Starting phenix.real_space_refine on Sun Aug 24 21:22:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v2y_31670/08_2025/7v2y_31670.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v2y_31670/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/7v2y_31670/08_2025/7v2y_31670.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v2y_31670/08_2025/7v2y_31670.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v2y_31670/08_2025/7v2y_31670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v2y_31670/08_2025/7v2y_31670.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.36, per 1000 atoms: 0.23 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: 2.03 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.89 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: 4.64 Time building geometry restraints manager: 2.67 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.530 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.420 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.010 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG A 110 TYR 0.028 0.002 TYR B 432 PHE 0.023 0.002 PHE B 889 TRP 0.019 0.002 TRP C 280 HIS 0.006 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00476 (23549) covalent geometry : angle 0.96139 (31826) hydrogen bonds : bond 0.33529 ( 759) hydrogen bonds : angle 10.17165 ( 2229) *********************** 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 : 0.948 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: 0.1864 time to fit residues: 125.8223 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 : 0.965 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN 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 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 88 ASN D 93 GLN E 74 GLN E 79 GLN F 282 GLN F 330 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.189998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.132896 restraints weight = 31254.952| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.68 r_work: 0.3465 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1929 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= 0.125 Angle : 0.602 8.047 31826 Z= 0.316 Chirality : 0.042 0.181 3596 Planarity : 0.005 0.081 4055 Dihedral : 5.694 47.682 3074 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.07 % Favored : 92.86 % Rotamer: Outliers : 1.68 % Allowed : 13.03 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.60 (0.12), residues: 2828 helix: -3.06 (0.10), residues: 1471 sheet: -1.51 (0.37), residues: 195 loop : -3.18 (0.14), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 67 TYR 0.021 0.001 TYR A 552 PHE 0.030 0.001 PHE B 948 TRP 0.024 0.001 TRP C 174 HIS 0.010 0.001 HIS B 805 Details of bonding type rmsd covalent geometry : bond 0.00266 (23549) covalent geometry : angle 0.60192 (31826) hydrogen bonds : bond 0.05696 ( 759) hydrogen bonds : angle 5.13004 ( 2229) *********************** 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 400 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 356 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ASN cc_start: 0.8578 (t0) cc_final: 0.8012 (t0) REVERT: A 47 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6672 (mt-10) REVERT: A 153 MET cc_start: 0.8524 (ptp) cc_final: 0.8224 (ptm) REVERT: A 190 ASN cc_start: 0.8506 (t0) cc_final: 0.8171 (t0) REVERT: A 308 MET cc_start: 0.7423 (mmt) cc_final: 0.6397 (tmm) REVERT: A 340 LYS cc_start: 0.7673 (mttm) cc_final: 0.7419 (mtmm) REVERT: A 382 LEU cc_start: 0.8280 (tt) cc_final: 0.8020 (tp) REVERT: A 450 ASN cc_start: 0.8010 (m-40) cc_final: 0.7800 (m110) REVERT: B 47 ASP cc_start: 0.7690 (t0) cc_final: 0.7283 (t0) REVERT: B 194 TYR cc_start: 0.8588 (m-10) cc_final: 0.8185 (m-10) REVERT: B 338 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7067 (tp30) REVERT: B 351 MET cc_start: 0.7856 (mpp) cc_final: 0.7433 (mpp) REVERT: B 542 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7694 (mt) REVERT: B 556 ASP cc_start: 0.8169 (t70) cc_final: 0.7931 (t0) REVERT: B 638 GLU cc_start: 0.7909 (tp30) cc_final: 0.7644 (tp30) REVERT: B 660 LYS cc_start: 0.8151 (tmmt) cc_final: 0.7863 (ttpt) REVERT: B 746 ASP cc_start: 0.8206 (t70) cc_final: 0.7994 (t0) REVERT: B 932 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.6828 (t80) REVERT: B 937 LEU cc_start: 0.4672 (OUTLIER) cc_final: 0.4300 (pp) REVERT: B 978 MET cc_start: 0.4763 (mtp) cc_final: 0.3983 (pmm) REVERT: B 1076 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8640 (tttm) REVERT: B 1116 ARG cc_start: 0.8352 (tpt90) cc_final: 