Starting phenix.real_space_refine on Fri Jun 6 10:20:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w6n_37329/06_2025/8w6n_37329.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w6n_37329/06_2025/8w6n_37329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w6n_37329/06_2025/8w6n_37329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w6n_37329/06_2025/8w6n_37329.map" model { file = "/net/cci-nas-00/data/ceres_data/8w6n_37329/06_2025/8w6n_37329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w6n_37329/06_2025/8w6n_37329.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 55 5.16 5 Na 1 4.78 5 C 5110 2.51 5 N 1158 2.21 5 O 1292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 7616 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3857 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 30, 'TRANS': 463} Chain breaks: 3 Chain: "B" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3748 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 30, 'TRANS': 450} Chain breaks: 3 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' NA': 1, 'SO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.82, per 1000 atoms: 0.63 Number of scatterers: 7616 At special positions: 0 Unit cell: (91.308, 92.395, 105.439, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 Na 1 11.00 O 1292 8.00 N 1158 7.00 C 5110 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: 1.86 Conformation dependent library (CDL) restraints added in 995.4 milliseconds 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1842 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 2 sheets defined 65.1% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 4.145A pdb=" N LEU A 8 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 23 removed outlier: 3.611A pdb=" N LEU A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 30 removed outlier: 3.581A pdb=" N ILE A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 44 Processing helix chain 'A' and resid 44 through 50 removed outlier: 3.865A pdb=" N TRP A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 50' Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.516A pdb=" N LEU A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 84 through 93 removed outlier: 3.701A pdb=" N LEU A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 101 removed outlier: 3.728A pdb=" N GLU A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 4.520A pdb=" N MET A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.612A pdb=" N SER A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 139 through 145 Processing helix chain 'A' and resid 146 through 161 removed outlier: 4.230A pdb=" N ILE A 150 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 251 removed outlier: 4.146A pdb=" N THR A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS A 241 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 247 " --> pdb=" O CYS A 243 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.538A pdb=" N ASN A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 308 removed outlier: 3.681A pdb=" N SER A 288 " --> pdb=" O TRP A 284 " (cutoff:3.500A) Proline residue: A 290 - end of helix removed outlier: 3.837A pdb=" N ILE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 330 through 339 removed outlier: 4.000A pdb=" N LYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 338 " --> pdb=" O LYS A 334 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 362 removed outlier: 3.817A pdb=" N ILE A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 358 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 384 through 394 removed outlier: 3.886A pdb=" N VAL A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 434 through 453 removed outlier: 3.661A pdb=" N GLY A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 460 Processing helix chain 'A' and resid 471 through 485 removed outlier: 3.574A pdb=" N LEU A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 508 removed outlier: 3.627A pdb=" N ILE A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR A 495 " --> pdb=" O PRO A 491 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 496 " --> pdb=" O ALA A 492 " (cutoff:3.500A) Proline residue: A 499 - end of helix Proline residue: A 503 - end of helix removed outlier: 3.934A pdb=" N GLU A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 507 " --> pdb=" O PRO A 503 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'A' and resid 539 through 543 removed outlier: 3.808A pdb=" N TYR A 542 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 543 " --> pdb=" O