Starting phenix.real_space_refine on Thu Jul 2 13:26:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cqk_30442/07_2026/7cqk_30442.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cqk_30442/07_2026/7cqk_30442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cqk_30442/07_2026/7cqk_30442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cqk_30442/07_2026/7cqk_30442.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cqk_30442/07_2026/7cqk_30442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cqk_30442/07_2026/7cqk_30442.map" } resolution = 3.3 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 22 atoms to isotropic. 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 4 5.49 5 S 51 5.16 5 C 5706 2.51 5 N 1482 2.21 5 O 1616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8859 Number of models: 1 Model: "" Number of chains: 7 Chain: "S" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3268 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 399} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 3907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3907 Classifications: {'peptide': 497} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 18, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1030 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 389 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'GE0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.11, per 1000 atoms: 0.24 Number of scatterers: 8859 At special positions: 0 Unit cell: (92.88, 82.08, 120.96, 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 51 16.00 P 4 15.00 O 1616 8.00 N 1482 7.00 C 5706 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 468.6 milliseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 44.7% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'S' and resid 54 through 61 Processing helix chain 'S' and resid 114 through 124 removed outlier: 3.524A pdb=" N SER S 124 " --> pdb=" O ALA S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 124 through 129 removed outlier: 3.529A pdb=" N TYR S 128 " --> pdb=" O SER S 124 " (cutoff:3.500A) Processing helix chain 'S' and resid 142 through 156 removed outlier: 3.875A pdb=" N LEU S 146 " --> pdb=" O PHE S 142 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA S 153 " --> pdb=" O GLU S 149 " (cutoff:3.500A) Processing helix chain 'S' and resid 192 through 203 removed outlier: 3.573A pdb=" N GLY S 198 " --> pdb=" O ALA S 194 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA S 201 " --> pdb=" O LYS S 197 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG S 203 " --> pdb=" O LEU S 199 " (cutoff:3.500A) Processing helix chain 'S' and resid 213 through 230 removed outlier: 4.107A pdb=" N LEU S 217 " --> pdb=" O ASP S 213 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU S 223 " --> pdb=" O ARG S 219 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN S 224 " --> pdb=" O LEU S 220 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU S 227 " --> pdb=" O GLU S 223 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN S 229 " --> pdb=" O GLU S 225 " (cutoff:3.500A) Processing helix chain 'S' and resid 257 through 262 removed outlier: 3.921A pdb=" N LYS S 262 " --> pdb=" O PRO S 258 " (cutoff:3.500A) Processing helix chain 'S' and resid 289 through 294 Processing helix chain 'S' and resid 321 through 326 removed outlier: 3.629A pdb=" N ASP S 326 " --> pdb=" O SER S 322 " (cutoff:3.500A) Processing helix chain 'S' and resid 327 through 332 Processing helix chain 'S' and resid 332 through 337 Processing helix chain 'S' and resid 345 through 359 removed outlier: 3.534A pdb=" N GLU S 351 " --> pdb=" O ALA S 347 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET S 356 " --> pdb=" O ALA S 352 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU S 357 " --> pdb=" O LEU S 353 " (cutoff:3.500A) Processing helix chain 'S' and resid 363 through 368 Processing helix chain 'S' and resid 368 through 377 removed outlier: 3.715A pdb=" N GLN S 372 " --> pdb=" O GLU S 368 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE S 373 " --> pdb=" O LYS S 369 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS S 374 " --> pdb=" O CYS S 370 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA S 376 " --> pdb=" O GLN S 372 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU S 377 " --> pdb=" O ILE S 373 " (cutoff:3.500A) Processing helix chain 'S' and resid 404 through 420 removed outlier: 3.928A pdb=" N ILE S 415 " --> pdb=" O LEU S 411 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET S 420 " --> pdb=" O VAL S 416 " (cutoff:3.500A) Processing helix chain 'S' and resid 454 through 467 removed outlier: 3.549A pdb=" N GLU S 458 " --> pdb=" O GLU S 454 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG S 459 " --> pdb=" O GLU S 455 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA S 460 " --> pdb=" O GLU S 456 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE S 464 " --> pdb=" O ALA S 460 " (cutoff:3.500A) Processing helix chain 'T' and resid 69 through 91 removed outlier: 3.711A pdb=" N LEU T 73 " --> pdb=" O LEU T 69 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR T 75 " --> pdb=" O ALA T 71 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL T 76 " --> pdb=" O VAL T 72 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR T 86 " --> pdb=" O THR T 82 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU T 87 " --> pdb=" O LEU T 83 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG T 88 " --> pdb=" O PHE T 84 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP T 89 " --> pdb=" O GLY T 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 130 through 134 removed outlier: 3.519A pdb=" N ASN T 133 " --> pdb=" O ILE T 130 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP T 134 " --> pdb=" O ARG T 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 130 through 134' Processing helix chain 'T' and resid 177 through 181 removed outlier: 4.303A pdb=" N PHE T 181 " --> pdb=" O TYR T 178 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 200 removed outlier: 3.611A pdb=" N TYR T 199 " --> pdb=" O VAL T 195 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY T 200 " --> pdb=" O LEU T 196 " (cutoff:3.500A) Processing helix chain 'T' and resid 214 through 228 removed outlier: 3.859A pdb=" N GLU T 218 " --> pdb=" O ASP T 214 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU T 222 " --> pdb=" O GLU T 218 " (cutoff:3.500A) Processing helix chain 'T' and resid 238 through 250 removed outlier: 3.603A pdb=" N ASN T 242 " --> pdb=" O GLY T 238 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER T 243 " --> pdb=" O PHE T 239 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET T 244 " --> pdb=" O ALA T 240 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE T 246 " --> pdb=" O ASN T 242 " (cutoff:3.500A) Proline residue: T 247 - end of helix Processing helix chain 'T' and resid 263 through 270 Processing helix chain 'T' and resid 285 through 293 removed outlier: 3.854A pdb=" N LEU T 291 " --> pdb=" O SER T 287 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 338 removed outlier: 3.957A pdb=" N LEU T 333 " --> pdb=" O GLU T 329 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS T 335 " --> pdb=" O ILE T 331 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS T 336 " --> pdb=" O ALA T 332 " (cutoff:3.500A) Processing helix chain 'T' and resid 357 through 363 removed outlier: 3.871A pdb=" N GLU T 361 " --> pdb=" O ARG T 357 