0.8141 (tpp80) REVERT: B 1139 MET cc_start: 0.7593 (mmm) cc_final: 0.7383 (mmt) REVERT: B 1221 MET cc_start: 0.7676 (mtt) cc_final: 0.7359 (tmm) REVERT: C 320 TYR cc_start: 0.8080 (m-80) cc_final: 0.7851 (m-80) REVERT: C 353 TYR cc_start: 0.4591 (t80) cc_final: 0.4060 (t80) REVERT: C 355 MET cc_start: 0.5964 (OUTLIER) cc_final: 0.5758 (mtm) REVERT: D 93 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7804 (tp-100) REVERT: D 125 GLN cc_start: 0.7807 (mt0) cc_final: 0.7092 (tm-30) REVERT: F 152 ARG cc_start: 0.7059 (ttp-170) cc_final: 0.6781 (tmm-80) REVERT: F 242 GLN cc_start: 0.6657 (mp10) cc_final: 0.6434 (mt0) REVERT: F 259 ARG cc_start: 0.6977 (mmm-85) cc_final: 0.6731 (mpt-90) REVERT: F 354 ASP cc_start: 0.7213 (t70) cc_final: 0.6777 (t0) outliers start: 44 outliers final: 22 residues processed: 385 average time/residue: 0.1595 time to fit residues: 98.2269 Evaluate side-chains 332 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 304 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 B residue 245 LEU Chi-restraints excluded: chain B residue 432 TYR 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 1065 ILE Chi-restraints excluded: chain B residue 1076 LYS Chi-restraints excluded: chain B residue 1168 THR 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 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 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 3 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 215 optimal weight: 0.0770 chunk 104 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 94 optimal weight: 0.0570 chunk 176 optimal weight: 2.9990 chunk 239 optimal weight: 0.6980 chunk 224 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN B 805 HIS B 984 HIS B1161 HIS ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.191120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.146327 restraints weight = 31206.461| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 3.08 r_work: 0.3449 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23549 Z= 0.104 Angle : 0.547 9.038 31826 Z= 0.282 Chirality : 0.041 0.181 3596 Planarity : 0.004 0.074 4055 Dihedral : 5.133 46.776 3073 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.68 % Favored : 93.28 % Rotamer: Outliers : 2.17 % Allowed : 14.63 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.47 (0.14), residues: 2828 helix: -1.90 (0.12), residues: 1470 sheet: -1.33 (0.37), residues: 205 loop : -2.93 (0.15), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 950 TYR 0.018 0.001 TYR A 552 PHE 0.025 0.001 PHE B1010 TRP 0.025 0.001 TRP C 174 HIS 0.006 0.001 HIS B 805 Details of bonding type rmsd covalent geometry : bond 0.00219 (23549) covalent geometry : angle 0.54655 (31826) hydrogen bonds : bond 0.04173 ( 759) hydrogen bonds : angle 4.35661 ( 2229) *********************** 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 392 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 335 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASN cc_start: 0.8610 (t0) cc_final: 0.8135 (t0) REVERT: A 47 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6694 (mt-10) REVERT: A 190 ASN cc_start: 0.8619 (t0) cc_final: 0.8243 (t0) REVERT: A 308 MET cc_start: 0.7571 (mmt) cc_final: 0.6253 (tmm) REVERT: A 340 LYS cc_start: 0.7776 (mttm) cc_final: 0.7493 (mtmm) REVERT: A 382 LEU cc_start: 0.8283 (tt) cc_final: 0.7941 (tp) REVERT: A 450 ASN cc_start: 0.8248 (m-40) cc_final: 0.8015 (m110) REVERT: A 589 ARG cc_start: 0.7806 (mtt180) cc_final: 0.7109 (mtt180) REVERT: B 47 ASP cc_start: 0.7624 (t0) cc_final: 0.7236 (t0) REVERT: B 194 TYR cc_start: 0.8601 (m-10) cc_final: 0.8092 (m-10) REVERT: B 195 ASP cc_start: 0.7753 (t0) cc_final: 0.7456 (t0) REVERT: B 338 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7003 (tp30) REVERT: B 498 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.7982 (tt) REVERT: B 642 ILE cc_start: 0.8280 (mm) cc_final: 0.8013 (mm) REVERT: B 726 MET cc_start: 0.8387 (tpp) cc_final: 0.8172 (mmm) REVERT: B 781 ASP cc_start: 0.7896 (p0) cc_final: 0.7340 (p0) REVERT: B 937 LEU cc_start: 0.4351 (OUTLIER) cc_final: 0.4078 (pp) REVERT: B 978 MET cc_start: 0.4827 (mtp) cc_final: 0.3996 (pmm) REVERT: B 1076 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8378 (pttp) REVERT: B 1221 MET cc_start: 0.7492 (mtt) cc_final: 0.7221 (tmm) REVERT: B 1242 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6798 (mm) REVERT: C 350 LYS cc_start: 0.6440 (tppt) cc_final: 0.6106 (pttm) REVERT: C 352 TRP cc_start: 0.7954 (m100) cc_final: 0.7728 (m100) REVERT: C 