PHE A 540 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 539 through 543' Processing helix chain 'A' and resid 547 through 569 removed outlier: 3.642A pdb=" N ALA A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 565 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 18 removed outlier: 4.054A pdb=" N VAL B 17 " --> pdb=" O PHE B 13 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 13 through 18' Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 41 through 50 removed outlier: 3.544A pdb=" N THR B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.820A pdb=" N PHE B 69 " --> pdb=" O MET B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 79 through 82 removed outlier: 3.951A pdb=" N PHE B 82 " --> pdb=" O SER B 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 82' Processing helix chain 'B' and resid 84 through 93 removed outlier: 3.590A pdb=" N LEU B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 102 removed outlier: 3.622A pdb=" N SER B 98 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 removed outlier: 3.501A pdb=" N GLY B 126 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N MET B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 131 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 132 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 159 removed outlier: 3.549A pdb=" N VAL B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Proline residue: B 149 - end of helix removed outlier: 3.542A pdb=" N GLU B 152 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA B 153 " --> pdb=" O PRO B 149 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 159 " --> pdb=" O VAL B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 251 removed outlier: 3.693A pdb=" N LYS B 238 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA B 245 " --> pdb=" O CYS B 241 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 258 removed outlier: 3.610A pdb=" N GLY B 258 " --> pdb=" O THR B 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 258' Processing helix chain 'B' and resid 259 through 271 removed outlier: 3.800A pdb=" N LEU B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.632A pdb=" N PHE B 285 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 306 removed outlier: 3.559A pdb=" N LEU B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 338 removed outlier: 3.545A pdb=" N ALA B 330 " --> pdb=" O GLN B 326 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 333 " --> pdb=" O CYS B 329 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR B 337 " --> pdb=" O ILE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 360 removed outlier: 4.098A pdb=" N THR B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 394 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.914A pdb=" N ALA B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 444 " --> pdb=" O GLY B 440 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 445 " --> pdb=" O GLY B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 462 removed outlier: 3.590A pdb=" N TRP B 457 " --> pdb=" O GLY B 453 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 485 removed outlier: 3.601A pdb=" N ILE B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 508 removed outlier: 3.619A pdb=" N ILE B 494 " --> pdb=" O ASN B 490 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR B 495 " --> pdb=" O PRO B 491 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 497 " --> pdb=" O THR B 493 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 498 " --> pdb=" O ILE B 494 " (cutoff:3.500A) Proline residue: B 499 - end of helix removed outlier: 3.670A pdb=" N SER B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Proline residue: B 503 - end of helix removed outlier: 3.612A pdb=" N ALA B 507 " --> pdb=" O PRO B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 522 removed outlier: 3.926A pdb=" N ILE B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Proline residue: B 518 - end of helix removed outlier: 3.611A pdb=" N LEU B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS B 522 " --> pdb=" O PRO B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 534 through 539 removed outlier: 4.296A pdb=" N VAL B 539 " --> pdb=" O PRO B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 546 through 572 removed outlier: 3.561A pdb=" N VAL B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B 553 " --> pdb=" O ASP B 549 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY B 556 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 560 " --> pdb=" O GLY B 556 