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR T 362 " --> pdb=" O GLY T 358 " (cutoff:3.500A) Processing helix chain 'T' and resid 391 through 402 removed outlier: 3.790A pdb=" N TYR T 397 " --> pdb=" O GLU T 393 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THR T 400 " --> pdb=" O ASP T 396 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER T 402 " --> pdb=" O LEU T 398 " (cutoff:3.500A) Processing helix chain 'T' and resid 402 through 408 removed outlier: 4.018A pdb=" N VAL T 406 " --> pdb=" O SER T 402 " (cutoff:3.500A) Processing helix chain 'T' and resid 412 through 428 removed outlier: 3.704A pdb=" N GLU T 417 " --> pdb=" O PRO T 413 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN T 418 " --> pdb=" O PRO T 414 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE T 419 " --> pdb=" O VAL T 415 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER T 422 " --> pdb=" O GLN T 418 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N CYS T 425 " --> pdb=" O THR T 421 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE T 426 " --> pdb=" O SER T 422 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET T 427 " --> pdb=" O MET T 423 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY T 428 " --> pdb=" O LYS T 424 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 455 removed outlier: 3.626A pdb=" N GLN T 440 " --> pdb=" O LYS T 436 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU T 444 " --> pdb=" O GLN T 440 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR T 446 " --> pdb=" O LEU T 442 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG T 447 " --> pdb=" O ALA T 443 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU T 453 " --> pdb=" O PHE T 449 " (cutoff:3.500A) Processing helix chain 'T' and resid 476 through 489 removed outlier: 3.846A pdb=" N GLY T 480 " --> pdb=" O PRO T 476 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY T 483 " --> pdb=" O ILE T 479 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG T 484 " --> pdb=" O GLY T 480 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU T 487 " --> pdb=" O GLY T 483 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS T 488 " --> pdb=" O ARG T 484 " (cutoff:3.500A) Processing helix chain 'T' and resid 497 through 501 removed outlier: 4.476A pdb=" N ALA T 500 " --> pdb=" O GLY T 497 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 533 removed outlier: 3.539A pdb=" N THR T 523 " --> pdb=" O GLU T 519 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU T 527 " --> pdb=" O THR T 523 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU T 530 " --> pdb=" O LYS T 526 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP T 533 " --> pdb=" O ASP T 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 38 Processing helix chain 'A' and resid 47 through 66 removed outlier: 3.563A pdb=" N LEU A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 62 " --> pdb=" O MET A 58 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 90 through 93 Processing helix chain 'A' and resid 96 through 116 removed outlier: 3.698A pdb=" N PHE A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Proline residue: A 106 - end of helix removed outlier: 3.932A pdb=" N TYR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 114 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 115 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 136 removed outlier: 4.215A pdb=" N VAL A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 23 removed outlier: 3.604A pdb=" N PHE E 16 " --> pdb=" O GLN E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 55 removed outlier: 4.512A pdb=" N PHE E 37 " --> pdb=" O GLU E 33 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL E 42 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA E 48 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR E 50 " --> pdb=" O GLY E 46 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR E 51 " --> pdb=" O MET E 47 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 40 removed outlier: 3.754A pdb=" N LEU C 27 " --> pdb=" O TYR C 23 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE C 30 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'S' and resid 85 through 86 removed outlier: 4.148A pdb=" N VAL S 94 " --> pdb=" O SER S 86 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA S 425 " --> pdb=" O GLU S 99 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE S 101 " --> pdb=" O ALA S 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 160 through 164 removed outlier: 3.711A pdb=" N LEU S 302 " --> pdb=" O ILE S 271 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER S 304 " --> pdb=" O LEU S 273 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ARG S 240 " --> pdb=" O ARG S 270 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N PHE S 272 " --> pdb=" O ARG S 240 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE S 242 " --> pdb=" O PHE S 272 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE S 184 " --> pdb=" O PHE S 241 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL S 243 " --> pdb=" O ILE S 184 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE S 186 " --> pdb=" O VAL S 243 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL S 185 " --> pdb=" O LYS S 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 393 through 397 removed outlier: 3.865A pdb=" N PHE S 394 " --> pdb=" O VAL S 446 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE S 444 " --> pdb=" O LEU S 396 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR S 427 " --> pdb=" O ARG S 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'T' and resid 146 through 153 removed outlier: 3.504A pdb=" N VAL T 170 " --> pdb=" O VAL T 146 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ILE T 148 " --> pdb=" O LYS T 168 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS T 168 " --> pdb=" O ILE T 148 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU T 150 " --> pdb=" O ILE T 166 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE T 166 " --> pdb=" O GLU T 150 " (cutoff:3.500A) removed outlier: 11.339A pdb=" N GLN T 152 " --> pdb=" O GLY T 164 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N GLY T 164 " --> pdb=" O GLN T 152 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N GLY T 492 " --> pdb=" O GLY T 169 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE T 171 " --> pdb=" O GLY T 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 231 through 234 removed outlier: 3.909A pdb=" N ALA T 231 " --> pdb=" O GLY T 390 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY T 375 " --> pdb=" O TYR T 387 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LEU T 341 " --> pdb=" O VAL T 372 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N MET T 374 " --> pdb=" O LEU T 341 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU T 343 " --> pdb=" O MET T 374 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N THR T 376 " --> pdb=" O LEU T 343 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE T 310 " --> pdb=" O TYR T 340 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N TYR T 342 " --> pdb=" O ILE T 310 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE T 312 " --> pdb=" O TYR T 342 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASP T 344 " --> pdb=" O ILE T 312 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 471 through 472 removed outlier: 3.978A pdb=" N VAL T 494 " --> pdb=" O ARG T 509 " (cutoff:3.500A) 263 hydrogen bonds defined for protein. 