Starting phenix.real_space_refine on Thu Jun 19 23:32:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v2y_31670/06_2025/7v2y_31670.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v2y_31670/06_2025/7v2y_31670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v2y_31670/06_2025/7v2y_31670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v2y_31670/06_2025/7v2y_31670.map" model { file = "/net/cci-nas-00/data/ceres_data/7v2y_31670/06_2025/7v2y_31670.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v2y_31670/06_2025/7v2y_31670.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 14736 2.51 5 N 3862 2.21 5 O 4406 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 210 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23097 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4942 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 22, 'TRANS': 570} Chain breaks: 1 Chain: "B" Number of atoms: 9958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1226, 9958 Classifications: {'peptide': 1226} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 1191} Chain breaks: 1 Chain: "C" Number of atoms: 2606 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 333, 2606 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "D" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1106 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "E" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1459 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "F" Number of atoms: 3026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3026 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 15, 'TRANS': 360} Chain breaks: 1 Time building chain proxies: 15.10, per 1000 atoms: 0.65 Number of scatterers: 23097 At special positions: 0 Unit cell: (220.18, 149.33, 119.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 93 16.00 O 4406 8.00 N 3862 7.00 C 14736 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=0, symmetry=0 Time building additional restraints: 6.61 Conformation dependent library (CDL) restraints added in 3.2 seconds 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5506 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 14 sheets defined 55.4% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 3 through 20 removed outlier: 3.615A pdb=" N SER A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY A 13 " --> pdb=" O GLN A 9 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 32 removed outlier: 3.679A pdb=" N ILE A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N HIS A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.645A pdb=" N PHE A 46 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 removed outlier: 3.816A pdb=" N LYS A 53 " --> pdb=" O GLU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 79 removed outlier: 3.707A pdb=" N LEU A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 106 removed outlier: 4.117A pdb=" N GLU A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 131 removed outlier: 3.606A pdb=" N THR A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.590A pdb=" N LYS A 139 " --> pdb=" O SER A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 147 removed outlier: 3.619A pdb=" N SER A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 147 " --> pdb=" O TYR A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 removed outlier: 4.016A pdb=" N LYS A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 153' Processing helix chain 'A' and resid 177 through 191 removed outlier: 3.680A pdb=" N ASP A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 212 removed outlier: 3.583A pdb=" N GLU A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 266 Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.758A pdb=" N PHE A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.917A pdb=" N ASP A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Proline residue: A 290 - end of helix removed outlier: 3.563A pdb=" N ASP A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 321 removed outlier: 3.596A pdb=" N SER A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 305 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR A 312 " --> pdb=" O MET A 308 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 316 " --> pdb=" O THR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 removed outlier: 3.586A pdb=" N MET A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 360 removed outlier: 4.052A pdb=" N GLN A 357 " --> pdb=" O TRP A 353 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 388 removed outlier: 3.790A pdb=" N TYR A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLN A 388 " --> pdb=" O LYS A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 415 removed outlier: 3.827A pdb=" N ILE A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR A 405 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 407 " --> pdb=" O CYS A 403 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 415 " --> pdb=" O ASN A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 444 through 456 removed outlier: 3.600A pdb=" N GLY A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR A 454 " --> pdb=" O ASN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 471 through 492 removed outlier: 3.568A pdb=" N LYS A 477 " --> pdb=" O ARG A 473 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 483 " --> pdb=" O MET A 479 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 488 " --> pdb=" O LYS A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 532 removed outlier: 3.640A pdb=" N ASN A 529 " --> pdb=" O ASN A 525 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 565 removed outlier: 3.752A pdb=" N VAL A 551 " --> pdb=" O LYS A 547 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 562 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 564 " --> pdb=" O GLU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 Processing helix chain 'B' and resid 2 through 15 removed outlier: 3.900A pdb=" N SER B 8 " --> pdb=" O GLN B 4 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS B 9 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 removed outlier: 3.648A pdb=" N SER B 41 " --> pdb=" O TRP B 37 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 42 " --> pdb=" O PRO B 38 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 49 " --> pdb=" O CYS B 45 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 72 removed outlier: 3.554A pdb=" N GLU B 58 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 63 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 101 removed outlier: 3.737A pdb=" N GLU B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN B 99 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 100 " --> pdb=" O HIS B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 121 through 130 removed outlier: 3.788A pdb=" N THR B 125 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 142 removed outlier: 3.505A pdb=" N PHE B 140 " --> pdb=" O HIS B 136 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 142 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.821A pdb=" N HIS B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 192 removed outlier: 3.507A pdb=" N GLN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 removed outlier: 4.279A pdb=" N GLU B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY B 214 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 231 removed outlier: 3.914A pdb=" N ASP B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 240 through 248 removed outlier: 3.652A pdb=" N ALA B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 282 removed outlier: 3.589A pdb=" N ILE B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 307 removed outlier: 3.628A pdb=" N TYR B 297 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 304 " --> pdb=" O MET B 300 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS B 306 " --> pdb=" O CYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 317 removed outlier: 3.583A pdb=" N ASP B 317 " --> pdb=" O TYR B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 343 removed outlier: 4.039A pdb=" N GLU B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 415 removed outlier: 4.276A pdb=" N LEU B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE B 413 " --> pdb=" O GLU B 409 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 427 removed outlier: 3.699A pdb=" N GLN B 426 " --> pdb=" O HIS B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 431 removed outlier: 3.725A pdb=" N LEU B 431 " --> pdb=" O PRO B 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 428 through 431' Processing helix chain 'B' and resid 434 through 438 removed outlier: 3.809A pdb=" N LEU B 437 " --> pdb=" O SER B 434 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 438 " --> pdb=" O GLU B 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 434 through 438' Processing helix chain 'B' and resid 439 through 448 removed outlier: 3.702A pdb=" N VAL B 444 " --> pdb=" O TYR B 440 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 457 removed outlier: 3.655A pdb=" N SER B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 457 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 463 removed outlier: 3.601A pdb=" N GLU B 461 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 527 through 532 removed outlier: 3.741A pdb=" N TYR B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 541 Processing helix chain 'B' and resid 542 through 560 removed outlier: 3.628A pdb=" N LEU B 546 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER B 550 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 552 " --> pdb=" O LYS B 548 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 573 removed outlier: 3.993A pdb=" N TRP B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 581 removed outlier: 3.906A pdb=" N ARG B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS B 579 " --> pdb=" O ASP B 575 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE B 580 " --> pdb=" O TYR B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 603 removed outlier: 3.560A pdb=" N SER B 596 " --> pdb=" O PRO B 592 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 597 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 601 " --> pdb=" O GLU B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 625 through 640 removed outlier: 3.764A pdb=" N LYS B 629 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 631 " --> pdb=" O PRO B 627 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 636 " --> pdb=" O PHE B 632 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 637 " --> pdb=" O ASN B 633 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 665 removed outlier: 4.527A pdb=" N ARG B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG B 657 " --> pdb=" O LYS B 653 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 661 " --> pdb=" O ARG B 657 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 676 Processing helix chain 'B' and resid 683 through 691 removed outlier: 3.532A pdb=" N VAL B 688 " --> pdb=" O SER B 684 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR B 689 " --> pdb=" O GLU B 685 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 690 " --> pdb=" O LEU B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 694 No H-bonds generated for 'chain 'B' and resid 692 through 694' Processing helix chain 'B' and resid 697 through 711 removed outlier: 3.587A pdb=" N VAL B 701 " --> pdb=" O PHE B 697 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR B 711 " --> pdb=" O LEU B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 742 removed outlier: 3.886A pdb=" N LYS B 740 " --> pdb=" O ALA B 736 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN B 741 " --> pdb=" O GLY B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 758 removed outlier: 3.504A pdb=" N LYS B 756 " --> pdb=" O THR B 752 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR B 757 " --> pdb=" O TYR B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 776 removed outlier: 3.599A pdb=" N VAL B 766 " --> pdb=" O ASN B 762 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU B 771 " --> pdb=" O SER B 767 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 773 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 774 " --> pdb=" O LYS B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 793 Processing helix chain 'B' and resid 797 through 807 removed outlier: 3.703A pdb=" N GLN B 801 " --> pdb=" O SER B 797 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS B 805 " --> pdb=" O GLN B 801 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 807 " --> pdb=" O ALA B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 828 removed outlier: 3.536A pdb=" N SER B 818 " --> pdb=" O ASN B 814 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 824 " --> pdb=" O ARG B 820 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLN B 828 " --> pdb=" O PHE B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 845 removed outlier: 3.624A pdb=" N ILE B 835 " --> pdb=" O ILE B 831 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B 836 " --> pdb=" O SER B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 877 removed outlier: 3.634A pdb=" N SER B 868 " --> pdb=" O THR B 864 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 871 " --> pdb=" O TRP B 867 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 872 " --> pdb=" O SER B 868 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 886 removed outlier: 3.970A pdb=" N ASN B 885 " --> pdb=" O ALA B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 893 removed outlier: 3.653A pdb=" N ASN B 893 " --> pdb=" O PHE B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 916 removed outlier: 3.586A pdb=" N PHE B 904 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 906 " --> pdb=" O TRP B 902 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TRP B 907 " --> pdb=" O THR B 903 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP B 909 " --> pdb=" O HIS B 905 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR B 910 " --> pdb=" O ILE B 906 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN B 913 " --> pdb=" O ASP B 909 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN B 914 " --> pdb=" O TYR B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 927 removed outlier: 4.251A pdb=" N ASP B 924 " --> pdb=" O ASN B 920 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU B 925 " --> pdb=" O PHE B 921 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU B 926 " --> pdb=" O SER B 922 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE B 927 " --> pdb=" O ILE B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 951 removed outlier: 3.918A pdb=" N THR B 947 " --> pdb=" O ASP B 943 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TRP B 949 " --> pdb=" O PHE B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 974 removed outlier: 3.895A pdb=" N ARG B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 967 " --> pdb=" O TYR B 963 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 970 " --> pdb=" O ARG B 966 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 974 " --> pdb=" O LEU B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 1019 removed outlier: 4.023A pdb=" N LYS B 983 " --> pdb=" O SER B 979 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN B 987 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP B 992 " --> pdb=" O ASN B 988 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 994 " --> pdb=" O ILE B 990 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B1009 " --> pdb=" O LYS B1005 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B1010 " --> pdb=" O LYS B1006 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN B1016 " --> pdb=" O SER B1012 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL B1017 " --> pdb=" O GLU B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1034 Processing helix chain 'B' and resid 1035 through 1039 Processing helix chain 'B' and resid 1042 through 1047 removed outlier: 3.564A pdb=" N LEU B1047 " --> pdb=" O PRO B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1052 Processing helix chain 'B' and resid 1052 through 1057 removed outlier: 3.642A pdb=" N PHE B1057 " --> pdb=" O ILE B1053 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1071 removed outlier: 3.652A pdb=" N MET B1063 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B1064 " --> pdb=" O GLU B1060 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR B1068 " --> pdb=" O SER B1064 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS B1069 " --> pdb=" O ILE B1065 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B1070 " --> pdb=" O LEU B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1079 removed outlier: 3.682A pdb=" N LEU B1079 " --> pdb=" O LEU B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1107 removed outlier: 3.511A pdb=" N GLY B1091 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B1092 " --> pdb=" O GLY B1088 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B1094 " --> pdb=" O LEU B1090 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP B1096 " --> pdb=" O LEU B1092 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS B1100 " --> pdb=" O ASP B1096 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET B1104 " --> pdb=" O LYS B1100 " (cutoff:3.500A) Processing helix chain 'B' and resid 1111 through 1134 removed outlier: 3.549A pdb=" N LYS B1117 " --> pdb=" O GLN B1113 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS B1122 " --> pdb=" O LEU B1118 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B1123 " --> pdb=" O TYR B1119 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B1124 " --> pdb=" O GLU B1120 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B1130 " --> pdb=" O THR B1126 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP B1131 " --> pdb=" O GLU B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1151 removed outlier: 3.638A pdb=" N ASN B1143 " --> pdb=" O MET B1139 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS B1150 " --> pdb=" O GLU B1146 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B1151 " --> pdb=" O PHE B1147 " (cutoff:3.500A) Processing helix chain 'B' and resid 1158 through 1175 removed outlier: 3.616A pdb=" N ILE B1162 " --> pdb=" O VAL B1158 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B1163 " --> pdb=" O LYS B1159 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR B1167 " --> pdb=" O GLN B1163 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR B1168 " --> pdb=" O LEU B1164 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU B1169 " --> pdb=" O VAL B1165 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU B1170 " --> pdb=" O TYR B1166 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B1172 " --> pdb=" O THR B1168 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B1173 " --> pdb=" O LEU B1169 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASN B1175 " --> pdb=" O GLU B1171 " (cutoff:3.500A) Processing helix chain 'B' and resid 1181 through 1193 removed outlier: 3.536A pdb=" N SER B1185 " --> pdb=" O ILE B1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 1194 through 1196 No H-bonds generated for 'chain 'B' and resid 1194 through 1196' Processing helix chain 'B' and resid 1211 through 1232 removed outlier: 3.609A pdb=" N MET B1221 " --> pdb=" O ARG B1217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN B1228 " --> pdb=" O GLU B1224 " (cutoff:3.500A) Processing helix chain 'B' and resid 1241 through 1255 removed outlier: 3.605A pdb=" N ASN B1249 " --> pdb=" O GLN B1245 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS B1250 " --> pdb=" O LEU B1246 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER B1251 " --> pdb=" O GLU B1247 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 56 removed outlier: 3.502A pdb=" N SER