop : -2.07 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.020 0.001 TYR A 469 PHE 0.023 0.001 PHE B 250 TRP 0.014 0.001 TRP B 124 HIS 0.004 0.001 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 7521) covalent geometry : angle 0.66925 / 0.32 (10225) SS BOND : bond 0.00247 / 0.13 ( 1) SS BOND : angle 2.28884 / 1.13 ( 2) hydrogen bonds : bond 0.03619 / 2.33 ( 292) hydrogen bonds : angle 4.11674 / 2.90 ( 852) link_BETA1-4 : bond 0.00668 / 0.31 ( 4) link_BETA1-4 : angle 1.85916 / 1.14 ( 12) link_NAG-ASN : bond 0.00379 / 0.18 ( 4) link_NAG-ASN : angle 2.53975 / 1.40 ( 12) *********************** 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 150 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.8983 (mtm) cc_final: 0.8782 (mtm) REVERT: A 269 GLN cc_start: 0.7855 (tp40) cc_final: 0.7443 (tp40) REVERT: A 292 ASP cc_start: 0.9038 (t0) cc_final: 0.8605 (m-30) REVERT: A 325 ASP cc_start: 0.8969 (m-30) cc_final: 0.8302 (p0) REVERT: A 451 LEU cc_start: 0.8901 (tt) cc_final: 0.8680 (tp) REVERT: A 572 ASP cc_start: 0.8528 (m-30) cc_final: 0.8294 (p0) REVERT: A 611 GLU cc_start: 0.7779 (pm20) cc_final: 0.7578 (pp20) REVERT: B 162 ARG cc_start: 0.8440 (mtm-85) cc_final: 0.8033 (mtt180) REVERT: B 185 ARG cc_start: 0.8733 (mmm160) cc_final: 0.8063 (ptt180) REVERT: B 314 MET cc_start: 0.7390 (ptt) cc_final: 0.7140 (pmm) REVERT: B 327 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8519 (t80) REVERT: B 346 ARG cc_start: 0.8286 (ttm-80) cc_final: 0.8056 (ttm-80) REVERT: B 426 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8504 (t80) REVERT: B 456 MET cc_start: 0.8934 (ttp) cc_final: 0.8574 (ttt) REVERT: B 469 TRP cc_start: 0.6943 (t-100) cc_final: 0.6538 (t-100) outliers start: 35 outliers final: 18 residues processed: 139 average time/residue: 0.4090 time to fit residues: 61.5172 Evaluate side-chains 120 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 399 LEU Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 446 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 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 209 ILE 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 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 54 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 79 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3519 r_free = 0.3519 target = 0.108528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.083749 restraints weight = 12971.126| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.21 r_work: 0.2994 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.8235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7530 Z= 0.146 Angle : 0.731 9.851 10251 Z= 0.352 Chirality : 0.044 0.268 1201 Planarity : 0.004 0.056 1258 Dihedral : 7.085 56.910 1056 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.15 % Favored : 92.74 % Rotamer: Outliers : 4.06 % Allowed : 25.95 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.28), residues: 923 helix: 0.62 (0.24), residues: 488 sheet: 0.70 (0.69), residues: 51 loop : -1.99 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.018 0.001 TYR A 554 PHE 0.017 0.001 PHE B 250 TRP 0.010 0.001 TRP B 124 HIS 0.002 0.000 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 7521) covalent geometry : angle 0.72247 / 0.35 (10225) SS BOND : bond 0.00375 / 0.20 ( 1) SS BOND : angle 2.30509 / 1.12 ( 2) hydrogen bonds : bond 0.03928 / 2.50 ( 292) hydrogen bonds : angle 4.05457 / 2.86 ( 852) link_BETA1-4 : bond 0.00202 / 0.09 ( 4) link_BETA1-4 : angle 1.83748 / 1.11 ( 12) link_NAG-ASN : bond 0.00326 / 0.16 ( 4) link_NAG-ASN : angle 2.63880 / 1.44 ( 12) *********************** 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 135 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.285 Fit side-chains REVERT: A 197 MET cc_start: 0.9038 (mtm) cc_final: 0.8789 (mtm) REVERT: A 292 ASP cc_start: 0.9091 (t0) cc_final: 0.8651 (m-30) REVERT: A 325 ASP cc_start: 0.8948 (m-30) cc_final: 0.8385 (p0) REVERT: A 611 GLU cc_start: 0.8029 (pm20) cc_final: 0.7822 (pp20) REVERT: B 162 ARG cc_start: 0.8552 (mtm-85) cc_final: 0.8317 (mtt180) REVERT: B 185 ARG cc_start: 0.8731 (mmm160) cc_final: 0.8157 (ptt180) REVERT: B 260 ASP cc_start: 0.8848 (t0) cc_final: 0.8462 (p0) REVERT: B 314 MET