353 TYR cc_start: 0.5236 (t80) cc_final: 0.4921 (t80) REVERT: C 355 MET cc_start: 0.6177 (mtm) cc_final: 0.4615 (mtm) REVERT: E 85 LYS cc_start: 0.7645 (tppp) cc_final: 0.6872 (pptt) REVERT: E 102 GLU cc_start: 0.8393 (tp30) cc_final: 0.7879 (tt0) REVERT: E 160 TYR cc_start: 0.7055 (t80) cc_final: 0.6824 (t80) REVERT: F 152 ARG cc_start: 0.7082 (ttp-170) cc_final: 0.6713 (tmm-80) REVERT: F 242 GLN cc_start: 0.6753 (mp10) cc_final: 0.6474 (mt0) REVERT: F 259 ARG cc_start: 0.6835 (mmm-85) cc_final: 0.6575 (mpt-90) REVERT: F 336 VAL cc_start: 0.5707 (p) cc_final: 0.5351 (t) REVERT: F 354 ASP cc_start: 0.7118 (t70) cc_final: 0.6756 (t0) outliers start: 57 outliers final: 27 residues processed: 377 average time/residue: 0.1635 time to fit residues: 97.7976 Evaluate side-chains 332 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 301 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 541 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 498 LEU 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 1076 LYS 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 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 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 20 VAL Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 170 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 243 optimal weight: 2.9990 chunk 96 optimal weight: 0.0270 chunk 256 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 269 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 145 optimal weight: 0.1980 chunk 219 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 overall best weight: 2.4444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 ASN B 311 ASN B 749 ASN 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** D 59 GLN ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4272 r_free = 0.4272 target = 0.183794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.126125 restraints weight = 31701.126| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.64 r_work: 0.3340 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23549 Z= 0.228 Angle : 0.657 10.186 31826 Z= 0.336 Chirality : 0.046 0.180 3596 Planarity : 0.004 0.073 4055 Dihedral : 5.499 42.146 3071 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.10 % Favored : 91.83 % Rotamer: Outliers : 2.97 % Allowed : 16.35 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.18 (0.14), residues: 2828 helix: -1.61 (0.12), residues: 1508 sheet: -1.21 (0.37), residues: 209 loop : -2.89 (0.16), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1038 TYR 0.023 0.002 TYR C 353 PHE 0.028 0.002 PHE B1010 TRP 0.021 0.002 TRP C 174 HIS 0.009 0.001 HIS B 805 Details of bonding type rmsd covalent geometry : bond 0.00542 (23549) covalent geometry : angle 0.65725 (31826) hydrogen bonds : bond 0.04902 ( 759) hydrogen bonds : angle 4.63717 ( 2229) *********************** 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 406 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 328 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASN cc_start: 0.8703 (t0) cc_final: 0.8087 (t0) REVERT: A 47 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6656 (mt-10) REVERT: A 190 ASN cc_start: 0.8651 (t0) cc_final: 0.8239 (t0) REVERT: A 308 MET cc_start: 0.7660 (mmt) cc_final: 0.6397 (tmm) REVERT: A 340 LYS cc_start: 0.7839 (mttm) cc_final: 0.7540 (mtmm) REVERT: A 392 ASP cc_start: 0.7197 (t70) cc_final: 0.6809 (t70) REVERT: A 450 ASN cc_start: 0.8258 (m-40) cc_final: 0.8026 (m110) REVERT: A 589 ARG cc_start: 0.7884 (mtt180) cc_final: 0.7409 (mtt90) REVERT: B 47 ASP cc_start: 0.7800 (t0) cc_final: 0.7347 (t0) REVERT: B 128 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7263 (pp) REVERT: B 338 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7014 (tp30) REVERT: B 498 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8089 (tt) REVERT: B 638 GLU cc_start: 0.8079 (tp30) cc_final: 0.7848 (tp30) REVERT: B 937 LEU cc_start: 0.4547 (OUTLIER) cc_final: 0.4184 (pp) REVERT: B 1117 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8492 (mmtt) REVERT: B 1221 MET cc_start: 0.7447 (mtt) cc_final: 0.7224 (tmm) REVERT: B 1242 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6922 (mm) REVERT: C 65 GLU cc_start: 0.5787 (OUTLIER) cc_final: 0.4892 (tm-30) REVERT: C 352 TRP cc_start: 0.8017 (m100) cc_final: 0.7551 (m100) REVERT: C 366 PHE cc_start: 0.6258 (m-80) cc_final: 0.5880 (m-80) REVERT: E 85 LYS cc_start: 0.7692 (tppp) cc_final: 0.6944 (pptt) REVERT: E 102 GLU cc_start: 0.8542 (tp30) cc_final: 0.7873 (tt0) REVERT: E 160 TYR