C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'D' and resid 4 through 9 removed outlier: 3.515A pdb=" N ASP D 9 " --> pdb=" O GLN D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 removed outlier: 3.809A pdb=" N LYS D 14 " --> pdb=" O GLN D 10 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL D 15 " --> pdb=" O VAL D 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 10 through 15' Processing helix chain 'D' and resid 21 through 44 removed outlier: 3.713A pdb=" N ASP D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE D 30 " --> pdb=" O LYS D 26 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER D 40 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE D 42 " --> pdb=" O THR D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 100 removed outlier: 3.816A pdb=" N PHE D 72 " --> pdb=" O ALA D 68 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D 73 " --> pdb=" O HIS D 69 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP D 89 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 138 removed outlier: 4.057A pdb=" N ILE D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 112 " --> pdb=" O PRO D 108 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE D 113 " --> pdb=" O ASP D 109 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL D 133 " --> pdb=" O ASP D 129 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE D 134 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN D 135 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG D 136 " --> pdb=" O GLN D 132 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL D 138 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 37 removed outlier: 3.567A pdb=" N GLU E 16 " --> pdb=" O SER E 12 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN E 18 " --> pdb=" O CYS E 14 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU E 22 " --> pdb=" O GLN E 18 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER E 23 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE E 33 " --> pdb=" O ASN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 53 removed outlier: 4.326A pdb=" N LEU E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS E 52 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS E 53 " --> pdb=" O GLU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 84 removed outlier: 3.559A pdb=" N LEU E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG E 59 " --> pdb=" O PRO E 55 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU E 60 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE E 62 " --> pdb=" O HIS E 58 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN E 63 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG E 67 " --> pdb=" O ASN E 63 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG E 69 " --> pdb=" O SER E 65 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR E 75 " --> pdb=" O ASP E 71 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP E 83 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR E 84 " --> pdb=" O LEU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 104 removed outlier: 3.900A pdb=" N ILE E 100 " --> pdb=" O ASN E 96 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU E 102 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 109 Processing helix chain 'E' and resid 109 through 119 removed outlier: 3.747A pdb=" N ASP E 113 " --> pdb=" O HIS E 109 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG E 116 " --> pdb=" O ARG E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 162 removed outlier: 4.075A pdb=" N ILE E 156 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N CYS E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA E 162 " --> pdb=" O GLU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 184 removed outlier: 4.044A pdb=" N ALA E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN E 173 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN E 180 " --> pdb=" O ASN E 176 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE E 181 " --> pdb=" O TYR E 177 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS E 182 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA E 184 " --> pdb=" O GLN E 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 68 removed outlier: 3.529A pdb=" N PHE F 67 " --> pdb=" O PHE F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 81 removed outlier: 4.208A pdb=" N ILE F 78 " --> pdb=" O SER F 74 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP F 79 " --> pdb=" O ARG F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 98 removed outlier: 3.867A pdb=" N THR F 92 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE F 93 " --> pdb=" O GLN F 89 " (cutoff:3.500A) Proline residue: F 94 - end of helix removed outlier: 4.092A pdb=" N HIS F 98 " --> pdb=" O PRO F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 124 removed outlier: 4.551A pdb=" N PHE F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL F 117 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU F 118 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER F 119 " --> pdb=" O VAL F 115 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU F 121 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 151 removed outlier: 3.787A pdb=" N ALA F 143 " --> pdb=" O ALA F 139 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR F 144 " --> pdb=" O ARG F 140 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN F 145 " --> pdb=" O GLU F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 180 Processing helix chain 'F' and resid 181 through 184 Processing helix chain 'F' and resid 191 through 200 removed outlier: 4.568A pdb=" N ALA F 197 " --> pdb=" O GLY F 193 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU F 198 " --> pdb=" O ARG F 194 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL F 199 " --> pdb=" O LEU F 195 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG F 200 " --> pdb=" O LYS F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 222 removed outlier: 3.553A pdb=" N GLU F 222 " --> pdb=" O ASP F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 236 removed outlier: 3.569A pdb=" N ARG F 228 " --> pdb=" O LEU F 224 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU F 232 " --> pdb=" O ARG F 228 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE F 233 " --> pdb=" O ASP F 229 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 259 removed outlier: 3.809A pdb=" N ARG F 259 " --> pdb=" O ARG F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 302 removed outlier: 3.871A pdb=" N ASP F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 328 removed outlier: 3.679A pdb=" N GLU F 321 " --> pdb=" O THR F 317 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS F 324 " --> pdb=" O ASN F 320 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA F 328 " --> pdb=" O LYS F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 354 removed outlier: 3.559A pdb=" N ALA F 347 " --> pdb=" O GLU F 343 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR F 349 " --> pdb=" O ARG F 345 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE F 352 " --> pdb=" O ARG F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 368 removed outlier: 3.582A pdb=" N PHE F 366 " --> pdb=" O THR F 363 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY F 367 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG F 368 " --> pdb=" O VAL F 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 363 through 368' Processing helix chain 'F' and resid 389 through 394 Processing helix chain 'F' and resid 398 through 402 removed outlier: 4.181A pdb=" N GLY F 401 " --> pdb=" O GLY F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 426 removed outlier: 3.730A pdb=" N VAL F 418 " --> pdb=" O GLU F 414 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU F 419 " --> pdb=" O ASP F 415 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU F 424 " --> pdb=" O ALA F 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA2, first strand: chain 'B' and resid 484 through 486 Processing sheet with id=AA3, first strand: chain 'B' and resid 488 through 491 removed outlier: 6.162A pdb=" N TYR B 489 " --> pdb=" O VAL B 505 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 4.737A pdb=" N ARG C 44 " --> pdb=" O HIS C 365 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N HIS C 365 " --> pdb=" O ARG C 44 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C 353 " --> pdb=" O PHE C 366 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 69 through 70 removed outlier: 3.826A pdb=" N LYS C 70 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 115 through 120 removed outlier: 4.574A pdb=" N ASP C 117 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL C 131 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE C 137 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THR C 154 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU C 139 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 163 through 165 removed outlier: 3.596A pdb=" N THR C 165 " --> pdb=" O ALA C 178 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 174 through 175 removed outlier: 3.924A pdb=" N CYS C 197 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 214 through 217 removed outlier: 3.791A pdb=" N SER C 214 " --> pdb=" O GLY C 227 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU C 233 " --> pdb=" O LYS C 248 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS C 248 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE C 235 " --> pdb=" O CYS C 246 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.503A pdb=" N THR C 270 " --> pdb=" O TYR C 278 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR C 278 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL C 279 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 298 through 302 Processing sheet with id=AB3, first strand: chain 'C' and resid 318 through 320 Processing sheet with id=AB4, first strand: chain 'F' and resid 162 through 165 removed outlier: 6.392A pdb=" N ALA F 163 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL F 133 " --> pdb=" O VAL F 188 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ALA F 190 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL F 135 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL F 134 " --> pdb=" O VAL F 213 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ASP F 215 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE F 136 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL F 102 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET F 245 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS F 104 " --> pdb=" O MET F 245 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER F 247 " --> pdb=" O CYS F 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 333 through 335 removed outlier: 6.707A pdb=" N ILE F 334 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL F 309 " --> pdb=" O CYS F 360 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N SER F 362 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE F 311 " --> pdb=" O SER F 362 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE F 310 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA F 431 " --> pdb=" O GLN F 283 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR F 285 " --> pdb=" O ALA F 431 " (cutoff:3.500A) 759 hydrogen bonds defined for protein. 