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 565 " --> pdb=" O GLY B 561 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N CYS B 570 " --> pdb=" O MET B 566 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 403 removed outlier: 6.735A pdb=" N SER A 419 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 400 through 402 removed outlier: 6.809A pdb=" N SER B 419 " --> pdb=" O ALA B 401 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2166 1.34 - 1.46: 1872 1.46 - 1.58: 3712 1.58 - 1.69: 0 1.69 - 1.81: 86 Bond restraints: 7836 Sorted by residual: bond pdb=" N THR A 423 " pdb=" CA THR A 423 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.01e+00 bond pdb=" O3 SO4 B 701 " pdb=" S SO4 B 701 " ideal model delta sigma weight residual 1.499 1.457 0.042 2.00e-02 2.50e+03 4.33e+00 bond pdb=" O4 SO4 B 701 " pdb=" S SO4 B 701 " ideal model delta sigma weight residual 1.499 1.459 0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" O3 SO4 A 601 " pdb=" S SO4 A 601 " ideal model delta sigma weight residual 1.499 1.459 0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" O1 SO4 A 601 " pdb=" S SO4 A 601 " ideal model delta sigma weight residual 1.498 1.458 0.040 2.00e-02 2.50e+03 3.95e+00 ... (remaining 7831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.12: 10632 4.12 - 8.24: 77 8.24 - 12.36: 11 12.36 - 16.48: 0 16.48 - 20.60: 1 Bond angle restraints: 10721 Sorted by residual: angle pdb=" N ILE A 538 " pdb=" CA ILE A 538 " pdb=" C ILE A 538 " ideal model delta sigma weight residual 111.91 105.26 6.65 8.90e-01 1.26e+00 5.58e+01 angle pdb=" C ILE B 573 " pdb=" N VAL B 574 " pdb=" CA VAL B 574 " ideal model delta sigma weight residual 120.24 124.07 -3.83 6.30e-01 2.52e+00 3.70e+01 angle pdb=" CA LEU B 545 " pdb=" CB LEU B 545 " pdb=" CG LEU B 545 " ideal model delta sigma weight residual 116.30 136.90 -20.60 3.50e+00 8.16e-02 3.46e+01 angle pdb=" N VAL B 16 " pdb=" CA VAL B 16 " pdb=" C VAL B 16 " ideal model delta sigma weight residual 111.67 106.60 5.07 9.50e-01 1.11e+00 2.85e+01 angle pdb=" C VAL B 113 " pdb=" N MET B 114 " pdb=" CA MET B 114 " ideal model delta sigma weight residual 121.54 131.55 -10.01 1.91e+00 2.74e-01 2.75e+01 ... (remaining 10716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4097 17.68 - 35.36: 381 35.36 - 53.04: 50 53.04 - 70.72: 5 70.72 - 88.40: 2 Dihedral angle restraints: 4535 sinusoidal: 1697 harmonic: 2838 Sorted by residual: dihedral pdb=" CA ARG B 364 " pdb=" C ARG B 364 " pdb=" N ASP B 365 " pdb=" CA ASP B 365 " ideal model delta harmonic sigma weight residual 180.00 147.58 32.42 0 5.00e+00 4.00e-02 4.21e+01 dihedral pdb=" CA TYR B 582 " pdb=" C TYR B 582 " pdb=" N PRO B 583 " pdb=" CA PRO B 583 " ideal model delta harmonic sigma weight residual 180.00 -150.44 -29.56 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA LEU B 529 " pdb=" C LEU B 529 " pdb=" N PRO B 530 " pdb=" CA PRO B 530 " ideal model delta harmonic sigma weight residual -180.00 -152.29 -27.71 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 4532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 921 0.050 - 0.101: 286 0.101 - 0.151: 62 0.151 - 0.202: 18 0.202 - 0.252: 4 Chirality restraints: 1291 Sorted by residual: chirality pdb=" CB ILE A 508 " pdb=" CA ILE A 508 " pdb=" CG1 ILE A 508 " pdb=" CG2 ILE A 508 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE A 93 " pdb=" CA ILE A 93 " pdb=" CG1 ILE A 93 " pdb=" CG2 ILE A 93 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE A 538 " pdb=" CA ILE A 538 " pdb=" CG1 ILE A 538 " pdb=" CG2 ILE A 538 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1288 not shown) Planarity restraints: 1274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 534 " -0.070 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO B 535 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO B 535 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 535 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 24 " 0.053 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO A 25 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 25 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 25 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 534 " 0.053 5.00e-02 4.00e+02 7.85e-02 9.87e+00 pdb=" N PRO A 535 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " 0.044 5.00e-02 4.00e+02 ... (remaining 1271 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2493 2.83 - 3.35: 6502 3.35 - 3.86: 11967 3.86 - 4.38: 14678 4.38 - 4.90: 24704 Nonbonded interactions: 60344 Sorted by model distance: nonbonded pdb=" O ILE A 93 " pdb=" OG1 THR A 97 " model vdw 2.310 3.040 nonbonded pdb=" O LEU B 498 " pdb=" OG SER B 502 " model vdw 2.312 3.040 nonbonded pdb=" O SER A 139 " pdb=" OG1 THR A 143 " model vdw 2.318 3.040 nonbonded pdb=" OG1 THR B 141 " pdb=" O3 SO4 B 701 " model vdw 2.323 3.040 nonbonded pdb=" O ALA B 59 " pdb=" OH TYR B 81 " model vdw 2.326 3.040 ... (remaining 60339 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 161 or resid 233 through 309 or resid 325 throug \ h 403 or resid 418 through 588)) selection = (chain 'B' and resid 8 through 588) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.040 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 : 0.004 0.060 7836 Z= 0.208 Angle : 0.952 20.596 10721 Z= 0.511 Chirality : 0.053 0.252 1291 Planarity : 0.010 0.104 1274 Dihedral : 13.428 88.400 2693 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.09 % Favored : 92.81 % Rotamer: Outliers : 0.12 % Allowed : 7.06 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.03 (0.15), residues: 959 helix: -4.80 (0.06), residues: 635 sheet: None (None), residues: 0 loop : -3.88 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 424 HIS 0.004 0.001 HIS B 105 PHE 0.020 0.001 PHE A 540 TYR 0.024 0.001 TYR A 514 ARG 0.001 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.34547 ( 247) hydrogen bonds : angle 10.37725 ( 735) covalent geometry : bond 0.00435 ( 7836) covalent geometry : angle 0.95201 (10721) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.728 Fit side-chains REVERT: A 128 MET cc_start: 0.8936 (mtp) cc_final: 0.8664 (mtp) REVERT: A 338 GLN cc_start: 0.8248 (mm110) cc_final: 0.7952 (mm110) REVERT: A 480 MET cc_start: 0.8261 (ttm) cc_final: 0.8028 (ttm) REVERT: A 546 LYS cc_start: 0.8066 (mttt) cc_final: 0.7744 (mmtt) REVERT: B 430 PHE cc_start: 0.7864 (t80) cc_final: 0.7586 (t80) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.1844 time to fit residues: 45.3053 Evaluate side-chains 133 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 39 optimal weight: 0.1980 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS A 428 GLN B 86 HIS B 103 ASN B 160 ASN B 270 ASN B 325 GLN B 338 GLN B 346 GLN B 490 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.110813 restraints weight = 10337.629| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.60 r_work: 0.3146 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7836 Z= 0.120 Angle : 0.660 12.766 10721 Z= 0.333 Chirality : 0.042 0.153 1291 Planarity : 0.007 0.078 1274 Dihedral : 5.596 29.707 1012 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.63 % Allowed : 11.00 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.98 (0.21), residues: 959 helix: -3.15 (0.14), residues: 635 sheet: None (None), residues: 0 loop : -3.23 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 572 HIS 0.002 0.001 HIS B 86 PHE 0.015 0.001 PHE A 368 TYR 0.020 0.001 TYR A 514 ARG 0.006 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.04624 ( 247) hydrogen bonds : angle 4.72133 ( 735) covalent geometry : bond 0.00265 ( 7836) covalent geometry : angle 0.65982 (10721) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.828 Fit side-chains REVERT: A 128 MET cc_start: 0.8989 (mtp) cc_final: 0.8690 (mtp) REVERT: A 338 GLN cc_start: 0.8570 (mm110) cc_final: 0.8326 (mm110) REVERT: A 480 MET cc_start: 0.8694 (ttm) cc_final: 0.8342 (ttp) REVERT: A 546 LYS cc_start: 0.8139 (mttt) cc_final: 0.7750 (mttm) REVERT: B 430 PHE cc_start: 0.8103 (t80) cc_final: 0.7877 (t80) outliers start: 22 outliers final: 11 residues processed: 162 average time/residue: 0.1833 time to fit residues: 40.8881 Evaluate side-chains 142 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 343 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 HIS ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113923 restraints weight = 10558.683| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.70 r_work: 0.3034 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7836 Z= 0.135 Angle : 0.650 11.479 10721 Z= 0.322 Chirality : 0.043 0.147 1291 Planarity : 0.006 0.070 1274 Dihedral : 5.344 27.513 1012 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.47 % Allowed : 14.23 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.24), residues: 959 helix: -2.18 (0.18), residues: 642 sheet: None (None), residues: 0 loop : -2.93 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 572 HIS 0.002 0.001 HIS B 31 PHE 0.014 0.001 PHE A 368 TYR 0.017 0.001 TYR A 514 ARG 0.004 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 247) hydrogen bonds : angle 4.09833 ( 735) covalent