cc_start: 0.7241 (t80) cc_final: 0.6993 (t80) REVERT: F 157 MET cc_start: 0.5580 (OUTLIER) cc_final: 0.5040 (mtm) REVERT: F 219 LYS cc_start: 0.4392 (mmtm) cc_final: 0.3691 (tttm) REVERT: F 259 ARG cc_start: 0.6862 (mmm-85) cc_final: 0.6618 (mpt-90) REVERT: F 268 ILE cc_start: 0.6152 (mm) cc_final: 0.5682 (pt) REVERT: F 354 ASP cc_start: 0.7080 (t70) cc_final: 0.6589 (t0) outliers start: 78 outliers final: 46 residues processed: 385 average time/residue: 0.1599 time to fit residues: 100.0616 Evaluate side-chains 345 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 293 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 96 HIS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 311 ASN 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 570 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 669 SER Chi-restraints excluded: chain B residue 677 ILE 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 1098 LEU Chi-restraints excluded: chain B residue 1168 THR Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain B residue 1242 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 65 GLU 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 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 157 MET 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 260 optimal weight: 30.0000 chunk 83 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 263 optimal weight: 9.9990 chunk 198 optimal weight: 3.9990 chunk 271 optimal weight: 9.9990 chunk 118 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 HIS B 311 ASN B 590 ASN B 794 ASN B 805 HIS B 984 HIS ** B1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 HIS C 173 ASN ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 93 GLN D 135 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.188241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.142892 restraints weight = 31032.055| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.81 r_work: 0.3414 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23549 Z= 0.101 Angle : 0.553 9.501 31826 Z= 0.283 Chirality : 0.042 0.210 3596 Planarity : 0.003 0.068 4055 Dihedral : 5.010 42.337 3071 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.44 % Favored : 93.53 % Rotamer: Outliers : 2.44 % Allowed : 18.29 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.65 (0.15), residues: 2828 helix: -1.07 (0.13), residues: 1487 sheet: -1.05 (0.37), residues: 205 loop : -2.79 (0.16), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 67 TYR 0.026 0.001 TYR C 353 PHE 0.024 0.001 PHE B1010 TRP 0.029 0.001 TRP B 144 HIS 0.017 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00226 (23549) covalent geometry : angle 0.55302 (31826) hydrogen bonds : bond 0.03696 ( 759) hydrogen bonds : angle 4.11756 ( 2229) *********************** 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 381 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 317 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASN cc_start: 0.8676 (t0) cc_final: 0.8376 (t0) REVERT: A 190 ASN cc_start: 0.8589 (t0) cc_final: 0.8198 (t0) REVERT: A 308 MET cc_start: 0.7672 (mmt) cc_final: 0.6430 (tmm) REVERT: A 340 LYS cc_start: 0.7771 (mttm) cc_final: 0.7567 (mtmm) REVERT: A 450 ASN cc_start: 0.8256 (m-40) cc_final: 0.8026 (m110) REVERT: A 578 ARG cc_start: 0.7668 (mtt180) cc_final: 0.7425 (mtp-110) REVERT: A 589 ARG cc_start: 0.7870 (mtt180) cc_final: 0.7462 (mtt90) REVERT: B 47 ASP cc_start: 0.7696 (t0) cc_final: 0.7453 (t0) REVERT: B 194 TYR cc_start: 0.8618 (m-10) cc_final: 0.8196 (m-10) REVERT: B 338 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7018 (tp30) REVERT: B 351 MET cc_start: 0.8188 (mpp) cc_final: 0.7960 (mpp) REVERT: B 498 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8071 (tt) REVERT: B 937 LEU cc_start: 0.4402 (OUTLIER) cc_final: 0.4050 (pp) REVERT: B 1117 LYS cc_start: 0.8739 (mmtt) cc_final: 0.8494 (mmtt) REVERT: B 1148 MET cc_start: 0.8716 (mmm) cc_final: 0.8516 (mmm) REVERT: B 1221 MET cc_start: 0.7405 (mtt) cc_final: 0.7205 (tmm) REVERT: B 1242 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6810 (mm) REVERT: C 252 HIS cc_start: 0.7598 (OUTLIER) cc_final: 0.6892 (p-80) REVERT: C 350 LYS cc_start: 0.6579 (tppt) cc_final: 0.6177 (pttm) REVERT: C 352 TRP cc_start: 0.7871 (m100) cc_final: 0.7529 (m100) REVERT: C 353 TYR cc_start: 0.5134 (t80) cc_final: 0.4565 (t80) REVERT: C 355 MET cc_start: 0.6731 (mtm) cc_final: 0.6346 (mtm) REVERT: C 366 PHE cc_start: 0.6261 (m-80) cc_final: 0.5580 (m-80) REVERT: D 93 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7512 (tp-100) REVERT: E 85 LYS cc_start: 0.7697 (tppp) cc_final: 0.6916 (pptt) REVERT: E 102 GLU cc_start: 0.8387 (tp30) cc_final: 0.7755 (tt0) REVERT: E 160 TYR cc_start: 0.7197 (t80) cc_final: 0.6974 (t80) REVERT: E 180 GLN cc_start: 0.5324 (tm-30) cc_final: 0.4762 (tt0) REVERT: F 152 ARG cc_start: 0.7105 (ttp-170) cc_final: 0.6725 (tmm-80) REVERT: F 157 MET cc_start: 0.5709 (OUTLIER) cc_final: 0.5191 (mtm) REVERT: F 194 ARG cc_start: 0.3764 (tpt170) cc_final: 0.3172 (mtt180) REVERT: F 219 LYS cc_start: 0.4253 (mmtm) cc_final: 0.3584 (tttm) REVERT: F 242 GLN cc_start: 0.6687 (mp10) cc_final: 0.6234 (tt0) REVERT: F 259 ARG cc_start: 0.6857 (mmm-85) cc_final: 0.6635 (mpt-90) REVERT: F 268 ILE cc_start: 0.6171 (mm) cc_final: 0.5711 (pt) REVERT: F 354 ASP cc_start: 0.6984 (t70) cc_final: 0.6634 (t0) outliers start: 64 outliers final: 39 residues processed: 367 average time/residue: 0.1594 time to fit residues: 93.4976 Evaluate side-chains 341 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 296 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 157 VAL 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 541 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 585 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1045 ASP 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 196 VAL Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 252 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 20 VAL Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain D residue 119 LEU 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 157 MET 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 129 optimal weight: 0.8980 chunk 218 optimal weight: 0.0670 chunk 94 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 163 optimal weight: 0.5980 chunk 187 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 268 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.189215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.143869 restraints weight = 31056.374| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.78 r_work: 0.3423 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3425 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 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 = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23549 Z= 0.099 Angle : 0.540 9.296 31826 Z= 0.275 Chirality : 0.041 0.179 3596 Planarity : 0.003 0.069 4055 Dihedral : 4.733 41.034 3071 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.79 % Favored : 93.18 % Rotamer: Outliers : 2.36 % Allowed : 19.74 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.22 (0.15), residues: 2828 helix: -0.65 (0.13), residues: 1468 sheet: -1.06 (0.38), residues: 195 loop : -2.61 (0.16), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 67 TYR 0.024 0.001 TYR C 353 PHE 0.023 0.001 PHE B1010 TRP 0.031 0.001 TRP B 144 HIS 0.008 0.001 HIS B 805 Details of bonding type rmsd covalent geometry : bond 0.00217 (23549) covalent geometry : angle 0.53998 (31826) hydrogen bonds : bond 0.03395 ( 759) hydrogen bonds : angle 3.90236 ( 2229) *********************** 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 380 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 318 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASN cc_start: 0.8677 (t0) cc_final: 0.8419 (t0) REVERT: A 293 ASP cc_start: 0.7490 (m-30) cc_final: 0.7179 (p0) REVERT: A 308 MET cc_start: 0.7665 (mmt) cc_final: 0.6448 (tmm) REVERT: A 340 LYS cc_start: 0.7763 (mttm) cc_final: 0.7504 (mtmm) REVERT: A 372 MET cc_start: 0.8080 (mtp) cc_final: 0.7342 (mmm) REVERT: A 387 THR cc_start: 0.7843 (m) cc_final: 0.7572 (t) REVERT: A 450 ASN cc_start: 0.8177 (m-40) cc_final: 0.7830 (t0) REVERT: A 578 ARG cc_start: 0.7685 (mtt180) cc_final: 0.7447 (mtp-110) REVERT: A 589 ARG cc_start: 0.7916 (mtt180) cc_final: 0.7542 (mtt90) REVERT: B 47 ASP cc_start: 0.7827 (t0) cc_final: 0.7472 (t0) REVERT: B 48 PHE cc_start: 0.7727 (t80) cc_final: 0.7507 (t80) REVERT: B 194 TYR cc_start: 0.8626 (m-10) cc_final: 0.8157 (m-10) REVERT: B 338 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7037 (tp30) REVERT: B 351 MET cc_start: 0.8227 (mpp) cc_final: 0.8007 (mpp) REVERT: B 498 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8063 (tt) REVERT: B 909 ASP cc_start: 0.7672 (t0) cc_final: 0.7471 (m-30) REVERT: B 937 LEU cc_start: 0.4058 (OUTLIER) cc_final: 0.3786 (pp) REVERT: B 1127 GLU cc_start: 0.8479 (pt0) cc_final: 0.8141 (pt0) REVERT: B 1221 MET cc_start: 0.7366 (mtt) cc_final: 0.7137 (tmm) REVERT: B 1242 