2229 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: 9.18 Time building geometry restraints manager: 7.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7452 1.34 - 1.46: 4899 1.46 - 1.58: 11053 1.58 - 1.70: 0 1.70 - 1.82: 145 Bond restraints: 23549 Sorted by residual: bond pdb=" C LEU B1183 " pdb=" N PRO B1184 " ideal model delta sigma weight residual 1.337 1.375 -0.038 1.24e-02 6.50e+03 9.35e+00 bond pdb=" C PHE C 346 " pdb=" N TYR C 347 " ideal model delta sigma weight residual 1.330 1.367 -0.037 1.37e-02 5.33e+03 7.28e+00 bond pdb=" C THR C 62 " pdb=" N PRO C 63 " ideal model delta sigma weight residual 1.334 1.396 -0.062 2.34e-02 1.83e+03 6.94e+00 bond pdb=" C PHE B1155 " pdb=" N PRO B1156 " ideal model delta sigma weight residual 1.334 1.394 -0.060 2.34e-02 1.83e+03 6.60e+00 bond pdb=" C THR C 59 " pdb=" N PRO C 60 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.83e+00 ... (remaining 23544 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 31084 2.54 - 5.08: 625 5.08 - 7.62: 91 7.62 - 10.17: 22 10.17 - 12.71: 4 Bond angle restraints: 31826 Sorted by residual: angle pdb=" N VAL B 683 " pdb=" CA VAL B 683 " pdb=" C VAL B 683 " ideal model delta sigma weight residual 113.53 106.07 7.46 9.80e-01 1.04e+00 5.80e+01 angle pdb=" C HIS B 561 " pdb=" N GLY B 562 " pdb=" CA GLY B 562 " ideal model delta sigma weight residual 121.41 132.17 -10.76 1.96e+00 2.60e-01 3.01e+01 angle pdb=" C ILE B 625 " pdb=" N LEU B 626 " pdb=" CA LEU B 626 " ideal model delta sigma weight residual 119.78 126.07 -6.29 1.24e+00 6.50e-01 2.57e+01 angle pdb=" N LYS B 960 " pdb=" CA LYS B 960 " pdb=" C LYS B 960 " ideal model delta sigma weight residual 114.56 108.32 6.24 1.27e+00 6.20e-01 2.42e+01 angle pdb=" C TYR C 168 " pdb=" N ASP C 169 " pdb=" CA ASP C 169 " ideal model delta sigma weight residual 120.68 128.03 -7.35 1.52e+00 4.33e-01 2.34e+01 ... (remaining 31821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12459 17.94 - 35.88: 1555 35.88 - 53.82: 267 53.82 - 71.76: 47 71.76 - 89.70: 34 Dihedral angle restraints: 14362 sinusoidal: 5911 harmonic: 8451 Sorted by residual: dihedral pdb=" CA LEU A 335 " pdb=" C LEU A 335 " pdb=" N PRO A 336 " pdb=" CA PRO A 336 " ideal model delta harmonic sigma weight residual -180.00 -138.85 -41.15 0 5.00e+00 4.00e-02 6.77e+01 dihedral pdb=" CA PHE A 437 " pdb=" C PHE A 437 " pdb=" N GLU A 438 " pdb=" CA GLU A 438 " ideal model delta harmonic sigma weight residual -180.00 -146.36 -33.64 0 5.00e+00 4.00e-02 4.53e+01 dihedral pdb=" CA LEU E 124 " pdb=" C LEU E 124 " pdb=" N SER E 125 " pdb=" CA SER E 125 " ideal model delta harmonic sigma weight residual 180.00 148.42 31.58 0 5.00e+00 4.00e-02 3.99e+01 ... (remaining 14359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3085 0.067 - 0.134: 445 0.134 - 0.200: 55 0.200 - 0.267: 8 0.267 - 0.334: 3 Chirality restraints: 3596 Sorted by residual: chirality pdb=" CB ILE C 61 " pdb=" CA ILE C 61 " pdb=" CG1 ILE C 61 " pdb=" CG2 ILE C 61 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB VAL B 257 " pdb=" CA VAL B 257 " pdb=" CG1 VAL B 257 " pdb=" CG2 VAL B 257 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB ILE A 374 " pdb=" CA ILE A 374 " pdb=" CG1 ILE A 374 " pdb=" CG2 ILE A 374 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3593 not shown) Planarity restraints: 4055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 141 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO A 142 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 671 " 0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO B 672 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 672 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 672 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 289 " 0.047 5.00e-02 4.00e+02 7.05e-02 7.96e+00 pdb=" N PRO A 290 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " 0.040 5.00e-02 4.00e+02 ... (remaining 4052 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6445 2.80 - 3.33: 19605 3.33 - 3.85: 35326 3.85 - 4.38: 42188 4.38 - 4.90: 71886 Nonbonded interactions: 175450 Sorted by model distance: nonbonded pdb=" OH TYR B 453 " pdb=" O SER C 284 " model vdw 2.276 3.040 nonbonded pdb=" O ALA B 112 " pdb=" OG1 THR B 116 " model vdw 2.301 3.040 nonbonded pdb=" OG1 THR C 165 " pdb=" O ALA C 178 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR A 365 " pdb=" O LYS D 106 " model vdw 2.311 3.040 nonbonded pdb=" O ASP A 60 " pdb=" OG SER A 63 " model vdw 2.312 3.040 ... (remaining 175445 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=0.38 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.970 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 57.980 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.005 0.062 23549 Z= 0.225 Angle : 0.961 12.707 31826 Z= 0.564 Chirality : 0.049 0.334 3596 Planarity : 0.006 0.100 4055 Dihedral : 16.295 89.699 8856 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.46 % Favored : 92.43 % Rotamer: Outliers : 0.34 % Allowed : 8.54 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.23 (0.10), residues: 2828 helix: -4.67 (0.05), residues: 1485 sheet: -2.00 (0.35), residues: 195 loop : -3.52 (0.13), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 280 HIS 0.006 0.001 HIS B 211 PHE 0.023 0.002 PHE B 889 TYR 0.028 0.002 TYR B 432 ARG 0.006 0.001 ARG A 110 Details of bonding type rmsd hydrogen bonds : bond 0.33529 ( 759) hydrogen bonds : angle 10.17165 ( 2229) covalent geometry : bond 0.00476 (23549) covalent geometry : angle 0.96139 (31826) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 437 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ASN cc_start: 0.7798 (t0) cc_final: 0.7456 (t0) REVERT: A 308 MET cc_start: 0.7344 (mmt) cc_final: 0.6711 (tmm) REVERT: A 339 MET cc_start: 0.7779 (mtm) cc_final: 0.7397 (mtm) REVERT: A 340 LYS cc_start: 0.7758 (mttm) cc_final: 0.7515 (mtmm) REVERT: A 416 ASP cc_start: 0.7204 (t0) cc_final: 0.6829 (t0) REVERT: A 455 ILE cc_start: 0.8508 (tp) cc_final: 0.8116 (tp) REVERT: A 479 MET cc_start: 0.7800 (mtp) cc_final: 0.7507 (mtp) REVERT: A 553 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7226 (tp30) REVERT: A 578 ARG cc_start: 0.8043 (mtt180) cc_final: 0.7687 (mtp-110) REVERT: B 47 ASP cc_start: 0.7278 (t0) cc_final: 0.6823 (t0) REVERT: B 194 TYR cc_start: 0.8183 (m-10) cc_final: 0.7895 (m-10) REVERT: B 298 MET cc_start: 0.8323 (mmm) cc_final: 0.8073 (tpt) REVERT: B 338 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7723 (tm-30) REVERT: B 542 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7663 (mt) REVERT: B 660 LYS cc_start: 0.7831 (tmmt) cc_final: 0.7568 (ttpt) REVERT: B 802 TYR cc_start: 0.8023 (t80) cc_final: 0.7567 (t80) REVERT: B 937 LEU cc_start: 0.4420 (OUTLIER) cc_final: 0.4200 (pp) REVERT: B 978 MET cc_start: 0.4967 (mtp) cc_final: 0.4003 (pmm) REVERT: B 1117 LYS cc_start: 0.8459 (mmtm) cc_final: 0.8078 (tptm) REVERT: B 1139 MET cc_start: 0.7280 (mmm) cc_final: 0.7070 (mmt) REVERT: D 10 GLN cc_start: 0.8590 (mt0) cc_final: 0.8389 (mt0) REVERT: D 37 LEU cc_start: 0.9140 (tp) cc_final: 0.8926 (tp) REVERT: D 109 ASP cc_start: 0.8357 (t0) cc_final: 0.8156 (t0) REVERT: D 125 GLN cc_start: 0.7770 (mt0) cc_final: 0.7363 (tm-30) REVERT: F 189 VAL cc_start: 0.6627 (m) cc_final: 0.6315 (p) REVERT: F 253 GLU cc_start: 0.5686 (tm-30) cc_final: 0.4848 (pm20) REVERT: F 299 GLN cc_start: 0.7467 (tt0) cc_final: 0.7242 (tm-30) REVERT: F 354 ASP cc_start: 0.7386 (t70) cc_final: 0.7106 (t0) outliers start: 9 outliers final: 3 residues processed: 445 average time/residue: 0.3806 time to fit residues: 257.4717 Evaluate side-chains 318 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 313 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 144 optimal weight: 0.0060 chunk 114 optimal weight: 0.9980 chunk 221 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS A 260 ASN A 309 ASN A 355 ASN A 397 GLN A 407 ASN A 556 GLN B 11 ASN B 121 ASN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN B 311 ASN B 422 HIS B 590 ASN B 679 ASN B 703 GLN B 762 ASN B 801 GLN B 805 HIS B 984 HIS B1019 ASN B1061 ASN B1067 ASN B1163 GLN C 47 HIS C 72 HIS C 193 HIS C 328 ASN ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN D 59 GLN D 88 ASN D 93 GLN E 74 GLN E 79 GLN F 282 GLN F 330 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.187399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.130220 restraints weight = 31260.559| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.82 r_work: 0.3400 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23549 Z= 0.159 Angle : 0.635 8.416 31826 Z= 0.333 Chirality : 0.043 0.183 3596 Planarity : 0.005 0.083 4055 Dihedral : 5.887 46.705 3074 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.60 % Favored : 92.33 % Rotamer: Outliers : 2.02 % Allowed : 13.00 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.12), residues: 2828 helix: -2.99 (0.10), residues: 1474 sheet: -1.51 (0.36), residues: 197 loop : -3.19 (0.15), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 174 HIS 0.011 0.001 HIS B 805 PHE 0.032 0.002 PHE B 948 TYR 0.022 0.001 TYR A 552 ARG 0.005 0.000 ARG B 950 Details of bonding type rmsd hydrogen bonds : bond 0.05645 ( 759) hydrogen bonds : angle 5.19944 ( 2229) covalent geometry : bond 0.00360 (23549) covalent geometry : angle 0.63468 (31826) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 350 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASN cc_start: 0.8640 (t0) cc_final: 0.7776 (t0) REVERT: A 47 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6776 (mt-10) REVERT: A 153 MET cc_start: 0.8669 (ptp) cc_final: 0.8376 (ptm) REVERT: A 190 ASN cc_start: 0.8566 (t0) cc_final: 0.8225 (t0) REVERT: A 308 MET cc_start: 0.7438 (mmt) cc_final: 0.6423 (tmm) REVERT: A 340 LYS cc_start: 0.7807 (mttm) cc_final: 0.7553 (mtmm) REVERT: A 382 LEU cc_start: 0.8342 (tt) cc_final: 0.8031 (tp) REVERT: A 450 ASN cc_start: 0.8019 (m-40) cc_final: 0.7800 (m110) REVERT: B 47 ASP cc_start: 0.7713 (t0) cc_final: 0.7051 (t0) REVERT: B 194 TYR cc_start: 0.8617 (m-10) cc_final: 0.8077 (m-10) REVERT: B 195 ASP cc_start: 0.7745 (t0) cc_final: 0.7285 (t0) REVERT: B 338 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7160 (tp30) REVERT: B 351 MET cc_start: 0.7858 (mpp) cc_final: 0.7427 (mpp) REVERT: B 416 CYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7975 (m) REVERT: B 638 GLU cc_start: 0.8013 (tp30) cc_final: 0.7806 (tp30) REVERT: B 660 LYS cc_start: 0.8245 (tmmt) cc_final: 0.7946 (ttpt) REVERT: B 746 ASP cc_start: 0.8302 (t70) cc_final: 0.8098 (t0) REVERT: B 932 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.6863 (t80) REVERT: B 937 LEU cc_start: 0.4463 (OUTLIER) cc_final: 0.4134 (pp) REVERT: B 978 MET cc_start: 0.4788 (mtp) cc_final: 0.3970 (pmm) REVERT: B 1116 ARG cc_start: 0.8367 (tpt90) cc_final: 0.7767 (tpt90) REVERT: B 1139 MET cc_start: 0.7621 (mmm) cc_final: 0.7396 (mmt) REVERT: B 1221 MET cc_start: 0.7742 (mtt) cc_final: 0.7343 (tmm) REVERT: B 1242 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6866 (mm) REVERT: C 320 TYR cc_start: 0.8181 (m-80) cc_final: 0.7946 (m-80) REVERT: C 350 LYS cc_start: 0.6626 (tppt) cc_final: 0.6118 (pttm) REVERT: C 353 TYR cc_start: 0.4803 (t80) cc_final: 0.4321 (t80) REVERT: C 355 MET cc_start: 0.6035 (OUTLIER) cc_final: 0.5807 (mtm) REVERT: D 90 GLU cc_start: 0.8596 (tp30) cc_final: 0.8342 (tp30) REVERT: D 93 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7805 (tp-100) REVERT: D 125 GLN cc_start: 0.7855 (mt0) cc_final: 0.7137 (tm-30) REVERT: F 152 ARG cc_start: 0.7119 (ttp-170) cc_final: 0.6810 (tmm-80) REVERT: F 354 ASP cc_start: 0.7223 (t70) cc_final: 0.6766 (t0) outliers start: 53 outliers final: 31 residues processed: 387 average time/residue: 0.3445 time to fit residues: 213.4707 Evaluate side-chains 340 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 303 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 932 PHE Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1045 ASP Chi-restraints excluded: chain B residue 1065 ILE Chi-restraints excluded: chain B residue 1168 THR Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 1242 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 207 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 88 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 272 optimal weight: 5.9990 chunk 235 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 123 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 11 ASN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN B 749 ASN B 805 HIS ** B 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 HIS ** B1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 93 GLN ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.185958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.127259 restraints weight = 30956.486| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.77 r_work: 0.3369 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23549 Z= 0.155 Angle : 0.604 10.921 31826 Z= 0.311 Chirality : 0.043 0.181 3596 Planarity : 0.004 0.075 4055 Dihedral : 5.551 43.983 3074 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.67 % Favored : 92.29 % Rotamer: Outliers : 2.55 % Allowed : 15.97 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.14), residues: 2828 helix: -2.05 (0.12), residues: 1489 sheet: -1.35 (0.36), residues: 206 loop : -3.00 (0.15), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 174 HIS 0.007 0.001 HIS B 805 PHE 0.024 0.002 PHE A 437 TYR 0.023 0.001 TYR C 353 ARG 0.005 0.000 ARG B 950 Details of bonding type rmsd hydrogen bonds : bond 0.04830 ( 759) hydrogen bonds : angle 4.66869 ( 2229) covalent geometry : bond 0.00364 (23549) covalent geometry : angle 0.60364 (31826) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 332 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8414 (tpt) cc_final: 0.8084 (tpp) REVERT: A 45 ASN cc_start: 0.8705 (t0) cc_final: 0.7898 (t0) REVERT: A 47 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6547 (mt-10) REVERT: A 190 ASN cc_start: 0.8621 (t0) cc_final: 0.8270 (t0) REVERT: A 308 MET cc_start: 0.7727 (mmt) cc_final: 0.6473 (tmm) REVERT: A 340 LYS cc_start: 0.7854 (mttm) cc_final: 0.7570 (mtmm) REVERT: A 382 LEU cc_start: 0.8382 (tt) cc_final: 0.7983 (tp) REVERT: A 450 ASN cc_start: 0.8248 (m-40) cc_final: 0.8020 (m110) REVERT: A 589 ARG cc_start: 0.7885 (mtt180) cc_final: 0.7155 (mtt180) REVERT: B 47 ASP cc_start: 0.7712 (t0) cc_final: 0.7288 (t0) REVERT: B 109 MET cc_start: 0.8253 (mmt) cc_final: 0.8049 (mmt) REVERT: B 128 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7178 (pp) REVERT: B 194 TYR cc_start: 0.8661 (m-10) cc_final: 0.8062 (m-10) REVERT: B 195 ASP cc_start: 0.7952 (t0) cc_final: 0.7689 (t0) REVERT: B 338 GLU cc_start: 0.7423 (tm-30) cc_final: 0.6928 (tp30) REVERT: B 416 CYS cc_start: 0.8242 (OUTLIER) cc_final: 0.8002 (m) REVERT: B 498 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.7976 (tt) REVERT: B 746 ASP cc_start: 0.8337 (t70) cc_final: 0.8098 (t0) REVERT: B 937 LEU cc_start: 0.4521 (OUTLIER) cc_final: 0.4176 (pp) REVERT: B 1139 MET cc_start: 0.7610 (mmm) cc_final: 0.7405 (mmt) REVERT: B 1221 MET cc_start: 0.7463 (mtt) cc_final: 0.7194 (tmm) REVERT: C 350 LYS cc_start: 0.6508 (tppt) cc_final: 0.6158 (pttm) REVERT: C 352 TRP cc_start: 0.7978 (m100) cc_final: 0.7741 (m100) REVERT: C 353 TYR cc_start: 0.5512 (t80) cc_final: 0.5201 (t80) REVERT: C 355 MET cc_start: 0.6657 (mtm) cc_final: 0.5177 (mtm) REVERT: D 63 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8227 (tm-30) REVERT: E 85 LYS cc_start: 0.7655 (tppp) cc_final: 0.6893 (pptt) REVERT: E 102 GLU cc_start: 0.8497 (tp30) cc_final: 0.7905 (tt0) REVERT: E 160 TYR cc_start: 0.7203 (t80) cc_final: 0.6991 (t80) REVERT: F 152 ARG cc_start: 0.6998 (ttp-170) cc_final: 0.6644 (tmm-80) REVERT: F 259 ARG cc_start: 0.6839 (mmm-85) cc_final: 0.6577 (mpt-90) REVERT: F 268 ILE cc_start: 0.6112 (mm) cc_final: 0.5694 (pt) REVERT: F 299 GLN cc_start: 0.7484 (tt0) cc_final: 0.6961 (tm-30) REVERT: F 336 VAL cc_start: 0.5958 (p) cc_final: 0.5642 (t) REVERT: F 354 ASP cc_start: 0.7104 (t70) cc_final: 0.6656 (t0) outliers start: 67 outliers final: 38 residues processed: 383 average time/residue: 0.3287 time to fit residues: 202.9904 Evaluate side-chains 346 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 303 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1045 ASP Chi-restraints excluded: chain B residue 1065 ILE Chi-restraints excluded: chain B residue 1168 THR Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 207 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 86 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 56 optimal weight: 8.9990 chunk 140 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 HIS ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN B 805 HIS B 984 HIS B1161 HIS C 47 HIS C 173 ASN ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN E 74 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.188168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.132277 restraints weight = 31392.475| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.97 r_work: 0.3442 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23549 Z= 0.112 Angle : 0.554 9.428 31826 Z= 0.284 Chirality : 0.042 0.161 3596 Planarity : 0.004 0.070 4055 Dihedral : 5.092 42.398 3072 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.04 % Favored : 92.93 % Rotamer: Outliers : 2.63 % Allowed : 17.42 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.14), residues: 2828 helix: -1.39 (0.13), residues: 1484 sheet: -1.19 (0.37), residues: 210 loop : -2.84 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 144 HIS 0.009 0.001 HIS B 805 PHE 0.016 0.001 PHE B 948 TYR 0.035 0.001 TYR C 353 ARG 0.004 0.000 ARG B 950 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 759) hydrogen bonds : angle 4.20500 ( 2229) covalent geometry : bond 0.00256 (23549) covalent geometry : angle 0.55446 (31826) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 339 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8364 (tpt) cc_final: 0.8018 (tpp) REVERT: A 45 ASN cc_start: 0.8790 (t0) cc_final: 0.8504 (t0) REVERT: A 190 ASN cc_start: 0.8653 (t0) cc_final: 0.8279 (t0) REVERT: A 308 MET cc_start: 0.7810 (mmt) cc_final: 0.6399 (tmm) REVERT: A 340 LYS cc_start: 0.7722 (mttm) cc_final: 0.7444 (mtmm) REVERT: A 345 MET cc_start: 0.7603 (tpp) cc_final: 0.7368 (ttt) REVERT: A 361 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7688 (pt0) REVERT: A 450 ASN cc_start: 0.8386 (m-40) cc_final: 0.8136 (m110) REVERT: A 589 ARG cc_start: 0.7939 (mtt180) cc_final: 0.7424 (mtt180) REVERT: B 47 ASP cc_start: 0.7798 (t0) cc_final: 0.7448 (t0) REVERT: B 194 TYR cc_start: 0.8740 (m-10) cc_final: 0.8291 (m-10) REVERT: B 195 ASP cc_start: 0.7927 (t0) cc_final: 0.7713 (t0) REVERT: B 338 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7015 (tp30) REVERT: B 498 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8066 (tt) REVERT: B 746 ASP cc_start: 0.8465 (t70) cc_final: 0.8071 (t0) REVERT: B 937 LEU cc_start: 0.4556 (OUTLIER) cc_final: 0.4186 (pp) REVERT: B 1118 LEU cc_start: 0.7704 (mp) cc_final: 0.7495 (mp) REVERT: B 1221 MET cc_start: 0.7500 (mtt) cc_final: 0.7233 (tmm) REVERT: B 1242 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6652 (mm) REVERT: C 350 LYS cc_start: 0.6602 (tppt) cc_final: 0.6305 (pttm) REVERT: C 352 TRP cc_start: 0.8013 (m100) cc_final: 0.7540 (m100) REVERT: C 366 PHE cc_start: 0.6144 (m-80) cc_final: 0.5568 (m-80) REVERT: D 94 GLN cc_start: 0.8261 (mm-40) cc_final: 0.8050 (mm-40) REVERT: E 85 LYS cc_start: 0.7624 (tppp) cc_final: 0.6825 (pptt) REVERT: E 102 GLU cc_start: 0.8625 (tp30) cc_final: 0.8036 (tt0) REVERT: E 160 TYR cc_start: 0.7181 (t80) cc_final: 0.6919 (t80) REVERT: E 180 GLN cc_start: 0.5279 (tm-30) cc_final: 0.4696 (tt0) REVERT: F 152 ARG cc_start: 0.7033 (ttp-170) cc_final: 0.6686 (tmm-80) REVERT: F 219 LYS cc_start: 0.4298 (mmtm) cc_final: 0.3619 (tttm) REVERT: F 259 ARG cc_start: 0.6841 (mmm-85) cc_final: 0.6581 (mpt-90) REVERT: F 268 ILE cc_start: 0.6145 (mm) cc_final: 0.5704 (pt) REVERT: F 299 GLN cc_start: 0.7520 (tt0) cc_final: 0.6934 (tm-30) REVERT: F 336 VAL cc_start: 0.6161 (p) cc_final: 0.5834 (t) REVERT: F 354 ASP cc_start: 0.7038 (t70) cc_final: 0.6678 (t0) outliers start: 69 outliers final: 39 residues processed: 392 average time/residue: 0.3338 time to fit residues: 208.9794 Evaluate side-chains 348 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 306 time to evaluate : 3.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1045 ASP Chi-restraints excluded: chain B residue 1242 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 207 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 54 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 242 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 248 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN B 95 ASN B 96 HIS ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 HIS ** B 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 HIS ** B1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 93 GLN E 74 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.183768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.125479 restraints weight = 31442.975| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.74 r_work: 0.3329 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23549 Z= 0.200 Angle : 0.634 9.627 31826 Z= 0.325 Chirality : 0.045 0.214 3596 Planarity : 0.004 0.072 4055 Dihedral : 5.409 41.411 3072 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.20 % Favored : 91.73 % Rotamer: Outliers : 3.24 % Allowed : 18.75 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.15), residues: 2828 helix: -1.28 (0.13), residues: 1518 sheet: -1.14 (0.37), residues: 209 loop : -2.84 (0.16), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 144 HIS 0.030 0.002 HIS B 96 PHE 0.028 0.002 PHE B1010 TYR 0.034 0.002 TYR C 353 ARG 0.004 0.000 ARG E 76 Details of bonding type rmsd hydrogen bonds : bond 0.04573 ( 759) hydrogen bonds : angle 4.48421 ( 2229) covalent geometry : bond 0.00477 (23549) covalent geometry : angle 0.63417 (31826) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 321 time to evaluate : 2.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8446 (tpt) cc_final: 0.8054 (tpp) REVERT: A 45 ASN cc_start: 0.8755 (t0) cc_final: 0.8355 (t0) REVERT: A 47 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6486 (mt-10) REVERT: A 190 ASN cc_start: 0.8670 (t0) cc_final: 0.8274 (t0) REVERT: A 231 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7329 (pp) REVERT: A 308 MET cc_start: 0.7700 (mmt) cc_final: 0.6493 (tmm) REVERT: A 340 LYS cc_start: 0.7841 (mttm) cc_final: 0.7515 (mtmm) REVERT: A 345 MET cc_start: 0.7675 (tpp) cc_final: 0.7388 (ttt) REVERT: A 392 ASP cc_start: 0.7262 (t70) cc_final: 0.6879 (t70) REVERT: A 450 ASN cc_start: 0.8286 (m-40) cc_final: 0.7898 (t0) REVERT: A 578 ARG cc_start: 0.7698 (mtt180) cc_final: 0.7383 (mtp-110) REVERT: A 589 ARG cc_start: 0.8000 (mtt180) cc_final: 0.7558 (mtt90) REVERT: B 47 ASP cc_start: 0.7809 (t0) cc_final: 0.7419 (t0) REVERT: B 109 MET cc_start: 0.8329 (mmt) cc_final: 0.7920 (mmm) REVERT: B 128 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7153 (pp) REVERT: B 338 GLU cc_start: 0.7479 (tm-30) cc_final: 0.6993 (tp30) REVERT: B 498 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8075 (tt) REVERT: B 746 ASP cc_start: 0.8333 (t70) cc_final: 0.8081 (t0) REVERT: B 937 LEU cc_start: 0.4541 (OUTLIER) cc_final: 0.4253 (pp) REVERT: B 1242 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6735 (mm) REVERT: C 252 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.7187 (p-80) REVERT: C 350 LYS cc_start: 0.6512 (tppt) cc_final: 0.6184 (pttm) REVERT: C 352 TRP cc_start: 0.7887 (m100) cc_final: 0.7341 (m100) REVERT: C 353 TYR cc_start: 0.6091 (t80) cc_final: 0.5657 (t80) REVERT: C 366 PHE cc_start: 0.6501 (m-80) cc_final: 0.5987 (m-80) REVERT: D 63 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7696 (pt0) REVERT: D 93 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7600 (tp-100) REVERT: D 94 GLN cc_start: 0.8307 (mm-40) cc_final: 0.8064 (mm-40) REVERT: E 85 LYS cc_start: 0.7675 (tppp) cc_final: 0.6905 (pptt) REVERT: E 160 TYR cc_start: 0.7484 (t80) cc_final: 0.7162 (t80) REVERT: E 180 GLN cc_start: 0.4969 (tm-30) cc_final: 0.4466 (tt0) REVERT: F 242 GLN cc_start: 0.6679 (mp10) cc_final: 0.6073 (tt0) REVERT: F 259 ARG cc_start: 0.6869 (mmm-85) cc_final: 0.6633 (mpt-90) REVERT: F 268 ILE cc_start: 0.6273 (mm) cc_final: 0.5796 (pt) REVERT: F 299 GLN cc_start: 0.7580 (tt0) cc_final: 0.6999 (tm-30) REVERT: F 354 ASP cc_start: 0.6996 (t70) cc_final: 0.6558 (t0) outliers start: 85 outliers final: 53 residues processed: 380 average time/residue: 0.3389 time to fit residues: 204.8014 Evaluate side-chains 362 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 301 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1045 ASP Chi-restraints excluded: chain B residue 1065 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1168 THR Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 1242 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 207 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 3 optimal weight: 9.9990 chunk 181 optimal weight: 0.1980 chunk 132 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 189 optimal weight: 0.6980 chunk 249 optimal weight: 0.0570 chunk 255 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 102 optimal weight: 0.0870 chunk 16 optimal weight: 1.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 211 HIS ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 HIS B 984 HIS ** B1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 93 GLN F 98 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.188557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.142435 restraints weight = 30812.758| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.89 r_work: 0.3413 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23549 Z= 0.096 Angle : 0.549 11.194 31826 Z= 0.279 Chirality : 0.041 0.184 3596 Planarity : 0.003 0.066 4055 Dihedral : 4.867 41.793 3072 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.05 % Favored : 93.92 % Rotamer: Outliers : 1.98 % Allowed : 20.81 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.15), residues: 2828 helix: -0.71 (0.13), residues: 1479 sheet: -1.00 (0.37), residues: 203 loop : -2.66 (0.16), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 144 HIS 0.015 0.001 HIS C 47 PHE 0.011 0.001 PHE B1054 TYR 0.031 0.001 TYR C 353 ARG 0.005 0.000 ARG E 76 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 759) hydrogen bonds : angle 3.96920 ( 2229) covalent geometry : bond 0.00210 (23549) covalent geometry : angle 0.54949 (31826) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 332 time to evaluate : 2.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8504 (tpt) cc_final: 0.7944 (tpp) REVERT: A 45 ASN cc_start: 0.8693 (t0) cc_final: 0.8440 (t0) REVERT: A 190 ASN cc_start: 0.8458 (t0) cc_final: 0.8071 (t0) REVERT: A 293 ASP cc_start: 0.7596 (m-30) cc_final: 0.7224 (p0) REVERT: A 308 MET cc_start: 0.7709 (mmt) cc_final: 0.6436 (tmm) REVERT: A 340 LYS cc_start: 0.7828 (mttm) cc_final: 0.7568 (mtmm) REVERT: A 372 MET cc_start: 0.8065 (mtp) cc_final: 0.7235 (mmm) REVERT: A 450 ASN cc_start: 0.8229 (m-40) cc_final: 0.7833 (t0) REVERT: A 468 ASP cc_start: 0.7856 (p0) cc_final: 0.7524 (p0) REVERT: A 578 ARG cc_start: 0.7638 (mtt180) cc_final: 0.7411 (mtp-110) REVERT: A 589 ARG cc_start: 0.7960 (mtt180) cc_final: 0.7208 (mtp85) REVERT: B 47 ASP cc_start: 0.7683 (t0) cc_final: 0.7348 (t0) REVERT: B 48 PHE cc_start: 0.7843 (t80) cc_final: 0.7544 (t80) REVERT: B 109 MET cc_start: 0.8280 (mmt) cc_final: 0.7942 (mmm) REVERT: B 194 TYR cc_start: 0.8610 (m-10) cc_final: 0.8216 (m-10) REVERT: B 338 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7063 (tp30) REVERT: B 498 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8082 (tt) REVERT: B 802 TYR cc_start: 0.7883 (t80) cc_final: 0.7517 (t80) REVERT: B 937 LEU cc_start: 0.4135 (OUTLIER) cc_final: 0.3866 (pp) REVERT: B 1127 GLU cc_start: 0.8474 (pt0) cc_final: 0.8117 (pt0) REVERT: C 350 LYS cc_start: 0.6319 (tppt) cc_final: 0.6044 (pttm) REVERT: C 352 TRP cc_start: 0.7714 (m100) cc_final: 0.7205 (m100) REVERT: C 355 MET cc_start: 0.7092 (mtm) cc_final: 0.6502 (mtm) REVERT: C 362 LEU cc_start: 0.2710 (OUTLIER) cc_final: 