765 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: 1.08 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2770 1.34 - 1.46: 2027 1.46 - 1.58: 4160 1.58 - 1.71: 10 1.71 - 1.83: 84 Bond restraints: 9051 Sorted by residual: bond pdb=" OBQ GE0 A 201 " pdb=" PAS GE0 A 201 " ideal model delta sigma weight residual 1.495 1.615 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" OBS GE0 A 201 " pdb=" PAQ GE0 A 201 " ideal model delta sigma weight residual 1.501 1.616 -0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" O3' GE0 A 201 " pdb=" PAY GE0 A 201 " ideal model delta sigma weight residual 1.728 1.618 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" O4P PLS T 601 " pdb=" P PLS T 601 " ideal model delta sigma weight residual 1.712 1.610 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" OBA GE0 A 201 " pdb=" PAY GE0 A 201 " ideal model delta sigma weight residual 1.521 1.610 -0.089 2.00e-02 2.50e+03 1.97e+01 ... (remaining 9046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 11692 2.84 - 5.68: 471 5.68 - 8.52: 67 8.52 - 11.35: 19 11.35 - 14.19: 9 Bond angle restraints: 12258 Sorted by residual: angle pdb=" C PHE T 498 " pdb=" N PRO T 499 " pdb=" CA PRO T 499 " ideal model delta sigma weight residual 119.84 130.70 -10.86 1.25e+00 6.40e-01 7.55e+01 angle pdb=" N GLU S 399 " pdb=" CA GLU S 399 " pdb=" C GLU S 399 " ideal model delta sigma weight residual 111.28 120.49 -9.21 1.09e+00 8.42e-01 7.15e+01 angle pdb=" N MET T 423 " pdb=" CA MET T 423 " pdb=" C MET T 423 " ideal model delta sigma weight residual 111.69 101.72 9.97 1.23e+00 6.61e-01 6.57e+01 angle pdb=" C GLU E 30 " pdb=" N PRO E 31 " pdb=" CA PRO E 31 " ideal model delta sigma weight residual 119.84 129.77 -9.93 1.25e+00 6.40e-01 6.32e+01 angle pdb=" N ASN S 212 " pdb=" CA ASN S 212 " pdb=" C ASN S 212 " ideal model delta sigma weight residual 112.86 121.12 -8.26 1.22e+00 6.72e-01 4.59e+01 ... (remaining 12253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 4636 17.47 - 34.94: 402 34.94 - 52.41: 248 52.41 - 69.89: 95 69.89 - 87.36: 12 Dihedral angle restraints: 5393 sinusoidal: 2163 harmonic: 3230 Sorted by residual: dihedral pdb=" C VAL T 372 " pdb=" N VAL T 372 " pdb=" CA VAL T 372 " pdb=" CB VAL T 372 " ideal model delta harmonic sigma weight residual -122.00 -134.83 12.83 0 2.50e+00 1.60e-01 2.63e+01 dihedral pdb=" N ARG S 189 " pdb=" C ARG S 189 " pdb=" CA ARG S 189 " pdb=" CB ARG S 189 " ideal model delta harmonic sigma weight residual 122.80 134.15 -11.35 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" N VAL T 372 " pdb=" C VAL T 372 " pdb=" CA VAL T 372 " pdb=" CB VAL T 372 " ideal model delta harmonic sigma weight residual 123.40 134.31 -10.91 0 2.50e+00 1.60e-01 1.90e+01 ... (remaining 5390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1004 0.080 - 0.160: 293 0.160 - 0.241: 54 0.241 - 0.321: 13 0.321 - 0.401: 9 Chirality restraints: 1373 Sorted by residual: chirality pdb=" CA VAL T 372 " pdb=" N VAL T 372 " pdb=" C VAL T 372 " pdb=" CB VAL T 372 " both_signs ideal model delta sigma weight residual False 2.44 2.04 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA ALA T 144 " pdb=" N ALA T 144 " pdb=" C ALA T 144 " pdb=" CB ALA T 144 " both_signs ideal model delta sigma weight residual False 2.48 2.09 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CA ARG S 189 " pdb=" N ARG S 189 " pdb=" C ARG S 189 " pdb=" CB ARG S 189 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 1370 not shown) Planarity restraints: 1547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE T 498 " 0.055 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO T 499 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO T 499 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO T 499 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU T 444 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.42e+00 pdb=" C GLU T 444 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU T 444 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN T 445 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU S 63 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.42e+00 pdb=" C GLU S 63 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU S 63 " -0.020 2.00e-02 2.50e+03 pdb=" N TRP S 64 " -0.018 2.00e-02 2.50e+03 ... (remaining 1544 not shown) Histogram of nonbonded interaction distances: 0.96 - 1.75: 5 1.75 - 2.54: 81 2.54 - 3.33: 10122 3.33 - 4.11: 19986 4.11 - 4.90: 38149 Warning: very small nonbonded interaction distances. Nonbonded interactions: 68343 Sorted by model distance: nonbonded pdb=" OG SER S 423 " pdb=" NH2 ARG S 459 " model vdw 0.963 3.120 nonbonded pdb=" O LEU T 91 " pdb=" NE1 TRP T 94 " model vdw 1.487 3.120 nonbonded pdb=" OD2 ASP T 344 " pdb=" CE MET T 374 " model vdw 1.568 3.460 nonbonded pdb=" CD1 LEU T 196 " pdb=" CB GLU T 417 " model vdw 1.668 3.860 nonbonded pdb=" CG LEU T 196 " pdb=" OE1 GLU T 417 " model vdw 1.735 3.470 ... (remaining 68338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.80 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.250 Find NCS groups from input model: 0.040 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 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 : 0.011 0.526 9052 Z= 0.728 Angle : 1.364 14.192 12258 Z= 0.815 Chirality : 0.082 0.401 1373 Planarity : 0.007 0.082 1547 Dihedral : 19.185 87.358 3325 Min Nonbonded Distance : 0.963 Molprobity Statistics. All-atom Clashscore : 30.94 Ramachandran Plot: Outliers : 1.00 % Allowed : 11.32 % Favored : 87.68 % Rotamer: Outliers : 21.66 % Allowed : 10.25 % Favored : 68.09 % Cbeta Deviations : 0.29 % 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: -5.35 (0.19), residues: 1104 helix: -4.21 (0.14), residues: 449 sheet: -2.77 (0.49), residues: 100 loop : -3.09 (0.22), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 445 TYR 0.047 0.002 TYR T 474 PHE 0.036 0.003 PHE T 280 TRP 0.022 0.002 TRP T 134 HIS 0.011 0.001 HIS S 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00956 / 0.47 ( 9051) covalent geometry : angle 1.36445 / 0.82 (12258) hydrogen bonds : bond 0.32662 / 22.11 ( 263) hydrogen bonds : angle 10.64614 / 7.54 ( 765) Misc. bond : bond 0.52590 / 27.68 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 208 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 57 LYS cc_start: 0.8370 (mtmt) cc_final: 0.7886 (tmtt) REVERT: S 160 GLU cc_start: 0.7702 (tt0) cc_final: 0.7500 (tt0) REVERT: S 203 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7676 (mmt-90) REVERT: S 217 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8648 (tp) REVERT: S 264 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8535 (tttt) REVERT: S 388 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: S 401 SER cc_start: 0.8552 (OUTLIER) cc_final: 0.8321 (t) REVERT: S 418 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: S 434 LYS cc_start: 0.7038 (mptt) cc_final: 0.6838 (mmtt) REVERT: T 50 GLN cc_start: 0.6206 (OUTLIER) cc_final: 0.5875 (tp40) REVERT: T 57 ARG cc_start: 0.8168 (ttm170) cc_final: 0.7859 (ptm160) REVERT: T 88 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7802 (mmm160) REVERT: T 113 SER cc_start: 0.7664 (OUTLIER) cc_final: 0.7380 (m) REVERT: T 189 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.7338 (tp40) REVERT: T 261 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8653 (pp) REVERT: T 440 GLN cc_start: 0.8432 (mm110) cc_final: 0.8154 (mt0) REVERT: T 506 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.8115 (p) REVERT: T 543 