geometry : bond 0.00319 ( 7836) covalent geometry : angle 0.64971 (10721) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.8989 (mtp) cc_final: 0.8674 (mtp) REVERT: A 546 LYS cc_start: 0.8158 (mttt) cc_final: 0.7740 (mttm) REVERT: B 430 PHE cc_start: 0.8135 (t80) cc_final: 0.7898 (t80) REVERT: B 480 MET cc_start: 0.8223 (ttm) cc_final: 0.7738 (ttp) outliers start: 29 outliers final: 18 residues processed: 162 average time/residue: 0.1746 time to fit residues: 39.0081 Evaluate side-chains 153 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 458 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 53 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 157 GLN B 234 HIS ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.131597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.105947 restraints weight = 10609.173| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.57 r_work: 0.3046 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7836 Z= 0.124 Angle : 0.628 10.553 10721 Z= 0.309 Chirality : 0.042 0.146 1291 Planarity : 0.006 0.065 1274 Dihedral : 5.167 26.549 1012 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.47 % Allowed : 15.91 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.26), residues: 959 helix: -1.57 (0.20), residues: 641 sheet: None (None), residues: 0 loop : -2.72 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 572 HIS 0.002 0.000 HIS B 86 PHE 0.013 0.001 PHE A 368 TYR 0.017 0.001 TYR A 514 ARG 0.002 0.000 ARG B 12 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 247) hydrogen bonds : angle 3.80947 ( 735) covalent geometry : bond 0.00294 ( 7836) covalent geometry : angle 0.62786 (10721) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.9065 (mtp) cc_final: 0.8766 (mtp) REVERT: A 378 GLU cc_start: 0.7782 (mp0) cc_final: 0.7568 (mp0) REVERT: A 480 MET cc_start: 0.8642 (ttm) cc_final: 0.8371 (ttp) REVERT: A 546 LYS cc_start: 0.8122 (mttt) cc_final: 0.7691 (mttm) REVERT: B 368 PHE cc_start: 0.7318 (m-10) cc_final: 0.6939 (m-80) REVERT: B 430 PHE cc_start: 0.8147 (t80) cc_final: 0.7913 (t80) REVERT: B 480 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7713 (ttp) outliers start: 29 outliers final: 21 residues processed: 158 average time/residue: 0.1791 time to fit residues: 38.8811 Evaluate side-chains 153 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 39 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.135242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.110021 restraints weight = 10448.217| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.53 r_work: 0.3069 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7836 Z= 0.112 Angle : 0.603 10.190 10721 Z= 0.297 Chirality : 0.042 0.145 1291 Planarity : 0.006 0.065 1274 Dihedral : 4.949 25.650 1012 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.59 % Allowed : 16.15 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.27), residues: 959 helix: -1.18 (0.20), residues: 645 sheet: None (None), residues: 0 loop : -2.58 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 471 HIS 0.001 0.000 HIS B 86 PHE 0.012 0.001 PHE A 368 TYR 0.018 0.001 TYR B 273 ARG 0.004 0.000 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.02953 ( 247) hydrogen bonds : angle 3.64155 ( 735) covalent geometry : bond 0.00261 ( 7836) covalent geometry : angle 0.60269 (10721) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.9068 (mtp) cc_final: 0.8774 (mtp) REVERT: A 378 GLU cc_start: 0.7695 (mp0) cc_final: 0.7493 (mp0) REVERT: A 480 MET cc_start: 0.8767 (ttm) cc_final: 0.8522 (ttp) REVERT: A 546 LYS cc_start: 0.8186 (mttt) cc_final: 0.7784 (mttm) REVERT: B 368 PHE cc_start: 0.7313 (m-10) cc_final: 0.6951 (m-80) REVERT: B 430 PHE cc_start: 0.8098 (t80) cc_final: 0.7877 (t80) REVERT: B 451 GLU cc_start: 0.8228 (mp0) cc_final: 0.7882 (mp0) REVERT: B 480 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7680 (ttp) outliers start: 30 outliers final: 19 residues processed: 161 average time/residue: 0.1896 time to fit residues: 42.2960 Evaluate side-chains 153 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 42 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 59 optimal weight: 0.0570 chunk 7 optimal weight: 0.0670 chunk 38 optimal weight: 0.9980 chunk 90 optimal weight: 0.0030 chunk 4 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 overall best weight: 0.2846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.137861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113387 restraints weight = 10430.028| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.46 