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6933 (mm) REVERT: C 47 HIS cc_start: 0.3621 (OUTLIER) cc_final: 0.3414 (p-80) REVERT: C 353 TYR cc_start: 0.5446 (t80) cc_final: 0.4706 (t80) REVERT: C 355 MET cc_start: 0.6922 (mtm) cc_final: 0.6613 (mtm) REVERT: C 366 PHE cc_start: 0.6336 (m-80) cc_final: 0.5661 (m-80) REVERT: E 81 LEU cc_start: 0.8695 (tp) cc_final: 0.8480 (tt) REVERT: E 85 LYS cc_start: 0.7653 (tppp) cc_final: 0.6862 (pptt) REVERT: E 102 GLU cc_start: 0.8382 (tp30) cc_final: 0.7913 (tt0) REVERT: E 160 TYR cc_start: 0.7253 (t80) cc_final: 0.7032 (t80) REVERT: E 180 GLN cc_start: 0.4947 (tm-30) cc_final: 0.4450 (tt0) REVERT: F 157 MET cc_start: 0.5450 (OUTLIER) cc_final: 0.5198 (mtm) REVERT: F 194 ARG cc_start: 0.3626 (tpt170) cc_final: 0.2707 (ptp-170) REVERT: F 219 LYS cc_start: 0.4247 (mmtm) cc_final: 0.3571 (tttm) REVERT: F 242 GLN cc_start: 0.6740 (mp10) cc_final: 0.6293 (tt0) REVERT: F 259 ARG cc_start: 0.6854 (mmm-85) cc_final: 0.6645 (mpt-90) REVERT: F 268 ILE cc_start: 0.6137 (mm) cc_final: 0.5667 (pt) REVERT: F 354 ASP cc_start: 0.6974 (t70) cc_final: 0.6704 (t0) outliers start: 62 outliers final: 41 residues processed: 363 average time/residue: 0.1631 time to fit residues: 94.0967 Evaluate side-chains 347 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 301 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 278 LEU 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 245 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 305 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 570 ILE Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1045 ASP 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 47 HIS 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 21 ASP Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 119 LEU 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 157 MET Chi-restraints excluded: chain F residue 207 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 160 optimal weight: 1.9990 chunk 262 optimal weight: 6.9990 chunk 191 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 275 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 270 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 109 ASN B 96 HIS ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN 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** D 59 GLN D 93 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.186691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.133063 restraints weight = 31061.632| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.47 r_work: 0.3444 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 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 = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23549 Z= 0.134 Angle : 0.574 11.434 31826 Z= 0.290 Chirality : 0.043 0.170 3596 Planarity : 0.003 0.068 4055 Dihedral : 4.831 40.378 3071 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.25 % Favored : 92.72 % Rotamer: Outliers : 2.71 % Allowed : 20.31 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.15), residues: 2828 helix: -0.55 (0.13), residues: 1479 sheet: -1.13 (0.37), residues: 199 loop : -2.56 (0.16), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 730 TYR 0.025 0.001 TYR C 353 PHE 0.025 0.001 PHE B1010 TRP 0.034 0.001 TRP B 144 HIS 0.009 0.001 HIS B 805 Details of bonding type rmsd covalent geometry : bond 0.00317 (23549) covalent geometry : angle 0.57403 (31826) hydrogen bonds : bond 0.03656 ( 759) hydrogen bonds : angle 3.97170 ( 2229) *********************** 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 387 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 316 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASN cc_start: 0.8766 (t0) cc_final: 0.8498 (t0) REVERT: A 190 ASN cc_start: 0.8578 (t0) cc_final: 0.8169 (t0) REVERT: A 293 ASP cc_start: 0.7854 (m-30) cc_final: 0.7397 (p0) REVERT: A 308 MET cc_start: 0.7720 (mmt) cc_final: 0.6495 (tmm) REVERT: A 340 LYS cc_start: 0.7806 (mttm) cc_final: 0.7529 (mtmm) REVERT: A 372 MET cc_start: 0.8138 (mtp) cc_final: 0.7167 (mmm) REVERT: A 450 ASN cc_start: 0.8222 (m-40) cc_final: 0.7836 (t0) REVERT: A 589 ARG cc_start: 0.7987 (mtt180) cc_final: 0.7221 (mtt180) REVERT: B 47 ASP cc_start: 0.7968 (t0) cc_final: 0.7623 (t0) REVERT: B 48 PHE cc_start: 0.7856 (t80) cc_final: 0.7512 (t80) REVERT: B 194 TYR cc_start: 0.8684 (m-10) cc_final: 0.8158 (m-10) REVERT: B 195 ASP cc_start: 0.7648 (t0) cc_final: 0.7081 (t0) REVERT: B 338 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7045 (tp30) REVERT: B 351 MET cc_start: 0.8375 (mpp) cc_final: 