Starting phenix.real_space_refine on Fri Jun 6 13:27:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w8s_32358/06_2025/7w8s_32358.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w8s_32358/06_2025/7w8s_32358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w8s_32358/06_2025/7w8s_32358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w8s_32358/06_2025/7w8s_32358.map" model { file = "/net/cci-nas-00/data/ceres_data/7w8s_32358/06_2025/7w8s_32358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w8s_32358/06_2025/7w8s_32358.cif" } resolution = 2.85 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= -0.001 sd= 0.288 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1513 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4127 2.51 5 N 1079 2.21 5 O 1211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6455 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4899 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 30, 'TRANS': 564} Chain: "B" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1527 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.56, per 1000 atoms: 0.71 Number of scatterers: 6455 At special positions: 0 Unit cell: (76.54, 91.16, 126.42, 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) Zn 1 29.99 S 37 16.00 O 1211 8.00 N 1079 7.00 C 4127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN A 53 " Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 887.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 378 " 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1486 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 6 sheets defined 53.0% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 20 through 52 removed outlier: 3.759A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 38 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 77 removed outlier: 3.833A pdb=" N GLN A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 67 " --> pdb=" O ASN A 63 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.721A pdb=" N TYR A 83 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.691A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 88' Processing helix chain 'A' and resid 90 through 98 removed outlier: 3.628A pdb=" N GLN A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 4.048A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 removed outlier: 3.548A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.831A pdb=" N MET A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 172 removed outlier: 3.906A pdb=" N TRP A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.701A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 removed outlier: 3.526A pdb=" N ARG A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 220 through 231 removed outlier: 3.912A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.628A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.697A pdb=" N LEU A 278 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Proline residue: A 280 - end of helix No H-bonds generated for 'chain 'A' and resid 275 through 282' Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.701A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.131A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 removed outlier: 3.571A pdb=" N ALA A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 4.083A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.770A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA A 412 " --> pdb=" O MET A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 removed outlier: 3.677A pdb=" N ASN A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 444 removed outlier: 3.518A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.607A pdb=" N GLU A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 458 " --> pdb=" O TYR A 454 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP A 459 " --> pdb=" O MET A 455 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.733A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP A 477 " --> pdb=" O TRP A 473 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 removed outlier: 3.521A pdb=" N ALA A 502 " --> pdb=" O ASP A 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 499 through 502' Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.528A pdb=" N ALA A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.715A pdb=" N THR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.572A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.559A pdb=" N GLN A 552 " --> pdb=" O ARG A 548 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 559 " --> pdb=" O HIS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 removed