r_work: 0.3130 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7836 Z= 0.100 Angle : 0.585 9.844 10721 Z= 0.287 Chirality : 0.041 0.140 1291 Planarity : 0.005 0.066 1274 Dihedral : 4.679 24.131 1012 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.75 % Allowed : 17.94 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.28), residues: 959 helix: -0.81 (0.21), residues: 647 sheet: None (None), residues: 0 loop : -2.57 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 471 HIS 0.001 0.000 HIS B 86 PHE 0.011 0.001 PHE A 368 TYR 0.011 0.001 TYR B 379 ARG 0.003 0.000 ARG B 272 Details of bonding type rmsd hydrogen bonds : bond 0.02522 ( 247) hydrogen bonds : angle 3.47413 ( 735) covalent geometry : bond 0.00224 ( 7836) covalent geometry : angle 0.58455 (10721) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.9076 (mtp) cc_final: 0.8829 (mtp) REVERT: A 540 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8452 (m-80) REVERT: A 546 LYS cc_start: 0.8150 (mttt) cc_final: 0.7805 (mttm) REVERT: A 580 TYR cc_start: 0.7739 (m-10) cc_final: 0.7425 (m-10) REVERT: B 368 PHE cc_start: 0.7118 (m-10) cc_final: 0.6607 (m-80) REVERT: B 451 GLU cc_start: 0.8168 (mp0) cc_final: 0.7866 (mp0) REVERT: B 480 MET cc_start: 0.8264 (ttm) cc_final: 0.7838 (ttp) outliers start: 23 outliers final: 15 residues processed: 167 average time/residue: 0.1807 time to fit residues: 41.6792 Evaluate side-chains 149 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 47 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 0.0170 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN B 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.112030 restraints weight = 10444.484| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.52 r_work: 0.3117 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7836 Z= 0.108 Angle : 0.595 9.668 10721 Z= 0.293 Chirality : 0.041 0.145 1291 Planarity : 0.005 0.069 1274 Dihedral : 4.646 23.690 1012 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.11 % Allowed : 18.42 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.28), residues: 959 helix: -0.61 (0.21), residues: 651 sheet: None (None), residues: 0 loop : -2.57 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 471 HIS 0.002 0.000 HIS B 86 PHE 0.011 0.001 PHE A 368 TYR 0.019 0.001 TYR B 273 ARG 0.004 0.000 ARG A 12 Details of bonding type rmsd hydrogen bonds : bond 0.02672 ( 247) hydrogen bonds : angle 3.47274 ( 735) covalent geometry : bond 0.00255 ( 7836) covalent geometry : angle 0.59511 (10721) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.9090 (mtp) cc_final: 0.8822 (mtp) REVERT: A 546 LYS cc_start: 0.8113 (mttt) cc_final: 0.7783 (mttm) REVERT: A 580 TYR cc_start: 0.7752 (m-10) cc_final: 0.7440 (m-10) REVERT: B 368 PHE cc_start: 0.7142 (m-10) cc_final: 0.6652 (m-80) REVERT: B 451 GLU cc_start: 0.8170 (mp0) cc_final: 0.7860 (mp0) REVERT: B 480 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7911 (ttp) outliers start: 26 outliers final: 21 residues processed: 155 average time/residue: 0.1762 time to fit residues: 38.0487 Evaluate side-chains 154 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 70 optimal weight: 2.9990 chunk 8 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 79 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.142004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116275 restraints weight = 10572.884| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.72 r_work: 0.3091 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7836 Z= 0.113 Angle : 0.601 9.618 10721 Z= 0.296 Chirality : 0.042 0.144 1291 Planarity : 0.005 0.068 1274 Dihedral : 4.660 24.369 1012 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.87 % Allowed : 19.14 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.28), residues: 959 helix: -0.53 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -2.62 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 471 HIS 0.002 0.000 HIS B 86 PHE 0.011 0.001 PHE A 368 TYR 0.015 0.001 TYR B 379 ARG 0.004 0.000 ARG B 12 Details of bonding type rmsd hydrogen bonds : bond 0.02758 ( 247) hydrogen bonds : angle 3.46321 ( 735) covalent geometry : bond 0.00269 ( 7836) covalent geometry : angle 0.60120 (10721) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 546 LYS cc_start: 0.8131 (mttt) cc_final: 0.7721 (mttm) REVERT: B 368 PHE cc_start: 0.7233 (m-10) cc_final: 0.6737 (m-80) REVERT: B 480 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7834 (ttp) outliers start: 24 outliers final: 21 residues processed: 151 average time/residue: 