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6460 (ttt180) REVERT: A 17 MET cc_start: 0.5155 (pp-130) cc_final: 0.3616 (mtt) REVERT: A 77 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.7950 (mp10) REVERT: A 138 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7031 (mmtt) REVERT: A 146 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.5667 (mmm-85) REVERT: E 33 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: C 37 ARG cc_start: 0.7030 (mpt-90) cc_final: 0.6148 (tpt90) outliers start: 203 outliers final: 101 residues processed: 372 average time/residue: 0.1061 time to fit residues: 52.0948 Evaluate side-chains 257 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 139 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 127 LYS Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 151 ARG Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 203 ARG Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 234 LYS Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain S residue 244 VAL Chi-restraints excluded: chain S residue 249 MET Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 257 LEU Chi-restraints excluded: chain S residue 264 LYS Chi-restraints excluded: chain S residue 267 TYR Chi-restraints excluded: chain S residue 277 LEU Chi-restraints excluded: chain S residue 291 GLU Chi-restraints excluded: chain S residue 300 ILE Chi-restraints excluded: chain S residue 313 SER Chi-restraints excluded: chain S residue 331 SER Chi-restraints excluded: chain S residue 362 ILE Chi-restraints excluded: chain S residue 377 LEU Chi-restraints excluded: chain S residue 381 SER Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 396 LEU Chi-restraints excluded: chain S residue 401 SER Chi-restraints excluded: chain S residue 408 ASP Chi-restraints excluded: chain S residue 411 LEU Chi-restraints excluded: chain S residue 414 GLU Chi-restraints excluded: chain S residue 418 GLN Chi-restraints excluded: chain S residue 423 SER Chi-restraints excluded: chain S residue 435 GLU Chi-restraints excluded: chain S residue 448 VAL Chi-restraints excluded: chain S residue 449 THR Chi-restraints excluded: chain S residue 451 GLU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain S residue 459 ARG Chi-restraints excluded: chain S residue 467 VAL Chi-restraints excluded: chain T residue 50 GLN Chi-restraints excluded: chain T residue 54 LEU Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 99 CYS Chi-restraints excluded: chain T residue 111 PHE Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 116 GLN Chi-restraints excluded: chain T residue 124 ARG Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 189 GLN Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 273 SER Chi-restraints excluded: chain T residue 297 VAL Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 314 VAL Chi-restraints excluded: chain T residue 315 GLU Chi-restraints excluded: chain T residue 320 MET Chi-restraints excluded: chain T residue 324 ILE Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain T residue 344 ASP Chi-restraints excluded: chain T residue 349 ILE Chi-restraints excluded: chain T residue 352 LEU Chi-restraints excluded: chain T residue 357 ARG Chi-restraints excluded: chain T residue 371 ASP Chi-restraints excluded: chain T residue 373 MET Chi-restraints excluded: chain T residue 374 MET Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 496 VAL Chi-restraints excluded: chain T residue 503 ILE Chi-restraints excluded: chain T residue 504 ILE Chi-restraints excluded: chain T residue 506 SER Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain T residue 543 ARG Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 34 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 65 GLN S 77 HIS S 211 HIS S 309 ASN S 413 GLN T 212 ASN T 263 HIS T 286 GLN T 445 ASN A 18 ASN A 53 ASN A 57 ASN A 85 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.104186 restraints weight = 13162.463| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.97 r_work: 0.3013 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9052 Z= 0.149 Angle : 0.718 8.526 12258 Z= 0.363 Chirality : 0.046 0.178 1373 Planarity : 0.006 0.065 1547 Dihedral : 15.631 102.726 1505 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.16 % Favored : 93.66 % Rotamer: Outliers : 9.50 % Allowed : 17.93 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -3.94 (0.22), residues: 1104 helix: -2.73 (0.19), residues: 458 sheet: -2.18 (0.48), residues: 113 loop : -2.54 (0.24), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 129 TYR 0.018 0.002 TYR T 474 PHE 0.015 0.002 PHE T 111 TRP 0.010 0.001 TRP A 86 HIS 0.006 0.001 HIS S 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 9051) covalent geometry : angle 0.71768 / 0.36 (12258) hydrogen bonds : bond 0.05594 / 3.75 ( 263) hydrogen bonds : angle 6.03424 / 4.26 ( 765) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 159 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: S 57 LYS cc_start: 0.8191 (mtmt) cc_final: 0.7609 (tttt) REVERT: S 388 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8035 (mp0) REVERT: S 390 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8568 (pp) REVERT: S 408 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: S 418 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: T 57 ARG cc_start: 0.8325 (ttm170) cc_final: 0.8007 (ptm160) REVERT: T 88 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8055 (mmt90) REVERT: T 189 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.6539 (tp40) REVERT: T 261 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8892 (pp) REVERT: T 327 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8697 (tp) REVERT: T 357 ARG cc_start: 0.9375 (OUTLIER) cc_final: 0.8740 (tpp-160) REVERT: T 506 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8584 (p) REVERT: A 17 MET cc_start: 0.5177 (pp-130) cc_final: 0.3475 (mtt) REVERT: A 68 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.7187 (mtmm) REVERT: A 138 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7268 (mmtt) REVERT: A 146 ARG cc_start: 0.6738 (OUTLIER) cc_final: 0.5811 (mmm-85) REVERT: E 50 TYR cc_start: 0.7124 (t80) cc_final: 0.6823 (t80) REVERT: C 37 ARG cc_start: 0.6663 (mpt-90) cc_final: 0.5912 (tpt90) outliers start: 89 outliers final: 48 residues processed: 226 average time/residue: 0.0884 time to fit residues: 27.9481 Evaluate side-chains 190 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 129 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 77 HIS Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain S residue 244 VAL Chi-restraints excluded: chain S residue 249 MET Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 257 LEU Chi-restraints excluded: chain S residue 277 LEU Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 390 LEU Chi-restraints excluded: chain S residue 396 LEU Chi-restraints excluded: chain S residue 408 ASP Chi-restraints excluded: chain S residue 411 LEU Chi-restraints excluded: chain S residue 418 GLN Chi-restraints excluded: chain S residue 423 SER Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 448 VAL Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain T residue 54 LEU Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 111 PHE Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 189 GLN Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 344 ASP Chi-restraints excluded: chain T residue 357 ARG Chi-restraints excluded: chain T residue 371 ASP Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 