0.8044 (mpp) REVERT: B 498 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8114 (tt) REVERT: B 937 LEU cc_start: 0.4330 (OUTLIER) cc_final: 0.4023 (pp) REVERT: B 1127 GLU cc_start: 0.8525 (pt0) cc_final: 0.8182 (pt0) REVERT: B 1242 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6939 (mm) REVERT: C 47 HIS cc_start: 0.3639 (OUTLIER) cc_final: 0.3332 (p-80) REVERT: C 350 LYS cc_start: 0.6565 (tppt) cc_final: 0.6129 (pttp) REVERT: C 352 TRP cc_start: 0.7838 (m100) cc_final: 0.7336 (m100) REVERT: C 353 TYR cc_start: 0.5490 (t80) cc_final: 0.4678 (t80) REVERT: C 355 MET cc_start: 0.7033 (mtm) cc_final: 0.6671 (mtm) REVERT: C 366 PHE cc_start: 0.6506 (m-80) cc_final: 0.5986 (m-80) REVERT: D 63 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7272 (pt0) REVERT: D 93 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7618 (tp-100) REVERT: E 85 LYS cc_start: 0.7619 (tppp) cc_final: 0.6778 (pptt) REVERT: E 102 GLU cc_start: 0.8481 (tp30) cc_final: 0.7941 (tt0) REVERT: E 160 TYR cc_start: 0.7321 (t80) cc_final: 0.7095 (t80) REVERT: E 180 GLN cc_start: 0.5096 (tm-30) cc_final: 0.4673 (tt0) REVERT: F 140 ARG cc_start: 0.2415 (mtm-85) cc_final: 0.1759 (mmm160) REVERT: F 157 MET cc_start: 0.5487 (OUTLIER) cc_final: 0.5227 (mtm) REVERT: F 242 GLN cc_start: 0.6834 (mp10) cc_final: 0.6393 (tt0) REVERT: F 268 ILE cc_start: 0.6145 (mm) cc_final: 0.5668 (pt) REVERT: F 354 ASP cc_start: 0.6910 (t70) cc_final: 0.6574 (t0) outliers start: 71 outliers final: 50 residues processed: 367 average time/residue: 0.1443 time to fit residues: 85.8906 Evaluate side-chains 362 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 305 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 278 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 96 HIS Chi-restraints excluded: chain B residue 119 ASN 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 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 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 47 HIS 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 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 8 THR 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 157 MET 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 72 optimal weight: 0.0020 chunk 275 optimal weight: 0.0670 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 144 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 231 optimal weight: 0.4980 chunk 192 optimal weight: 5.9990 overall best weight: 0.3726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 HIS ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 HIS B 848 GLN B 984 HIS ** B1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN F 98 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.190187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.144222 restraints weight = 30996.989| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.79 r_work: 0.3444 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 23549 Z= 0.093 Angle : 0.544 9.271 31826 Z= 0.275 Chirality : 0.041 0.174 3596 Planarity : 0.003 0.067 4055 Dihedral : 4.578 39.666 3071 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.12 % Favored : 93.85 % Rotamer: Outliers : 2.21 % Allowed : 20.92 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.15), residues: 2828 helix: -0.22 (0.14), residues: 1477 sheet: -0.96 (0.37), residues: 197 loop : -2.49 (0.16), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 291 TYR 0.023 0.001 TYR C 353 PHE 0.024 0.001 PHE B1010 TRP 0.035 0.001 TRP B 144 HIS 0.008 0.001 HIS B 805 Details of bonding type rmsd covalent geometry : bond 0.00208 (23549) covalent geometry : angle 0.54354 (31826) hydrogen bonds : bond 0.03142 ( 759) hydrogen bonds : angle 3.74558 ( 2229) *********************** 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 372 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 314 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASN cc_start: 0.8667 (t0) cc_final: 0.8445 (t0) REVERT: A 190 ASN cc_start: 0.8528 (t0) cc_final: 0.8131 (t0) REVERT: A 293 ASP cc_start: 0.7474 (m-30) cc_final: 0.7224 (p0) REVERT: A 308 MET cc_start: 0.7635 (mmt) cc_final: 0.6465 (tmm) REVERT: A 372 MET cc_start: 0.8021 (mtp) cc_final: 0.7444 (mmm) REVERT: A 387 THR cc_start: 0.7766 (m) cc_final: 0.7469 (t) REVERT: A 450 ASN cc_start: 0.8093 (m-40) cc_final: 0.7804 (t0) REVERT: A 589 ARG cc_start: 0.7925 (mtt180) cc_final: 0.7319 (mtt180) REVERT: B 194 TYR cc_start: 0.8589 (m-10) cc_final: 0.8204 (m-10) REVERT: B 338 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7143 (tp30) REVERT: B 351 MET cc_start: 0.8325 (mpp) cc_final: 0.8033 (mpp) REVERT: B 498 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8092 (tt) REVERT: B 542 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7660 (mt) REVERT: B 848 GLN cc_start: 0.7655 (tp-100) cc_final: 0.7233 (tp-100) REVERT: B 871 GLU cc_start: 0.8667 (tp30) cc_final: 0.8312 (tp30) REVERT: B 937 LEU cc_start: 0.4667 (OUTLIER) cc_final: 0.4339 (pp) REVERT: B 1127 GLU cc_start: 0.8447 (pt0) cc_final: 0.8097 (pt0) REVERT: B 1132 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8581 (tp) REVERT: B 1221 MET cc_start: 0.7334 (mtt) cc_final: 0.7086 (tmm) REVERT: C 47 HIS cc_start: 0.3707 (OUTLIER) cc_final: 0.3420 (p-80) REVERT: C 352 TRP cc_start: 0.7573 (m100) cc_final: 0.7147 (m100) REVERT: C 353 TYR cc_start: 0.5388 (t80) cc_final: 0.4581 (t80) REVERT: C 355 MET cc_start: 0.6935 (mtm) cc_final: 0.6545 (mtm) REVERT: C 366 PHE cc_start: 0.6294 (m-80) cc_final: 0.5934 (m-80) REVERT: D 63 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7221 (pt0) REVERT: E 85 LYS cc_start: 0.7668 (tppp) cc_final: 0.6849 (pptt) REVERT: E 102 GLU cc_start: 0.8358 (tp30) cc_final: 0.7833 (tt0) REVERT: E 180 GLN cc_start: 0.5030 (tm-30) cc_final: 0.4597 (tt0) REVERT: F 157 MET cc_start: 0.5440 (OUTLIER) cc_final: 0.5212 (mtm) REVERT: F 194 ARG cc_start: 0.3870 (tpt170) cc_final: 0.3042 (mtt-85) REVERT: F 219 LYS cc_start: 0.4428 (mmtp) cc_final: 0.3750 (tttm) REVERT: F 242 GLN cc_start: 0.6809 (mp10) cc_final: 0.6378 (tt0) REVERT: F 268 ILE cc_start: 0.6138 (mm) cc_final: 0.5671 (pt) REVERT: F 354 ASP cc_start: 0.6800 (t70) cc_final: 0.6520 (t0) outliers start: 58 outliers final: 36 residues processed: 359 average time/residue: 0.1352 time to fit residues: 78.0220 Evaluate side-chains 341 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 299 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 374 ILE 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 156 THR 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 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 1098 LEU Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain B residue 1168 THR Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 59 THR 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 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 21 ASP Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain F residue 207 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.0959 > 50: distance: 40 - 64: 7.213 distance: 60 - 64: 3.950 distance: 64 - 65: 5.063 distance: 65 - 66: 8.672 distance: 66 - 67: 13.203 distance: 66 - 70: 4.560 distance: 68 - 69: 14.104 distance: 70 - 71: 3.762 distance: 71 - 72: 4.159 distance: 72 - 73: 16.041 distance: 72 - 79: 17.637 distance: 74 - 75: 7.292 distance: 75 - 76: 4.048 distance: 76 - 77: 10.287 distance: 76 - 78: 6.727 distance: 79 - 80: 5.469 distance: 80 - 81: 22.512 distance: 80 - 83: 20.877 distance: 81 - 82: 25.621 distance: 81 - 87: 43.996 distance: 83 - 84: 15.278 distance: 84 - 85: 13.576 distance: 84 - 86: 5.552 distance: 87 - 88: 28.249 distance: 88 - 89: 25.443 distance: 88 - 91: 21.229 distance: 89 - 90: 16.628 distance: 89 - 95: 9.567 distance: 91 - 92: 3.154 distance: 92 - 93: 28.397 distance: 92 - 94: 15.550 distance: 95 - 96: 3.568 distance: 95 - 101: 11.958 distance: 96 - 97: 14.625 distance: 97 - 98: 7.255 distance: 97 - 102: 14.216 distance: 99 - 100: 13.565 distance: 100 - 101: 17.077 distance: 102 - 103: 6.106 distance: 103 - 104: 13.538 distance: 103 - 106: 8.954 distance: 104 - 105: 18.094 distance: 104 - 110: 7.431 distance: 106 - 107: 24.775 distance: 106 - 108: 16.322 distance: 107 - 109: 11.490 distance: 110 - 111: 13.436 distance: 111 - 112: 22.733 distance: 111 - 114: 13.798 distance: 112 - 113: 20.924 distance: 112 - 118: 9.594 distance: 114 - 115: 12.248 distance: 115 - 116: 6.341 distance: 115 - 117: 6.331 distance: 118 - 119: 4.552 distance: 119 - 120: 9.747 distance: 119 - 122: 8.527 distance: 120 - 121: 14.167 distance: 120 - 127: 17.575 distance: 122 - 123: 12.699 distance: 123 - 124: 7.848 distance: 124 - 125: 8.448 distance: 124 - 126: 7.195 distance: 127 - 128: 7.938 distance: 128 - 129: 18.943 distance: 128 - 131: 7.726 distance: 129 - 130: 21.956 distance: 129 - 136: 10.977 distance: 131 - 132: 18.810 distance: 132 - 133: 17.918 distance: 133 - 134: 5.292 distance: 133 - 135: 6.946 distance: 136 - 137: 11.443 distance: 137 - 138: 10.261 distance: 137 - 140: 19.434 distance: 138 - 139: 19.637 distance: 138 - 142: 6.579 distance: 140 - 141: 4.969