cc_start: 0.7332 (ptt) cc_final: 0.7130 (pmm) REVERT: B 327 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8468 (t80) REVERT: B 347 GLU cc_start: 0.8348 (tt0) cc_final: 0.8028 (tp30) REVERT: B 426 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8651 (t80) REVERT: B 436 PHE cc_start: 0.7996 (m-10) cc_final: 0.7648 (t80) REVERT: B 456 MET cc_start: 0.9000 (ttp) cc_final: 0.8603 (ttt) outliers start: 31 outliers final: 15 residues processed: 125 average time/residue: 0.4395 time to fit residues: 59.3129 Evaluate side-chains 100 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 597 LEU 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 304 VAL Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 327 PHE 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 82 optimal weight: 0.7980 chunk 57 optimal weight: 0.0770 chunk 15 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 67 optimal weight: 0.0770 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 0.0370 chunk 39 optimal weight: 2.9990 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 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 = 0.3535 r_free = 0.3535 target = 0.109843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.085347 restraints weight = 12671.229| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.16 r_work: 0.3019 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.8340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7530 Z= 0.118 Angle : 0.689 8.873 10251 Z= 0.333 Chirality : 0.044 0.264 1201 Planarity : 0.004 0.056 1258 Dihedral : 6.948 56.180 1056 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.61 % Favored : 93.28 % Rotamer: Outliers : 3.15 % Allowed : 27.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.28), residues: 923 helix: 0.80 (0.24), residues: 487 sheet: 0.76 (0.70), residues: 51 loop : -2.00 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.015 0.001 TYR B 253 PHE 0.014 0.001 PHE B 250 TRP 0.016 0.001 TRP B 124 HIS 0.002 0.001 HIS B 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 7521) covalent geometry : angle 0.67872 / 0.33 (10225) SS BOND : bond 0.00284 / 0.15 ( 1) SS BOND : angle 2.12130 / 1.06 ( 2) hydrogen bonds : bond 0.03415 / 2.19 ( 292) hydrogen bonds : angle 4.05895 / 2.85 ( 852) link_BETA1-4 : bond 0.00447 / 0.21 ( 4) link_BETA1-4 : angle 1.81503 / 1.10 ( 12) link_NAG-ASN : bond 0.00437 / 0.22 ( 4) link_NAG-ASN : angle 2.93748 / 1.64 ( 12) *********************** 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 117 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.283 Fit side-chains REVERT: A 292 ASP cc_start: 0.9072 (t0) cc_final: 0.8671 (m-30) REVERT: A 325 ASP cc_start: 0.8944 (m-30) cc_final: 0.8298 (p0) REVERT: A 366 ASN cc_start: 0.6525 (t0) cc_final: 0.6245 (t0) REVERT: A 583 ASP cc_start: 0.8433 (m-30) cc_final: 0.7651 (p0) REVERT: A 611 GLU cc_start: 0.8040 (pm20) cc_final: 0.7827 (pp20) REVERT: B 162 ARG cc_start: 0.8528 (mtm-85) cc_final: 0.8278 (mtt180) REVERT: B 185 ARG cc_start: 0.8754 (mmm160) cc_final: 0.8149 (ptt180) REVERT: B 260 ASP cc_start: 0.8726 (t0) cc_final: 0.8459 (p0) REVERT: B 327 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8498 (t80) REVERT: B 347 GLU cc_start: 0.8308 (tt0) cc_final: 0.7988 (tp30) REVERT: B 426 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8623 (t80) REVERT: B 436 PHE cc_start: 0.8037 (m-10) cc_final: 0.7632 (t80) REVERT: B 456 MET cc_start: 0.8967 (ttp) cc_final: 0.8624 (ttt) outliers start: 24 outliers final: 14 residues processed: 109 average time/residue: 0.3752 time to fit residues: 44.3649 Evaluate side-chains 102 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 399 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 597 LEU Chi-restraints excluded: chain B residue 76 LEU 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 327 PHE Chi-restraints excluded: chain B residue 426 PHE 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: 1.9990 chunk 84 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 89 optimal weight: 0.0970 chunk 28 optimal weight: 0.0980 chunk 72 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS B 406 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.109543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.084929 