496 VAL Chi-restraints excluded: chain T residue 504 ILE Chi-restraints excluded: chain T residue 506 SER Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 32 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 53 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 77 HIS T 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.129702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.105120 restraints weight = 12922.027| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.98 r_work: 0.3028 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9052 Z= 0.134 Angle : 0.645 8.134 12258 Z= 0.322 Chirality : 0.045 0.165 1373 Planarity : 0.005 0.060 1547 Dihedral : 12.293 67.893 1359 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.80 % Favored : 94.11 % Rotamer: Outliers : 6.94 % Allowed : 20.92 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -3.08 (0.24), residues: 1104 helix: -1.86 (0.22), residues: 462 sheet: -2.25 (0.49), residues: 102 loop : -2.10 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 459 TYR 0.013 0.001 TYR T 539 PHE 0.016 0.001 PHE T 111 TRP 0.011 0.001 TRP C 34 HIS 0.013 0.001 HIS S 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 9051) covalent geometry : angle 0.64487 / 0.32 (12258) hydrogen bonds : bond 0.04575 / 3.00 ( 263) hydrogen bonds : angle 5.23221 / 3.72 ( 765) Misc. bond : bond 0.00144 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 138 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: S 57 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7626 (tttt) REVERT: S 77 HIS cc_start: 0.6906 (OUTLIER) cc_final: 0.5779 (m-70) REVERT: S 321 ARG cc_start: 0.8714 (ttp80) cc_final: 0.8501 (mtp-110) REVERT: S 362 ILE cc_start: 0.8663 (pt) cc_final: 0.8339 (pt) REVERT: S 388 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: S 390 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8362 (pp) REVERT: S 418 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8183 (tt0) REVERT: T 57 ARG cc_start: 0.8284 (ttm170) cc_final: 0.7965 (ptm160) REVERT: T 88 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8057 (mmm160) REVERT: T 90 PHE cc_start: 0.7169 (m-10) cc_final: 0.6722 (t80) REVERT: T 257 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8755 (mt) REVERT: T 327 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8640 (tp) REVERT: T 369 ASP cc_start: 0.8382 (m-30) cc_final: 0.8091 (m-30) REVERT: A 17 MET cc_start: 0.5027 (pp-130) cc_final: 0.3616 (mtm) REVERT: A 138 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7323 (mmtt) REVERT: A 146 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.5930 (mmm-85) REVERT: E 11 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7627 (tppt) REVERT: E 12 GLN cc_start: 0.8152 (pp30) cc_final: 0.7742 (pp30) REVERT: E 50 TYR cc_start: 0.7231 (t80) cc_final: 0.6986 (t80) outliers start: 65 outliers final: 36 residues processed: 188 average time/residue: 0.0885 time to fit residues: 23.2005 Evaluate side-chains 176 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 130 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 77 HIS Chi-restraints excluded: chain S residue 81 ASN Chi-restraints excluded: chain S residue 166 TYR Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain S residue 249 MET Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 390 LEU Chi-restraints excluded: chain S residue 396 LEU Chi-restraints excluded: chain S residue 418 GLN Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 448 VAL Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 103 THR Chi-restraints excluded: chain T residue 111 PHE Chi-restraints excluded: chain T residue 257 LEU Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 344 ASP Chi-restraints excluded: chain T residue 371 ASP Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 496 VAL Chi-restraints excluded: chain T residue 504 ILE Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 32 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 0.0020 chunk 91 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 chunk 21 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 0.0670 chunk 96 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.4528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 77 HIS S 107 ASN S 372 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.107018 restraints weight = 13156.569| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.00 r_work: 0.3083 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 9052 Z= 0.107 Angle : 0.596 8.318 12258 Z= 0.297 Chirality : 0.044 0.188 1373 Planarity : 0.005 0.063 1547 Dihedral : 10.388 62.902 1316 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.53 % Favored : 94.38 % Rotamer: Outliers : 5.34 % Allowed : 22.20 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -2.55 (0.25), residues: 1104 helix: -1.31 (0.24), residues: 461 sheet: -1.84 (0.51), residues: 102 loop : -1.95 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 357 TYR 0.014 0.001 TYR A 26 PHE 0.012 0.001 PHE T 111 TRP 0.011 0.001 TRP C 34 HIS 0.019 0.001 HIS S 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 9051) covalent geometry : angle 0.59582 / 0.30 (12258) hydrogen bonds : bond 0.03742 / 2.42 ( 263) hydrogen bonds : angle 4.85970 / 3.46 ( 765) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: S 57 LYS cc_start: 0.8186 (mtmt) cc_final: 0.7595 (tttt) REVERT: S 77 HIS cc_start: 0.6947 (OUTLIER) cc_final: 0.6144 (m-70) REVERT: S 388 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8172 (mp0) REVERT: T 57 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7985 (ptm160) REVERT: T 88 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7980 (mmm160) REVERT: T 90 PHE cc_start: 0.7158 (m-10) cc_final: 0.6760 (t80) REVERT: T 261 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8831 (pp) REVERT: T 327 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8642 (tp) REVERT: T 369 ASP cc_start: 0.8315 (m-30) cc_final: 0.7918 (m-30) REVERT: A 17 MET cc_start: 0.5011 (pp-130) cc_final: 0.3554 (mtm) REVERT: A 135 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8056 (mm) REVERT: A 138 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7213 (mmtt) REVERT: A 146 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.5814 (mmm-85) REVERT: E 12 GLN cc_start: 0.8158 (pp30) cc_final: 0.7779 (pp30) outliers start: 50 outliers final: 26 residues processed: 186 average time/residue: 0.0977 time to fit residues: 25.3813 Evaluate side-chains 173 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 77 HIS Chi-restraints excluded: chain S residue 81 ASN Chi-restraints excluded: chain S residue 166 TYR Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain S residue 249 MET Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 396 LEU Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 103 THR Chi-restraints excluded: chain T residue 111 PHE Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 344 ASP Chi-restraints excluded: chain T residue 371 ASP Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 496 VAL Chi-restraints excluded: chain T residue 503 ILE Chi-restraints excluded: chain T residue 504 ILE Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain C residue 32 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 52 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 96 optimal weight: 0.0370 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.130113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.105496 restraints weight = 13035.019| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.98 