0.2433 (tt) REVERT: C 366 PHE cc_start: 0.6402 (m-80) cc_final: 0.5917 (m-80) REVERT: D 63 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7361 (pt0) REVERT: E 76 ARG cc_start: 0.8582 (tpt170) cc_final: 0.8186 (tpt170) REVERT: E 85 LYS cc_start: 0.7626 (tppp) cc_final: 0.6871 (pptt) REVERT: E 102 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8094 (tt0) REVERT: E 160 TYR cc_start: 0.7348 (t80) cc_final: 0.7058 (t80) REVERT: E 180 GLN cc_start: 0.5352 (tm-30) cc_final: 0.4893 (tt0) REVERT: F 194 ARG cc_start: 0.3515 (tpt170) cc_final: 0.2709 (ptp-170) REVERT: F 219 LYS cc_start: 0.4169 (mmtm) cc_final: 0.3530 (tttm) REVERT: F 242 GLN cc_start: 0.6844 (mp10) cc_final: 0.6333 (tt0) REVERT: F 259 ARG cc_start: 0.6816 (mmm-85) cc_final: 0.6598 (mpt-90) REVERT: F 268 ILE cc_start: 0.6316 (mm) cc_final: 0.5832 (pt) REVERT: F 299 GLN cc_start: 0.7430 (tt0) cc_final: 0.6852 (tm-30) REVERT: F 354 ASP cc_start: 0.6883 (t70) cc_final: 0.6558 (t0) outliers start: 52 outliers final: 36 residues processed: 371 average time/residue: 0.3359 time to fit residues: 198.6129 Evaluate side-chains 339 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 300 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1045 ASP Chi-restraints excluded: chain B residue 1168 THR Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 243 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 183 optimal weight: 0.9990 chunk 32 optimal weight: 20.0000 chunk 110 optimal weight: 0.6980 chunk 249 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 239 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN B 96 HIS B 805 HIS B 848 GLN B 984 HIS ** B1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN D 59 GLN D 93 GLN E 24 GLN F 392 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.186741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140971 restraints weight = 31146.555| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.09 r_work: 0.3381 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23549 Z= 0.122 Angle : 0.569 11.553 31826 Z= 0.287 Chirality : 0.042 0.171 3596 Planarity : 0.004 0.068 4055 Dihedral : 4.828 41.289 3072 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.97 % Favored : 93.00 % Rotamer: Outliers : 2.36 % Allowed : 21.34 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.15), residues: 2828 helix: -0.55 (0.13), residues: 1486 sheet: -0.95 (0.37), residues: 204 loop : -2.62 (0.16), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 144 HIS 0.013 0.001 HIS C 47 PHE 0.030 0.001 PHE B1010 TYR 0.029 0.001 TYR C 353 ARG 0.006 0.000 ARG E 76 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 759) hydrogen bonds : angle 3.97364 ( 2229) covalent geometry : bond 0.00288 (23549) covalent geometry : angle 0.56934 (31826) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 313 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8551 (tpt) cc_final: 0.7958 (tpp) REVERT: A 45 ASN cc_start: 0.8712 (t0) cc_final: 0.8463 (t0) REVERT: A 190 ASN cc_start: 0.8534 (t0) cc_final: 0.8145 (t0) REVERT: A 293 ASP cc_start: 0.7696 (m-30) cc_final: 0.7319 (p0) REVERT: A 308 MET cc_start: 0.7692 (mmt) cc_final: 0.6487 (tmm) REVERT: A 340 LYS cc_start: 0.7821 (mttm) cc_final: 0.7554 (mtmm) REVERT: A 372 MET cc_start: 0.8172 (mtp) cc_final: 0.7292 (mmm) REVERT: A 450 ASN cc_start: 0.8171 (m-40) cc_final: 0.7802 (t0) REVERT: A 578 ARG cc_start: 0.7672 (mtt180) cc_final: 0.7418 (mtp-110) REVERT: A 589 ARG cc_start: 0.7987 (mtt180) cc_final: 0.7497 (mtt90) REVERT: B 109 MET cc_start: 0.8330 (mmt) cc_final: 0.7964 (mmm) REVERT: B 128 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7356 (pp) REVERT: B 338 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6972 (tp30) REVERT: B 498 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8040 (tt) REVERT: B 802 TYR cc_start: 0.7888 (t80) cc_final: 0.7507 (t80) REVERT: B 848 GLN cc_start: 0.7745 (tp-100) cc_final: 0.7315 (tp-100) REVERT: B 937 LEU cc_start: 0.4276 (OUTLIER) cc_final: 0.4014 (pp) REVERT: B 1127 GLU cc_start: 0.8467 (pt0) cc_final: 0.8150 (pt0) REVERT: B 1242 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6947 (mm) REVERT: C 352 TRP cc_start: 0.7716 (m100) cc_final: 0.7212 (m100) REVERT: C 355 MET cc_start: 0.7294 (mtm) cc_final: 0.7056 (mtm) REVERT: C 362 LEU cc_start: 0.2811 (OUTLIER) cc_final: 0.2570 (tt) REVERT: C 366 PHE cc_start: 0.6524 (m-80) cc_final: 0.6091 (m-80) REVERT: D 63 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7288 (pt0) REVERT: E 85 LYS cc_start: 0.7633 (tppp) cc_final: 0.6870 (pptt) REVERT: E 102 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8029 (tt0) REVERT: E 160 TYR cc_start: 0.7329 (t80) cc_final: 0.7105 (t80) REVERT: E 180 GLN cc_start: 0.5042 (tm-30) cc_final: 0.4642 (tt0) REVERT: F 140 ARG cc_start: 0.2391 (mtm-85) cc_final: 0.1558 (mmm160) REVERT: F 242 GLN cc_start: 0.6882 (mp10) cc_final: 0.6386 (tt0) REVERT: F 259 ARG cc_start: 0.6826 (mmm-85) cc_final: 0.6622 (mpt-90) REVERT: F 268 ILE cc_start: 0.6328 (mm) cc_final: 0.5868 (pt) REVERT: F 299 GLN cc_start: 0.7555 (tt0) cc_final: 0.6990 (tm-30) REVERT: F 354 ASP cc_start: 0.6823 (t70) cc_final: 0.6490 (t0) outliers start: 62 outliers final: 39 residues processed: 358 average time/residue: 0.3319 time to fit residues: 191.1531 Evaluate side-chains 340 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 296 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1045 ASP Chi-restraints excluded: chain B residue 1168 THR Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 1242 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 207 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 153 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 chunk 212 optimal weight: 8.9990 chunk 272 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 262 optimal weight: 0.9980 chunk 236 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN B 794 ASN B 805 HIS ** B 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 HIS ** B1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN D 59 GLN D 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.185223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.133689 restraints weight = 31229.719| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.89 r_work: 0.3448 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23549 Z= 0.153 Angle : 0.603 11.018 31826 Z= 0.305 Chirality : 0.044 0.167 3596 Planarity : 0.004 0.081 4055 Dihedral : 4.986 41.023 3072 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.32 % Favored : 92.64 % Rotamer: Outliers : 2.13 % Allowed : 22.03 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.15), residues: 2828 helix: -0.52 (0.13), residues: 1496 sheet: -0.97 (0.37), residues: 206 loop : -2.63 (0.16), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 174 HIS 0.013 0.001 HIS C 47 PHE 0.017 0.001 PHE B 234 TYR 0.032 0.001 TYR C 353 ARG 0.009 0.000 ARG B1116 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 759) hydrogen bonds : angle 4.08603 ( 2229) covalent geometry : bond 0.00365 (23549) covalent geometry : angle 0.60335 (31826) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 308 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8587 (tpt) cc_final: 0.7981 (tpp) REVERT: A 45 ASN cc_start: 0.8790 (t0) cc_final: 0.8539 (t0) REVERT: A 293 ASP cc_start: 0.7853 (m-30) cc_final: 0.7354 (p0) REVERT: A 308 MET cc_start: 0.7713 (mmt) cc_final: 0.6502 (tmm) REVERT: A 340 LYS cc_start: 0.7895 (mttm) cc_final: 0.7610 (mtmm) REVERT: A 372 MET cc_start: 0.8292 (mtp) cc_final: 0.7293 (mmm) REVERT: A 450 ASN cc_start: 0.8227 (m-40) cc_final: 0.7821 (t0) REVERT: A 589 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7595 (mtt90) REVERT: B 128 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7427 (pp) REVERT: B 338 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7071 (tp30) REVERT: B 498 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8031 (tt) REVERT: B 937 LEU cc_start: 0.4451 (OUTLIER) cc_final: 0.4190 (pp) REVERT: B 1127 GLU cc_start: 0.8433 (pt0) cc_final: 0.8099 (pt0) REVERT: B 1242 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6862 (mm) REVERT: C 352 TRP cc_start: 0.8062 (m100) cc_final: 0.7503 (m100) REVERT: C 355 MET cc_start: 0.7386 (mtm) cc_final: 0.7172 (mtm) REVERT: C 362 LEU cc_start: 0.2972 (OUTLIER) cc_final: 0.2660 (tt) REVERT: C 366 PHE cc_start: 0.6585 (m-80) cc_final: 0.6292 (m-80) REVERT: D 63 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7279 (pt0) REVERT: D 93 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7553 (tp-100) REVERT: E 85 LYS cc_start: 0.7637 (tppp) cc_final: 0.6825 (pptt) REVERT: E 102 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8073 (tt0) REVERT: F 140 ARG cc_start: 0.2460 (mtm-85) cc_final: 0.1607 (mmm160) REVERT: F 242 GLN cc_start: 0.6835 (mp10) cc_final: 0.6376 (tt0) REVERT: F 268 ILE cc_start: 0.6332 (mm) cc_final: 0.5829 (pt) REVERT: F 299 GLN cc_start: 0.7628 (tt0) cc_final: 0.7090 (tm-30) REVERT: F 354 ASP cc_start: 0.6838 (t70) cc_final: 0.6479 (t0) outliers start: 56 outliers final: 40 residues processed: 347 average time/residue: 0.3381 time to fit residues: 188.9360 Evaluate side-chains 342 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 295 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1045 ASP Chi-restraints excluded: chain B residue 1168 THR Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 1242 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 325 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 103 optimal weight: 7.9990 chunk 110 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 225 optimal weight: 3.9990 chunk 118 optimal weight: 0.0020 chunk 133 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 264 optimal weight: 10.0000 chunk 273 optimal weight: 3.