0.1800 time to fit residues: 37.6434 Evaluate side-chains 153 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 7 optimal weight: 0.0470 chunk 28 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.136339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.111584 restraints weight = 10679.413| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.48 r_work: 0.3164 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7836 Z= 0.111 Angle : 0.601 9.578 10721 Z= 0.295 Chirality : 0.042 0.146 1291 Planarity : 0.005 0.068 1274 Dihedral : 4.620 24.428 1012 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.63 % Allowed : 19.74 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.28), residues: 959 helix: -0.38 (0.21), residues: 658 sheet: None (None), residues: 0 loop : -2.57 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 471 HIS 0.002 0.000 HIS B 86 PHE 0.011 0.001 PHE A 368 TYR 0.014 0.001 TYR B 580 ARG 0.003 0.000 ARG A 12 Details of bonding type rmsd hydrogen bonds : bond 0.02734 ( 247) hydrogen bonds : angle 3.46080 ( 735) covalent geometry : bond 0.00263 ( 7836) covalent geometry : angle 0.60077 (10721) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 546 LYS cc_start: 0.8158 (mttt) cc_final: 0.7934 (mttm) REVERT: A 580 TYR cc_start: 0.7649 (m-10) cc_final: 0.7374 (m-10) REVERT: B 368 PHE cc_start: 0.7038 (m-10) cc_final: 0.6583 (m-80) REVERT: B 480 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7928 (ttp) outliers start: 22 outliers final: 21 residues processed: 146 average time/residue: 0.1857 time to fit residues: 37.4231 Evaluate side-chains 154 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 72 optimal weight: 7.9990 chunk 48 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 14 optimal weight: 0.0770 chunk 44 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.142009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116387 restraints weight = 10584.824| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.71 r_work: 0.3145 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7836 Z= 0.111 Angle : 0.599 9.375 10721 Z= 0.294 Chirality : 0.042 0.148 1291 Planarity : 0.005 0.068 1274 Dihedral : 4.603 24.173 1012 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.39 % Allowed : 19.86 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.28), residues: 959 helix: -0.29 (0.21), residues: 658 sheet: None (None), residues: 0 loop : -2.56 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 471 HIS 0.001 0.000 HIS B 86 PHE 0.011 0.001 PHE A 368 TYR 0.019 0.001 TYR B 379 ARG 0.004 0.000 ARG A 12 Details of bonding type rmsd hydrogen bonds : bond 0.02730 ( 247) hydrogen bonds : angle 3.46360 ( 735) covalent geometry : bond 0.00263 ( 7836) covalent geometry : angle 0.59877 (10721) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 546 LYS cc_start: 0.8160 (mttt) cc_final: 0.7793 (mttm) REVERT: A 580 TYR cc_start: 0.7704 (m-10) cc_final: 0.7361 (m-10) REVERT: B 272 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7930 (ptm160) REVERT: B 368 PHE cc_start: 0.7101 (m-10) cc_final: 0.6644 (m-80) REVERT: B 480 MET cc_start: 0.8295 (ttm) cc_final: 0.7865 (ttp) outliers start: 20 outliers final: 20 residues processed: 147 average time/residue: 0.1906 time to fit residues: 38.4769 Evaluate side-chains 150 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 18 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 63 optimal weight: 0.0670 chunk 22 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.143228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117664 restraints weight = 10529.432| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.71 r_work: 0.3100 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7836 Z= 0.108 Angle : 0.595 9.373 10721 Z= 0.292 Chirality : 0.042 0.148 1291 Planarity : 0.005 0.068 1274 Dihedral : 4.565 23.719 1012 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.87 % Allowed : 19.86 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.28), residues: 959 helix: -0.21 (0.21), residues: 657 sheet: None (None), residues: 0 loop : -2.53 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 471 HIS 0.001 0.000 HIS B 86 PHE 0.011 0.001 PHE A 368 TYR 0.017 0.001 TYR B 379 ARG 0.004 0.000 ARG A 12 Details of bonding type rmsd hydrogen bonds : bond 0.02660 ( 247) hydrogen bonds : angle 3.45046 ( 735) covalent geometry : bond 0.00254 ( 7836) covalent geometry : angle 0.59507 (10721) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4384.06 seconds wall clock time: 76 minutes 8.82 seconds (4568.82 seconds total)