r_work: 0.2933 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9052 Z= 0.124 Angle : 0.585 7.025 12258 Z= 0.291 Chirality : 0.044 0.188 1373 Planarity : 0.005 0.069 1547 Dihedral : 9.596 59.663 1300 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.34 % Favored : 94.57 % Rotamer: Outliers : 5.44 % Allowed : 21.34 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -2.21 (0.25), residues: 1104 helix: -0.94 (0.24), residues: 469 sheet: -1.37 (0.50), residues: 114 loop : -1.93 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 151 TYR 0.016 0.001 TYR A 119 PHE 0.014 0.001 PHE T 111 TRP 0.011 0.001 TRP C 34 HIS 0.004 0.000 HIS S 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 9051) covalent geometry : angle 0.58530 / 0.29 (12258) hydrogen bonds : bond 0.03728 / 2.40 ( 263) hydrogen bonds : angle 4.64198 / 3.31 ( 765) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 142 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 57 LYS cc_start: 0.8226 (mtmt) cc_final: 0.7589 (tttt) REVERT: S 77 HIS cc_start: 0.6950 (OUTLIER) cc_final: 0.6435 (m-70) REVERT: S 388 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: S 418 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: T 57 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7952 (ptm160) REVERT: T 88 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7882 (mmm160) REVERT: T 90 PHE cc_start: 0.7228 (m-10) cc_final: 0.6775 (t80) REVERT: T 261 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8923 (pp) REVERT: T 327 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8664 (tp) REVERT: T 369 ASP cc_start: 0.8345 (m-30) cc_final: 0.7932 (m-30) REVERT: T 491 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.7930 (mt) REVERT: A 17 MET cc_start: 0.5353 (pp-130) cc_final: 0.3500 (mtm) REVERT: A 120 ASP cc_start: 0.7508 (m-30) cc_final: 0.7276 (m-30) REVERT: A 135 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8279 (mt) REVERT: A 138 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7181 (mmtt) REVERT: A 146 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.5776 (mmm-85) REVERT: E 11 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7974 (tppt) REVERT: E 12 GLN cc_start: 0.8247 (pp30) cc_final: 0.7876 (pp30) outliers start: 51 outliers final: 29 residues processed: 179 average time/residue: 0.0940 time to fit residues: 23.4651 Evaluate side-chains 173 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 77 HIS Chi-restraints excluded: chain S residue 81 ASN Chi-restraints excluded: chain S residue 166 TYR Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain S residue 249 MET Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 396 LEU Chi-restraints excluded: chain S residue 418 GLN Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 103 THR Chi-restraints excluded: chain T residue 111 PHE Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 344 ASP Chi-restraints excluded: chain T residue 371 ASP Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 503 ILE Chi-restraints excluded: chain T residue 504 ILE Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain T residue 545 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 43 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 103 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 56 optimal weight: 7.9990 chunk 95 optimal weight: 0.0170 chunk 50 optimal weight: 3.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 77 HIS A 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.127144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.102399 restraints weight = 13095.413| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.00 r_work: 0.3038 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9052 Z= 0.143 Angle : 0.593 7.975 12258 Z= 0.295 Chirality : 0.044 0.189 1373 Planarity : 0.005 0.074 1547 Dihedral : 9.360 59.957 1295 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.80 % Favored : 94.11 % Rotamer: Outliers : 5.44 % Allowed : 21.77 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -2.03 (0.25), residues: 1104 helix: -0.66 (0.25), residues: 471 sheet: -1.23 (0.51), residues: 114 loop : -2.00 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG S 321 TYR 0.016 0.001 TYR A 26 PHE 0.016 0.001 PHE T 111 TRP 0.010 0.001 TRP C 34 HIS 0.009 0.001 HIS S 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 ( 9051) covalent geometry : angle 0.59278 / 0.30 (12258) hydrogen bonds : bond 0.03850 / 2.46 ( 263) hydrogen bonds : angle 4.55525 / 3.25 ( 765) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 130 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 57 LYS cc_start: 0.8257 (mtmt) cc_final: 0.7662 (tttt) REVERT: S 77 HIS cc_start: 0.6851 (OUTLIER) cc_final: 0.6364 (m-70) REVERT: S 239 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7901 (ptt90) REVERT: S 388 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8222 (mp0) REVERT: S 418 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: T 57 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8022 (ptm160) REVERT: T 88 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7802 (mmm160) REVERT: T 90 PHE cc_start: 0.7235 (m-10) cc_final: 0.6845 (t80) REVERT: T 261 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8967 (pp) REVERT: T 327 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8710 (tp) REVERT: T 369 ASP cc_start: 0.8328 (m-30) cc_final: 0.8033 (m-30) REVERT: T 491 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.7933 (mt) REVERT: A 17 MET cc_start: 0.5557 (pp-130) cc_final: 0.3556 (mtm) REVERT: A 135 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8421 (mt) REVERT: A 138 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7572 (mptt) REVERT: A 146 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.5873 (mmm-85) REVERT: E 12 GLN cc_start: 0.8276 (pp30) cc_final: 0.7897 (pp30) outliers start: 51 outliers final: 31 residues processed: 168 average time/residue: 0.0958 time to fit residues: 22.4845 Evaluate side-chains 172 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 77 HIS Chi-restraints excluded: chain S residue 81 ASN Chi-restraints excluded: chain S residue 166 TYR Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain S residue 244 VAL Chi-restraints excluded: chain S residue 249 MET Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 297 ILE Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 396 LEU Chi-restraints excluded: chain S residue 418 GLN Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 103 THR Chi-restraints excluded: chain T residue 111 PHE Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 344 ASP Chi-restraints excluded: chain T residue 370 VAL Chi-restraints excluded: chain T residue 371 ASP Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 503 ILE Chi-restraints excluded: chain T residue 504 ILE Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain C residue 27 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.0370 chunk 16 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 77 HIS T 242 ASN T 300 GLN A 85 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.130580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.105829 restraints weight = 13025.061| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.98 r_work: 0.3081 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9052 Z= 0.102 Angle : 0.565 8.857 12258 Z= 0.279 Chirality : 0.043 0.190 1373 Planarity : 0.004 0.075 1547 Dihedral : 8.908 58.952 1293 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.75 % Rotamer: Outliers : 4.80 % Allowed : 22.63 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -1.83 (0.25), residues: 1104 helix: -0.39 (0.25), residues: 472 sheet: -1.15 (0.51), residues: 114 loop : -2.00 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG T 357 TYR 0.014 0.001 TYR A 26 PHE 0.011 0.001 PHE T 111 TRP 0.012 0.001 TRP C 34 HIS 0.010 0.001 HIS S 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 9051) covalent geometry : angle 0.56503 / 0.28 (12258) hydrogen bonds : bond 0.03324 / 2.13 ( 263) hydrogen bonds : angle 4.42156 / 3.16 ( 765) Misc. bond : bond 0.00128 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 57 LYS cc_start: 0.8252 (mtmt) cc_final: 0.7639 (tttt) REVERT: S 239 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8125 (ptt90) REVERT: S 362 ILE cc_start: 0.8673 (pt) cc_final: 0.8422 (pt) REVERT: S 388 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: S 418 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: T 57 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7947 (ptm160) REVERT: T 88 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7767 (mmm160) REVERT: T 90 PHE cc_start: 0.7078 (m-10) cc_final: 0.6672 (t80) REVERT: T 261 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8927 (pp) REVERT: T 300 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8019 (mp10) REVERT: T 327 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8701 (tp) REVERT: T 369 ASP cc_start: 0.8115 (m-30) cc_final: 0.7812 (m-30) REVERT: T 471 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8658 (tt) REVERT: A 17 MET cc_start: 0.5387 (pp-130) cc_final: 0.4917 (ptp) REVERT: A 135 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8254 (mt) REVERT: A 138 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7461 (mptt) REVERT: A 146 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.5849 (mmm-85) REVERT: E 12 GLN cc_start: 0.8217 (pp30) cc_final: 0.7860 (pp30) outliers start: 45 outliers final: 23 residues processed: 170 average time/residue: 0.0755 time to fit residues: 18.1174 Evaluate side-chains 167 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 81 ASN Chi-restraints excluded: chain S residue 166 TYR Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain S residue 247 LEU Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 418 GLN Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 111 PHE Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 344 ASP Chi-restraints excluded: chain T residue 370 VAL Chi-restraints excluded: chain T residue 371 ASP Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 471 LEU Chi-restraints excluded: chain T residue 503 ILE Chi-restraints excluded: chain T residue 504 ILE Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 41 optimal weight: 3.9990 chunk 95 optimal weight: 0.0570 chunk 103 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 107 ASN T 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.126317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.101526 restraints weight = 13074.773| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.97 r_work: 0.3018 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9052 Z= 0.111 Angle : 0.579 8.136 12258 Z= 0.288 Chirality : 0.044 0.220 1373 Planarity : 0.004 0.074 1547 Dihedral : 8.516 59.597 1288 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.34 % Favored : 94.57 % Rotamer: Outliers : 4.91 % Allowed : 22.73 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -1.59 (0.25), residues: 1104 helix: -0.12 (0.25), residues: 463 sheet: -1.13 (0.51), residues: 114 loop : -1.90 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG T 357 TYR 0.024 0.001 TYR T 298 PHE 0.012 0.001 PHE T 111 TRP 0.013 0.001 TRP C 34 HIS 0.001 0.000 HIS S 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 9051) covalent geometry : angle 0.57865 / 0.29 (12258) hydrogen bonds : bond 0.03296 / 2.11 ( 263) hydrogen bonds : angle 4.34497 / 3.10 ( 765) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 57 LYS cc_start: 0.8239 (mtmt) cc_final: 0.7588 (tttt) REVERT: S 239 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8073 (ptt90) REVERT: S 362 ILE cc_start: 0.8609 (pt) cc_final: 0.8330 (pt) REVERT: S 388 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: S 406 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8084 (mt-10) REVERT: S 418 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: T 57 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7938 (ptm160) REVERT: T 88 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7805 (mmm160) REVERT: T 90 PHE cc_start: 0.7007 (m-10) cc_final: 0.6634 (t80) REVERT: T 261 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8981 (pp) REVERT: T 298 TYR cc_start: 0.9145 (m-10) cc_final: 0.8685 (m-80) REVERT: T 300 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: T 327 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8690 (tp) REVERT: T 471 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8629 (tt) REVERT: T 491 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.7910 (mt) REVERT: A 17 MET cc_start: 0.5471 (pp-130) cc_final: 0.4853 (ptp) REVERT: A 119 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.6575 (m-80) REVERT: A 135 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8208 (mt) REVERT: A 138 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7483 (mptt) REVERT: A 146 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.5816 (mmm-85) REVERT: E 12 GLN cc_start: 0.8211 (pp30) cc_final: 0.7871 (pp30) outliers start: 46 outliers final: 27 residues processed: 171 average time/residue: 0.0852 time to fit residues: 20.4766 Evaluate side-chains 170 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 166 TYR Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain S residue 244 VAL Chi-restraints excluded: chain S residue 247 LEU Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 406 GLU Chi-restraints excluded: chain S residue 418 GLN Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain T residue 54 LEU Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 111 PHE Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 344 ASP Chi-restraints excluded: chain T residue 370 VAL Chi-restraints excluded: chain T residue 371 ASP Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 471 LEU Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 503 ILE Chi-restraints excluded: chain T residue 504 ILE Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 119 TYR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain C residue 27 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 0.0050 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.124485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.099528 restraints weight = 13290.670| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.00 r_work: 0.2978 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9052 Z= 0.142 Angle : 0.603 8.785 12258 Z= 0.299 Chirality : 0.045 0.191 1373 Planarity : 0.005 0.072 1547 Dihedral : 8.595 58.189 1288 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.62 % Favored : 94.20 % Rotamer: Outliers : 4.70 % Allowed : 23.16 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -1.55 (0.25), residues: 1104 helix: -0.09 (0.25), residues: 472 sheet: -1.15 (0.51), residues: 114 loop : -1.89 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG T 450 TYR 0.016 0.001 TYR T 298 PHE 0.015 0.001 PHE T 111 TRP 0.012 0.001 TRP C 34 HIS 0.002 0.000 HIS T 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 ( 9051) covalent geometry : angle 0.60253 / 0.30 (12258) hydrogen bonds : bond 0.03752 / 2.37 ( 263) hydrogen bonds : angle 4.42494 / 3.16 ( 765) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 131 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 57 LYS cc_start: 0.8262 (mtmt) cc_final: 0.7610 (tttt) REVERT: S 239 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8050 (ptt90) REVERT: S 388 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8152 (mp0) REVERT: S 406 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8099 (mt-10) REVERT: S 418 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: T 57 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7963 (ptm160) REVERT: T 88 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7802 (mmm160) REVERT: T 90 PHE cc_start: 0.6957 (m-10) cc_final: 0.6552 (t80) REVERT: T 261 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9016 (pp) REVERT: T 298 TYR cc_start: 0.9179 (m-10) cc_final: 0.8667 (m-80) REVERT: T 300 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: T 327 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8694 (tp) REVERT: T 471 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8647 (tt) REVERT: T 491 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.7913 (mt) REVERT: A 17 MET cc_start: 0.5556 (pp-130) cc_final: 0.4838 (ptp) REVERT: A 53 ASN cc_start: 0.8845 (t0) cc_final: 0.7983 (t0) REVERT: A 119 TYR cc_start: 0.6987 (m-80) cc_final: 0.6582 (m-80) REVERT: A 135 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8231 (mt) REVERT: A 138 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7498 (mptt) REVERT: A 146 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.5838 (mmm-85) REVERT: E 12 GLN cc_start: 0.8214 (pp30) cc_final: 0.7873 (pp30) outliers start: 44 outliers final: 26 residues processed: 164 average time/residue: 0.0992 time to fit residues: 22.4058 Evaluate side-chains 166 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 166 TYR Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain S residue 244 VAL Chi-restraints excluded: chain S residue 247 LEU Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 297 ILE Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 406 GLU Chi-restraints excluded: chain S residue 418 GLN Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain T residue 54 LEU Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 111 PHE Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 311 LEU Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 344 ASP Chi-restraints excluded: chain T residue 370 VAL Chi-restraints excluded: chain T residue 371 ASP Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 471 LEU Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 503 ILE Chi-restraints excluded: chain T residue 504 ILE Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain E residue 24 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 0.0020 chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 103 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 347 HIS A 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.102148 restraints weight = 13163.650| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.01 r_work: 0.3019 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9052 Z= 0.101 Angle : 0.564 7.824 12258 Z= 0.279 Chirality : 0.043 0.171 1373 Planarity : 0.004 0.069 1547 Dihedral : 8.289 57.114 1287 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.53 % Favored : 95.29 % Rotamer: Outliers : 4.06 % Allowed : 23.59 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -1.29 (0.26), residues: 1104 helix: 0.17 (0.25), residues: 467 sheet: -0.85 (0.57), residues: 98 loop : -1.81 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG T 357 TYR 0.017 0.001 TYR A 26 PHE 0.011 0.001 PHE T 111 TRP 0.016 0.001 TRP C 34 HIS 0.001 0.000 HIS S 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 9051) covalent geometry : angle 0.56416 / 0.28 (12258) hydrogen bonds : bond 0.03146 / 2.00 ( 263) hydrogen bonds : angle 4.31988 / 3.10 ( 765) Misc. bond : bond 0.00014 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 57 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7598 (tttt) REVERT: S 388 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8167 (mp0) REVERT: S 418 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: T 57 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7937 (ptm160) REVERT: T 88 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7787 (mmm160) REVERT: T 90 PHE cc_start: 0.6731 (m-10) cc_final: 0.6464 (t80) REVERT: T 261 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8995 (pp) REVERT: T 300 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.7843 (mp10) REVERT: T 327 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8690 (tp) REVERT: T 471 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8652 (tt) REVERT: T 491 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.7862 (mt) REVERT: A 17 MET cc_start: 0.5545 (pp-130) cc_final: 0.4863 (ptm) REVERT: A 119 TYR cc_start: 0.6858 (m-80) cc_final: 0.6453 (m-80) REVERT: A 135 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8166 (mt) REVERT: A 138 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7558 (mptt) REVERT: A 146 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.5799 (mmm-85) REVERT: E 12 GLN cc_start: 0.8146 (pp30) cc_final: 0.7833 (pp30) outliers start: 38 outliers final: 23 residues processed: 163 average time/residue: 0.0934 time to fit residues: 21.4510 Evaluate side-chains 162 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 166 TYR Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 244 VAL Chi-restraints excluded: chain S residue 247 LEU Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 418 GLN Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain T residue 54 LEU Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 111 PHE Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 344 ASP Chi-restraints excluded: chain T residue 370 VAL Chi-restraints excluded: chain T residue 371 ASP Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 471 LEU Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 503 ILE Chi-restraints excluded: chain T residue 504 ILE Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain E residue 24 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 469 GLN A 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.096871 restraints weight = 13061.835| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.98 r_work: 0.2931 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9052 Z= 0.215 Angle : 0.671 8.932 12258 Z= 0.333 Chirality : 0.047 0.205 1373 Planarity : 0.005 0.069 1547 Dihedral : 8.739 59.375 1283 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.70 % Favored : 93.12 % Rotamer: Outliers : 3.95 % Allowed : 23.91 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -1.54 (0.26), residues: 1104 helix: -0.09 (0.25), residues: 481 sheet: -1.17 (0.51), residues: 114 loop : -1.89 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 304 TYR 0.019 0.002 TYR T 539 PHE 0.020 0.002 PHE T 111 TRP 0.010 0.002 TRP T 94 HIS 0.003 0.001 HIS S 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.22 ( 9051) covalent geometry : angle 0.67052 / 0.33 (12258) hydrogen bonds : bond 0.04347 / 2.76 ( 263) hydrogen bonds : angle 4.48312 / 3.21 ( 765) Misc. bond : bond 0.00075 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2235.94 seconds wall clock time: 39 minutes 0.17 seconds (2340.17 seconds total)