outlier: 3.829A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG A 572 " --> pdb=" O PHE A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.537A pdb=" N TYR A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.511A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.291A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.090A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.061A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.637A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 501 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: 1.52 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2071 1.35 - 1.46: 1709 1.46 - 1.58: 2803 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6641 Sorted by residual: bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.80e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.78e+00 bond pdb=" C GLU A 145 " pdb=" N PRO A 146 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.69e+00 bond pdb=" C LYS A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.28e-02 6.10e+03 1.75e+00 bond pdb=" C TYR A 279 " pdb=" N PRO A 280 " ideal model delta sigma weight residual 1.337 1.351 -0.014 1.11e-02 8.12e+03 1.66e+00 ... (remaining 6636 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 8773 1.50 - 3.00: 203 3.00 - 4.50: 34 4.50 - 6.00: 6 6.00 - 7.50: 7 Bond angle restraints: 9023 Sorted by residual: angle pdb=" C ILE A 233 " pdb=" N LYS A 234 " pdb=" CA LYS A 234 " ideal model delta sigma weight residual 120.09 124.32 -4.23 1.25e+00 6.40e-01 1.15e+01 angle pdb=" N ARG A 582 " pdb=" CA ARG A 582 " pdb=" C ARG A 582 " ideal model delta sigma weight residual 109.81 116.21 -6.40 2.21e+00 2.05e-01 8.38e+00 angle pdb=" N ASP A 499 " pdb=" CA ASP A 499 " pdb=" C ASP A 499 " ideal model delta sigma weight residual 109.81 115.94 -6.13 2.21e+00 2.05e-01 7.70e+00 angle pdb=" CA ARG A 582 " pdb=" C ARG A 582 " pdb=" N PRO A 583 " ideal model delta sigma weight residual 118.44 122.79 -4.35 1.59e+00 3.96e-01 7.47e+00 angle pdb=" CA LEU A 450 " pdb=" C LEU A 450 " pdb=" N PRO A 451 " ideal model delta sigma weight residual 118.44 122.34 -3.90 1.59e+00 3.96e-01 6.03e+00 ... (remaining 9018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3712 17.84 - 35.68: 205 35.68 - 53.52: 31 53.52 - 71.36: 5 71.36 - 89.20: 2 Dihedral angle restraints: 3955 sinusoidal: 1639 harmonic: 2316 Sorted by residual: dihedral pdb=" CA CYS B 336 " pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " ideal model delta sinusoidal sigma weight residual 79.00 22.27 56.73 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA TYR A 497 " pdb=" C TYR A 497 " pdb=" N CYS A 498 " pdb=" CA CYS A 498 " ideal model delta harmonic sigma weight residual 180.00 164.65 15.35 0 5.00e+00 4.00e-02 9.42e+00 dihedral pdb=" N LEU A 570 " pdb=" CA LEU A 570 " pdb=" CB LEU A 570 " pdb=" CG LEU A 570 " ideal model delta sinusoidal sigma weight residual -180.00 -125.17 -54.83 3 1.50e+01 4.44e-03 9.31e+00 ... (remaining 3952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 536 0.033 - 0.065: 294 0.065 - 0.098: 59 0.098 - 0.131: 39 0.131 - 0.163: 7 Chirality restraints: 935 Sorted by residual: chirality pdb=" CA GLU A 145 " pdb=" N GLU A 145 " pdb=" C GLU A 145 " pdb=" CB GLU A 145 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA TYR A 279 " pdb=" N TYR A 279 " pdb=" C TYR A 279 " pdb=" CB TYR A 279 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA ARG A 177 " pdb=" N ARG A 177 " pdb=" C ARG A 177 " pdb=" CB ARG A 177 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 932 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " -0.042 5.00e-02 4.00e+02 6.36e-02 6.47e+00 pdb=" N PRO A 583 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 336 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO B 337 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " 0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO B 521 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " 0.028 5.00e-02 4.00e+02 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 40 2.66 - 3.22: 5074 3.22 - 3.78: 8522 3.78 - 4.34: 12521 4.34 - 4.90: 20834 Nonbonded interactions: 46991 Sorted by model distance: nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 801 " model vdw 2.102 2.230 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.307 3.040 nonbonded pdb=" O THR A 125 " pdb=" OG1 THR A 129 " model vdw 2.316 3.040 nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.374 3.040 nonbonded pdb=" OG SER A 170 " pdb=" OE1 GLU A 171 " model vdw 2.388 3.040 ... (remaining 46986 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=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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.810 