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN B 805 HIS B 848 GLN B 984 HIS B 988 ASN B1113 GLN ** B1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN D 59 GLN D 93 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.188219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.142487 restraints weight = 31047.840| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.96 r_work: 0.3409 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 23549 Z= 0.102 Angle : 0.562 11.663 31826 Z= 0.282 Chirality : 0.042 0.197 3596 Planarity : 0.003 0.064 4055 Dihedral : 4.712 41.917 3072 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.75 % Favored : 93.21 % Rotamer: Outliers : 1.64 % Allowed : 22.64 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.15), residues: 2828 helix: -0.25 (0.14), residues: 1500 sheet: -0.89 (0.36), residues: 206 loop : -2.57 (0.16), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 174 HIS 0.012 0.001 HIS C 47 PHE 0.015 0.001 PHE B 89 TYR 0.029 0.001 TYR C 353 ARG 0.006 0.000 ARG E 76 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 759) hydrogen bonds : angle 3.84654 ( 2229) covalent geometry : bond 0.00232 (23549) covalent geometry : angle 0.56171 (31826) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 309 time to evaluate : 2.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASN cc_start: 0.8688 (t0) cc_final: 0.8481 (t0) REVERT: A 293 ASP cc_start: 0.7578 (m-30) cc_final: 0.7235 (p0) REVERT: A 308 MET cc_start: 0.7685 (mmt) cc_final: 0.6586 (tmm) REVERT: A 372 MET cc_start: 0.8183 (mtp) cc_final: 0.7339 (mmm) REVERT: A 387 THR cc_start: 0.7851 (m) cc_final: 0.7552 (t) REVERT: A 450 ASN cc_start: 0.8189 (m-40) cc_final: 0.7851 (t0) REVERT: A 589 ARG cc_start: 0.7935 (mtt180) cc_final: 0.7531 (mtt90) REVERT: B 194 TYR cc_start: 0.8575 (m-10) cc_final: 0.8142 (m-10) REVERT: B 338 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7132 (tp30) REVERT: B 498 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8083 (tt) REVERT: B 848 GLN cc_start: 0.7902 (tp-100) cc_final: 0.7563 (tp-100) REVERT: B 937 LEU cc_start: 0.4805 (OUTLIER) cc_final: 0.4504 (pp) REVERT: B 1076 LYS cc_start: 0.8531 (tttm) cc_final: 0.8163 (tmtt) REVERT: B 1127 GLU cc_start: 0.8457 (pt0) cc_final: 0.8108 (pt0) REVERT: C 352 TRP cc_start: 0.7943 (m100) cc_final: 0.7460 (m100) REVERT: C 355 MET cc_start: 0.7271 (mtm) cc_final: 0.6951 (mtm) REVERT: C 362 LEU cc_start: 0.2866 (OUTLIER) cc_final: 0.2564 (tt) REVERT: C 366 PHE cc_start: 0.6417 (m-80) cc_final: 0.5886 (m-80) REVERT: D 63 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7317 (pt0) REVERT: D 93 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7486 (tp-100) REVERT: E 81 LEU cc_start: 0.8783 (tp) cc_final: 0.8580 (tt) REVERT: E 85 LYS cc_start: 0.7689 (tppp) cc_final: 0.6899 (pptt) REVERT: E 102 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8090 (tt0) REVERT: F 140 ARG cc_start: 0.2468 (mtm-85) cc_final: 0.1817 (mmm160) REVERT: F 242 GLN cc_start: 0.6767 (mp10) cc_final: 0.6356 (tt0) REVERT: F 268 ILE cc_start: 0.6309 (mm) cc_final: 0.5819 (pt) REVERT: F 299 GLN cc_start: 0.7555 (tt0) cc_final: 0.7045 (tm-30) REVERT: F 354 ASP cc_start: 0.6706 (t70) cc_final: 0.6396 (t0) outliers start: 43 outliers final: 35 residues processed: 338 average time/residue: 0.3389 time to fit residues: 182.7522 Evaluate side-chains 334 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 294 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1045 ASP Chi-restraints excluded: chain B residue 1168 THR Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 116 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 210 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 178 optimal weight: 20.0000 chunk 141 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN B 151 ASN ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 HIS ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN D 59 GLN D 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.187022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133653 restraints weight = 31220.314| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.56 r_work: 0.3443 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23549 Z= 0.122 Angle : 0.576 11.207 31826 Z= 0.289 Chirality : 0.042 0.175 3596 Planarity : 0.004 0.069 4055 Dihedral : 4.712 41.699 3071 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.21 % Favored : 92.75 % Rotamer: Outliers : 1.71 % Allowed : 22.64 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.15), residues: 2828 helix: -0.22 (0.14), residues: 1510 sheet: -0.99 (0.37), residues: 199 loop : -2.51 (0.17), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP C 174 HIS 0.012 0.001 HIS C 47 PHE 0.017 0.001 PHE B 948 TYR 0.039 0.001 TYR C 353 ARG 0.005 0.000 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 759) hydrogen bonds : angle 3.90997 ( 2229) covalent geometry : bond 0.00288 (23549) covalent geometry : angle 0.57623 (31826) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 305 time to evaluate : 2.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASN cc_start: 0.8796 (t0) cc_final: 0.8539 (t0) REVERT: A 293 ASP cc_start: 0.7877 (m-30) cc_final: 0.7383 (p0) REVERT: A 308 MET cc_start: 0.7724 (mmt) cc_final: 0.6588 (tmm) REVERT: A 372 MET cc_start: 0.8298 (mtp) cc_final: 0.7382 (mmm) REVERT: A 387 THR cc_start: 0.7891 (m) cc_final: 0.7589 (t) REVERT: A 450 ASN cc_start: 0.8282 (m-40) cc_final: 0.7874 (t0) REVERT: A 589 ARG cc_start: 0.7998 (mtt180) cc_final: 0.7569 (mtt90) REVERT: B 138 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8069 (mp0) REVERT: B 194 TYR cc_start: 0.8683 (m-10) cc_final: 0.8237 (m-10) REVERT: B 338 GLU cc_start: 0.7345 (tm-30) cc_final: 0.7053 (tp30) REVERT: B 498 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8022 (tt) REVERT: B 848 GLN cc_start: 0.7892 (tp-100) cc_final: 0.7527 (tp-100) REVERT: B 937 LEU cc_start: 0.4978 (OUTLIER) cc_final: 0.4661 (pp) REVERT: B 1076 LYS cc_start: 0.8542 (tttm) cc_final: 0.8180 (tmtt) REVERT: B 1127 GLU cc_start: 0.8498 (pt0) cc_final: 0.8176 (pt0) REVERT: C 352 TRP cc_start: 0.7976 (m100) cc_final: 0.7422 (m100) REVERT: C 355 MET cc_start: 0.7304 (mtm) cc_final: 0.6956 (mtm) REVERT: C 362 LEU cc_start: 0.2839 (OUTLIER) cc_final: 0.2548 (tt) REVERT: C 366 PHE cc_start: 0.6590 (m-80) cc_final: 0.5976 (m-80) REVERT: D 63 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7292 (pt0) REVERT: E 81 LEU cc_start: 0.8818 (tp) cc_final: 0.8606 (tt) REVERT: E 85 LYS cc_start: 0.7609 (tppp) cc_final: 0.6764 (pptt) REVERT: E 102 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8072 (tt0) REVERT: F 140 ARG cc_start: 0.2377 (mtm-85) cc_final: 0.1634 (mmm160) REVERT: F 194 ARG cc_start: 0.3957 (tpt170) cc_final: 0.3064 (tpt170) REVERT: F 242 GLN cc_start: 0.6813 (mp10) cc_final: 0.6390 (tt0) REVERT: F 268 ILE cc_start: 0.6278 (mm) cc_final: 0.5782 (pt) REVERT: F 299 GLN cc_start: 0.7566 (tt0) cc_final: 0.7017 (tm-30) REVERT: F 354 ASP cc_start: 0.6769 (t70) cc_final: 0.6431 (t0) outliers start: 45 outliers final: 37 residues processed: 335 average time/residue: 0.4648 time to fit residues: 254.2185 Evaluate side-chains 335 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 294 time to evaluate : 3.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1045 ASP Chi-restraints excluded: chain B residue 1168 THR Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.3504 > 50: distance: 140 - 159: 3.960 distance: 146 - 166: 30.584 distance: 155 - 185: 28.898 distance: 159 - 160: 27.321 distance: 160 - 161: 44.146 distance: 160 - 163: 49.628 distance: 161 - 162: 36.876 distance: 161 - 166: 49.297 distance: 162 - 197: 44.676 distance: 163 - 164: 56.455 distance: 163 - 165: 49.141 distance: 166 - 167: 36.502 distance: 167 - 168: 29.365 distance: 167 - 170: 36.830 distance: 168 - 169: 47.160 distance: 168 - 174: 46.986 distance: 169 - 205: 45.513 distance: 170 - 171: 39.686 distance: 171 - 172: 41.825 distance: 171 - 173: 17.382 distance: 174 - 175: 65.490 distance: 175 - 176: 69.066 distance: 175 - 178: 57.479 distance: 176 - 177: 24.032 distance: 176 - 185: 41.436 distance: 178 - 179: 39.422 distance: 179 - 180: 40.130 distance: 180 - 181: 15.056 distance: 181 - 182: 33.649 distance: 182 - 183: 27.269 distance: 182 - 184: 18.037 distance: 185 - 186: 43.493 distance: 186 - 187: 17.629 distance: 186 - 189: 46.201 distance: 187 - 188: 68.023 distance: 187 - 197: 61.030 distance: 189 - 190: 40.746 distance: 190 - 191: 26.574 distance: 190 - 192: 45.841 distance: 191 - 193: 34.320 distance: 192 - 194: 14.941 distance: 193 - 195: 46.312 distance: 194 - 195: 5.157 distance: 195 - 196: 16.705 distance: 197 - 198: 13.342 distance: 198 - 199: 29.367 distance: 198 - 201: 52.086 distance: 199 - 200: 43.830 distance: 199 - 205: 38.836 distance: 201 - 202: 69.238 distance: 201 - 203: 41.244 distance: 202 - 204: 23.052 distance: 205 - 206: 65.846 distance: 206 - 207: 40.014 distance: 206 - 209: 57.959 distance: 207 - 208: 54.785 distance: 207 - 213: 56.626 distance: 209 - 210: 7.963 distance: 210 - 211: 69.865 distance: 210 - 212: 55.785 distance: 213 - 214: 56.402 distance: 214 - 215: 60.146 distance: 214 - 217: 28.838 distance: 215 - 216: 41.147 distance: 215 - 221: 40.478 distance: 217 - 218: 28.431 distance: 218 - 219: 50.493 distance: 218 - 220: 25.173 distance: 221 - 222: 32.968 distance: 222 - 223: 23.000 distance: 222 - 225: 44.353 distance: 223 - 224: 58.556 distance: 223 - 229: 57.888 distance: 225 - 226: 48.563 distance: 226 - 227: 43.900 distance: 226 - 228: 38.617 distance: 229 - 230: 47.808 distance: 230 - 231: 44.844 distance: 230 - 233: 43.990 distance: 231 - 232: 46.516 distance: 231 - 238: 69.572 distance: 233 - 234: 66.904 distance: 234 - 235: 41.187 distance: 235 - 236: 57.516 distance: 236 - 237: 56.048 distance: 239 - 240: 40.337 distance: 239 - 242: 40.940 distance: 240 - 241: 56.664 distance: 240 - 249: 25.075 distance: 242 - 243: 56.886 distance: 243 - 244: 54.629 distance: 244 - 245: 54.938 distance: 245 - 246: 64.594 distance: 246 - 247: 40.682 distance: 246 - 248: 12.585