restraints weight = 12765.183| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.17 r_work: 0.3007 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.8573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7530 Z= 0.122 Angle : 0.705 11.847 10251 Z= 0.340 Chirality : 0.044 0.247 1201 Planarity : 0.004 0.059 1258 Dihedral : 6.840 55.344 1056 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.93 % Favored : 92.96 % Rotamer: Outliers : 2.62 % Allowed : 28.18 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.28), residues: 923 helix: 0.94 (0.25), residues: 486 sheet: 0.60 (0.70), residues: 51 loop : -1.98 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 346 TYR 0.016 0.001 TYR B 253 PHE 0.014 0.001 PHE B 250 TRP 0.036 0.001 TRP B 469 HIS 0.006 0.001 HIS B 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 7521) covalent geometry : angle 0.69626 / 0.34 (10225) SS BOND : bond 0.00318 / 0.17 ( 1) SS BOND : angle 2.14750 / 1.07 ( 2) hydrogen bonds : bond 0.03441 / 2.19 ( 292) hydrogen bonds : angle 4.04969 / 2.84 ( 852) link_BETA1-4 : bond 0.00530 / 0.25 ( 4) link_BETA1-4 : angle 1.77118 / 1.08 ( 12) link_NAG-ASN : bond 0.00295 / 0.15 ( 4) link_NAG-ASN : angle 2.65236 / 1.49 ( 12) ********************** 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 108 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.280 Fit side-chains REVERT: A 292 ASP cc_start: 0.9077 (t0) cc_final: 0.8753 (m-30) REVERT: A 325 ASP cc_start: 0.8955 (m-30) cc_final: 0.8329 (p0) REVERT: A 366 ASN cc_start: 0.6645 (t0) cc_final: 0.6353 (t0) REVERT: A 583 ASP cc_start: 0.8479 (m-30) cc_final: 0.7661 (p0) REVERT: A 611 GLU cc_start: 0.8084 (pm20) cc_final: 0.7859 (pp20) REVERT: B 162 ARG cc_start: 0.8516 (mtm-85) cc_final: 0.8116 (mtt180) REVERT: B 185 ARG cc_start: 0.8779 (mmm160) cc_final: 0.8083 (ptt180) REVERT: B 260 ASP cc_start: 0.8801 (t0) cc_final: 0.8598 (p0) REVERT: B 327 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8505 (t80) REVERT: B 340 LEU cc_start: 0.9271 (tt) cc_final: 0.9017 (tp) REVERT: B 426 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8632 (t80) REVERT: B 436 PHE cc_start: 0.8018 (m-10) cc_final: 0.7752 (t80) REVERT: B 456 MET cc_start: 0.8979 (ttp) cc_final: 0.8650 (ttt) REVERT: B 469 TRP cc_start: 0.7579 (t60) cc_final: 0.7215 (t60) outliers start: 20 outliers final: 14 residues processed: 101 average time/residue: 0.4028 time to fit residues: 44.0249 Evaluate side-chains 100 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 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 597 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 426 PHE 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 41 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 43 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3514 r_free = 0.3514 target = 0.108923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.084739 restraints weight = 12893.820| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.22 r_work: 0.3007 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.8849 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= 0.123 Angle : 0.712 8.957 10251 Z= 0.342 Chirality : 0.044 0.276 1201 Planarity : 0.004 0.056 1258 Dihedral : 6.806 54.278 1056 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.15 % Favored : 92.74 % Rotamer: Outliers : 2.62 % Allowed : 28.18 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.28), residues: 923 helix: 0.95 (0.25), residues: 488 sheet: 0.48 (0.71), residues: 51 loop : -1.97 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.016 0.001 TYR B 253 PHE 0.013 0.001 PHE B 250 TRP 0.014 0.001 TRP B 469 HIS 0.002 0.000 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 7521) covalent geometry : angle 0.70494 / 0.34 (10225) SS BOND : bond 0.00310 / 0.16 ( 1) SS BOND : angle 2.11055 / 1.05 ( 2) hydrogen bonds : bond 0.03428 / 2.19 ( 292) hydrogen bonds : angle 4.03100 / 2.82 ( 852) link_BETA1-4 : bond 0.00607 / 0.28 ( 4) link_BETA1-4 : angle 1.72089 / 1.05 ( 12) link_NAG-ASN : bond 0.00242 / 0.12 ( 4) link_NAG-ASN : angle 2.50820 / 1.41 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2234.90 seconds wall clock time: 38 minutes 55.66 seconds (2335.66 seconds total)