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 0.197 6652 Z= 0.186 Angle : 0.601 7.497 9043 Z= 0.322 Chirality : 0.045 0.163 935 Planarity : 0.007 0.064 1172 Dihedral : 11.074 89.201 2448 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.48 % Allowed : 3.77 % Favored : 92.75 % 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: -4.03 (0.24), residues: 784 helix: -4.51 (0.10), residues: 307 sheet: 1.25 (0.91), residues: 41 loop : -1.60 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.014 0.001 PHE B 453 TYR 0.021 0.001 TYR A 385 ARG 0.002 0.000 ARG B 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 1) link_NAG-ASN : angle 3.16573 ( 3) link_BETA1-4 : bond 0.00509 ( 1) link_BETA1-4 : angle 1.26074 ( 3) hydrogen bonds : bond 0.42099 ( 179) hydrogen bonds : angle 9.04772 ( 501) metal coordination : bond 0.19699 ( 2) SS BOND : bond 0.00194 ( 7) SS BOND : angle 1.07353 ( 14) covalent geometry : bond 0.00306 ( 6641) covalent geometry : angle 0.59743 ( 9023) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.874 Fit side-chains REVERT: A 89 GLN cc_start: 0.6046 (mp10) cc_final: 0.5703 (mp10) REVERT: A 92 ILE cc_start: 0.6990 (mm) cc_final: 0.6764 (mp) REVERT: A 383 MET cc_start: 0.8283 (mtp) cc_final: 0.7935 (mtm) REVERT: A 580 ASP cc_start: 0.7721 (t0) cc_final: 0.7240 (t0) REVERT: B 356 LYS cc_start: 0.7695 (ttmt) cc_final: 0.6962 (tttp) outliers start: 24 outliers final: 5 residues processed: 124 average time/residue: 1.5005 time to fit residues: 195.1811 Evaluate side-chains 87 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 70 optimal weight: 4.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 420 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.163352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.134770 restraints weight = 6836.238| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.75 r_work: 0.3484 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6652 Z= 0.171 Angle : 0.629 7.143 9043 Z= 0.330 Chirality : 0.045 0.140 935 Planarity : 0.006 0.043 1172 Dihedral : 5.165 31.952 914 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.75 % Allowed : 9.28 % Favored : 87.97 % 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: -3.12 (0.25), residues: 784 helix: -2.77 (0.21), residues: 343 sheet: 1.61 (0.99), residues: 36 loop : -1.72 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 163 HIS 0.009 0.002 HIS A 241 PHE 0.020 0.002 PHE A 28 TYR 0.022 0.002 TYR A 385 ARG 0.003 0.001 ARG B 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00093 ( 1) link_NAG-ASN : angle 3.81163 ( 3) link_BETA1-4 : bond 0.00317 ( 1) link_BETA1-4 : angle 2.01699 ( 3) hydrogen bonds : bond 0.08879 ( 179) hydrogen bonds : angle 4.97220 ( 501) metal coordination : bond 0.00223 ( 2) SS BOND : bond 0.00524 ( 7) SS BOND : angle 1.71742 ( 14) covalent geometry : bond 0.00374 ( 6641) covalent geometry : angle 0.62109 ( 9023) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.760 Fit side-chains REVERT: A 89 GLN cc_start: 0.5995 (mp10) cc_final: 0.5591 (mp10) REVERT: A 323 MET cc_start: 0.8490 (mmp) cc_final: 0.8202 (mmt) REVERT: A 383 MET cc_start: 0.8446 (mtp) cc_final: 0.8175 (mtm) REVERT: A 580 ASP cc_start: 0.8046 (t0) cc_final: 0.7656 (t0) outliers start: 19 outliers final: 11 residues processed: 95 average time/residue: 1.1937 time to fit residues: 119.9189 Evaluate side-chains 82 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.0670 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 0.0050 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 overall best weight: 0.9936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 401 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.164090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.135397 restraints weight = 6940.642| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.77 r_work: 0.3481 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6652 Z= 0.130 Angle : 0.530 5.945 9043 Z= 0.279 Chirality : 0.042 0.127 935 Planarity : 0.005 0.041 1172 Dihedral : 4.771 32.003 913 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.75 % Allowed : 10.14 % Favored : 87.10 % 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: -2.40 (0.26), residues: 784 helix: -1.80 (0.25), residues: 339 sheet: 1.33 (0.99), residues: 36 loop : -1.64 (0.26), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.008 0.001 HIS A 241 PHE 0.016 0.001 PHE A 28 TYR 0.016 0.001 TYR A 385 ARG 0.002 0.000 ARG B 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00059 ( 1) link_NAG-ASN : angle 3.37639 ( 3) link_BETA1-4 : bond 0.00304 ( 1) link_BETA1-4 : angle 1.56800 ( 3) hydrogen bonds : bond 0.07058 ( 179) hydrogen bonds : angle 4.57108 ( 501) metal coordination : bond 0.00313 ( 2) SS BOND : bond 0.00449 ( 7) SS BOND : angle 1.54660 ( 14) covalent geometry : bond 0.00279 ( 6641) covalent geometry : angle 0.52288 ( 9023) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.681 Fit side-chains REVERT: A 21 THR cc_start: 0.6886 (OUTLIER) cc_final: 0.6619 (m) REVERT: A 89 GLN cc_start: 0.5892 (mp10) cc_final: 0.5455 (mp10) REVERT: A 153 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7349 (mt-10) REVERT: A 171 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: A 323 MET cc_start: 0.8414 (mmp) cc_final: 0.8062 (mmt) REVERT: A 383 MET cc_start: 0.8392 (mtp) cc_final: 0.8156 (mtm) REVERT: A 580 ASP cc_start: 0.7903 (t0) cc_final: 0.7582 (m-30) REVERT: B 395 VAL cc_start: 0.7339 (OUTLIER) cc_final: 0.7106 (t) REVERT: B 465 GLU cc_start: 0.7867 (tt0) cc_final: 0.7198 (tm-30) outliers start: 19 outliers final: 9 residues processed: 87 average time/residue: 1.2493 time to fit residues: 114.4275 Evaluate side-chains 80 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 73 optimal weight: 0.1980 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 0.0770 chunk 24 optimal weight: 8.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.166462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.137842 restraints weight = 6954.434| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.77 r_work: 0.3508 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6652 Z= 0.100 Angle : 0.465 4.758 9043 Z= 0.243 Chirality : 0.041 0.130 935 Planarity : 0.004 0.038 1172 Dihedral : 4.425 31.604 913 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.75 % Allowed : 10.58 % Favored : 86.67 % 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: -1.88 (0.27), residues: 784 helix: -1.22 (0.27), residues: 339 sheet: 1.46 (0.98), residues: 36 loop : -1.48 (0.26), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.012 0.001 PHE A 28 TYR 0.011 0.001 TYR A 385 ARG 0.001 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 1) link_NAG-ASN : angle 2.89543 ( 3) link_BETA1-4 : bond 0.00364 ( 1) link_BETA1-4 : angle 1.29460 ( 3) hydrogen bonds : bond 0.05327 ( 179) hydrogen bonds : angle 4.25815 ( 501) metal coordination : bond 0.00222 ( 2) SS BOND : bond 0.00378 ( 7) SS BOND : angle 1.40022 ( 14) covalent geometry : bond 0.00211 ( 6641) covalent geometry : angle 0.45824 ( 9023) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.678 Fit side-chains REVERT: A 89 GLN cc_start: 0.5756 (mp10) cc_final: 0.5355 (mp10) REVERT: A 153 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7288 (mt-10) REVERT: A 323 MET cc_start: 0.8363 (mmp) cc_final: 0.8027 (mmt) REVERT: A 383 MET cc_start: 0.8343 (mtp) cc_final: 0.8057 (mtm) REVERT: A 580 ASP cc_start: 0.7719 (t0) cc_final: 0.7496 (m-30) REVERT: A 586 ASN cc_start: 0.7125 (m-40) cc_final: 0.6908 (t0) REVERT: B 465 GLU cc_start: 0.7916 (tt0) cc_final: 0.7247 (tm-30) REVERT: B 513 LEU cc_start: 0.7908 (mt) cc_final: 0.7663 (mp) outliers start: 19 outliers final: 12 residues processed: 93 average time/residue: 1.4373 time to fit residues: 140.2366 Evaluate side-chains 82 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 19 optimal weight: 0.0170 chunk 38 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 61 optimal weight: 20.0000 overall best weight: 1.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.163451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134585 restraints weight = 6972.254| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.77 r_work: 0.3479 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6652 Z= 0.135 Angle : 0.535 5.896 9043 Z= 0.280 Chirality : 0.043 0.127 935 Planarity : 0.004 0.039 1172 Dihedral : 4.519 31.338 912 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.48 % Allowed : 10.43 % Favored : 86.09 % 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: -1.81 (0.27), residues: 784 helix: -1.05 (0.28), residues: 339 sheet: 1.43 (0.98), residues: 36 loop : -1.56 (0.26), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.008 0.001 HIS A 241 PHE 0.017 0.001 PHE A 28 TYR 0.017 0.001 TYR A 385 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00020 ( 1) link_NAG-ASN : angle 3.41483 ( 3) link_BETA1-4 : bond 0.00204 ( 1) link_BETA1-4 : angle 1.58519 ( 3) hydrogen bonds : bond 0.06518 ( 179) hydrogen bonds : angle 4.31208 ( 501) metal coordination : bond 0.00383 ( 2) SS BOND : bond 0.00466 ( 7) SS BOND : angle 1.52149 ( 14) covalent geometry : bond 0.00296 ( 6641) covalent geometry : angle 0.52828 ( 9023) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 1.549 Fit side-chains REVERT: A 21 THR cc_start: 0.6850 (OUTLIER) cc_final: 0.6591 (m) REVERT: A 89 GLN cc_start: 0.5908 (mp10) cc_final: 0.5511 (mp10) REVERT: A 153 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7390 (mt-10) REVERT: A 323 MET cc_start: 0.8401 (mmp) cc_final: 0.8033 (mmp) REVERT: A 383 MET cc_start: 0.8409 (mtp) cc_final: 0.8161 (mtm) REVERT: A 580 ASP cc_start: 0.7900 (t0) cc_final: 0.7602 (m-30) REVERT: B 465 GLU cc_start: 0.7873 (tt0) cc_final: 0.7272 (tm-30) outliers start: 24 outliers final: 17 residues processed: 91 average time/residue: 1.6745 time to fit residues: 161.8000 Evaluate side-chains 88 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 0.0050 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 0.1980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 401 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.166916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.138106 restraints weight = 6947.039| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.78 r_work: 0.3525 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6652 Z= 0.093 Angle : 0.455 4.783 9043 Z= 0.236 Chirality : 0.041 0.125 935 Planarity : 0.004 0.037 1172 Dihedral : 4.200 31.695 912 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.17 % Allowed : 12.32 % Favored : 85.51 % 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: -1.49 (0.28), residues: 784 helix: -0.67 (0.28), residues: 346 sheet: 1.45 (0.99), residues: 36 loop : -1.49 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.010 0.001 PHE A 28 TYR 0.010 0.001 TYR B 351 ARG 0.001 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 1) link_NAG-ASN : angle 2.81168 ( 3) link_BETA1-4 : bond 0.00357 ( 1) link_BETA1-4 : angle 1.24216 ( 3) hydrogen bonds : bond 0.04825 ( 179) hydrogen bonds : angle 4.13420 ( 501) metal coordination : bond 0.00174 ( 2) SS BOND : bond 0.00324 ( 7) SS BOND : angle 1.16736 ( 14) covalent geometry : bond 0.00192 ( 6641) covalent geometry : angle 0.44943 ( 9023) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.677 Fit side-chains REVERT: A 21 THR cc_start: 0.6704 (OUTLIER) cc_final: 0.6426 (m) REVERT: A 89 GLN cc_start: 0.5786 (mp10) cc_final: 0.5368 (mp10) REVERT: A 153 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7320 (mt-10) REVERT: A 323 MET cc_start: 0.8388 (mmp) cc_final: 0.8033 (mmt) REVERT: A 383 MET cc_start: 0.8359 (mtp) cc_final: 0.8072 (mtm) REVERT: B 465 GLU cc_start: 0.7843 (tt0) cc_final: 0.7249 (tm-30) REVERT: B 513 LEU cc_start: 0.7938 (mt) cc_final: 0.7686 (mp) outliers start: 15 outliers final: 12 residues processed: 86 average time/residue: 1.3764 time to fit residues: 124.2323 Evaluate side-chains 82 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 0.0470 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 56 optimal weight: 0.1980 chunk 0 optimal weight: 6.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.166732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.137771 restraints weight = 6987.596| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.79 r_work: 0.3517 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6652 Z= 0.095 Angle : 0.459 5.165 9043 Z= 0.237 Chirality : 0.041 0.128 935 Planarity : 0.004 0.037 1172 Dihedral : 4.088 31.384 912 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.33 % Allowed : 12.03 % Favored : 84.64 % 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: -1.29 (0.28), residues: 784 helix: -0.38 (0.28), residues: 345 sheet: 1.36 (1.00), residues: 36 loop : -1.49 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.012 0.001 PHE A 28 TYR 0.011 0.001 TYR A 385 ARG 0.001 0.000 ARG B 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 1) link_NAG-ASN : angle 2.88227 ( 3) link_BETA1-4 : bond 0.00198 ( 1) link_BETA1-4 : angle 1.22590 ( 3) hydrogen bonds : bond 0.04835 ( 179) hydrogen bonds : angle 4.07376 ( 501) metal coordination : bond 0.00200 ( 2) SS BOND : bond 0.00315 ( 7) SS BOND : angle 1.15003 ( 14) covalent geometry : bond 0.00199 ( 6641) covalent geometry : angle 0.45397 ( 9023) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.682 Fit side-chains REVERT: A 21 THR cc_start: 0.6652 (OUTLIER) cc_final: 0.6388 (m) REVERT: A 89 GLN cc_start: 0.5784 (mp10) cc_final: 0.5361 (mp10) REVERT: A 189 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7509 (tp30) REVERT: A 323 MET cc_start: 0.8381 (mmp) cc_final: 0.8011 (mmt) REVERT: A 383 MET cc_start: 0.8361 (mtp) cc_final: 0.8073 (mtm) REVERT: B 465 GLU cc_start: 0.7866 (tt0) cc_final: 0.7254 (tm-30) outliers start: 23 outliers final: 14 residues processed: 89 average time/residue: 1.3645 time to fit residues: 127.4907 Evaluate side-chains 84 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.166999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.138106 restraints weight = 6981.738| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.78 r_work: 0.3523 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6652 Z= 0.093 Angle : 0.453 4.782 9043 Z= 0.234 Chirality : 0.041 0.126 935 Planarity : 0.004 0.036 1172 Dihedral : 4.015 31.442 912 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.19 % Allowed : 12.46 % Favored : 84.35 % 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: -1.09 (0.29), residues: 784 helix: -0.16 (0.29), residues: 345 sheet: 1.33 (1.01), residues: 36 loop : -1.43 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.011 0.001 PHE A 28 TYR 0.011 0.001 TYR A 385 ARG 0.001 0.000 ARG B 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00079 ( 1) link_NAG-ASN : angle 2.85080 ( 3) link_BETA1-4 : bond 0.00318 ( 1) link_BETA1-4 : angle 1.19935 ( 3) hydrogen bonds : bond 0.04687 ( 179) hydrogen bonds : angle 4.04977 ( 501) metal coordination : bond 0.00189 ( 2) SS BOND : bond 0.00300 ( 7) SS BOND : angle 1.09344 ( 14) covalent geometry : bond 0.00195 ( 6641) covalent geometry : angle 0.44744 ( 9023) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.810 Fit side-chains REVERT: A 21 THR cc_start: 0.6611 (OUTLIER) cc_final: 0.6351 (m) REVERT: A 89 GLN cc_start: 0.5746 (mp10) cc_final: 0.5318 (mp10) REVERT: A 189 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7493 (tp30) REVERT: A 323 MET cc_start: 0.8356 (mmp) cc_final: 0.7972 (mmt) REVERT: A 383 MET cc_start: 0.8351 (mtp) cc_final: 0.8060 (mtm) REVERT: B 465 GLU cc_start: 0.7882 (tt0) cc_final: 0.7270 (tm-30) REVERT: B 513 LEU cc_start: 0.7953 (mt) cc_final: 0.7714 (mp) outliers start: 22 outliers final: 16 residues processed: 85 average time/residue: 1.3520 time to fit residues: 120.9330 Evaluate side-chains 86 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.163594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.134332 restraints weight = 7024.919| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.80 r_work: 0.3468 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6652 Z= 0.141 Angle : 0.543 6.001 9043 Z= 0.282 Chirality : 0.044 0.129 935 Planarity : 0.004 0.037 1172 Dihedral : 4.386 30.396 912 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.04 % Allowed : 12.75 % Favored : 84.20 % 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: -1.36 (0.28), residues: 784 helix: -0.42 (0.28), residues: 351 sheet: 1.27 (0.99), residues: 36 loop : -1.55 (0.27), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.009 0.001 HIS A 241 PHE 0.017 0.001 PHE A 28 TYR 0.017 0.001 TYR A 385 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 1) link_NAG-ASN : angle 3.45496 ( 3) link_BETA1-4 : bond 0.00166 ( 1) link_BETA1-4 : angle 1.55997 ( 3) hydrogen bonds : bond 0.06361 ( 179) hydrogen bonds : angle 4.22820 ( 501) metal coordination : bond 0.00400 ( 2) SS BOND : bond 0.00426 ( 7) SS BOND : angle 1.41709 ( 14) covalent geometry : bond 0.00312 ( 6641) covalent geometry : angle 0.53614 ( 9023) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.657 Fit side-chains REVERT: A 89 GLN cc_start: 0.5889 (mp10) cc_final: 0.5479 (mp10) REVERT: A 189 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7493 (tp30) REVERT: A 323 MET cc_start: 0.8382 (mmp) cc_final: 0.8077 (mmp) REVERT: A 383 MET cc_start: 0.8407 (mtp) cc_final: 0.8145 (mtm) REVERT: B 406 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: B 465 GLU cc_start: 0.7871 (tt0) cc_final: 0.7240 (tm-30) outliers start: 21 outliers final: 15 residues processed: 83 average time/residue: 1.1763 time to fit residues: 102.9039 Evaluate side-chains 84 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 0.0670 chunk 41 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.164548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135419 restraints weight = 7019.745| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.80 r_work: 0.3490 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6652 Z= 0.119 Angle : 0.506 5.592 9043 Z= 0.263 Chirality : 0.042 0.127 935 Planarity : 0.004 0.036 1172 Dihedral : 4.343 30.539 912 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.61 % Allowed : 13.48 % Favored : 83.91 % 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: -1.20 (0.28), residues: 784 helix: -0.23 (0.29), residues: 341 sheet: 1.27 (0.98), residues: 36 loop : -1.49 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.007 0.001 HIS A 241 PHE 0.014 0.001 PHE A 28 TYR 0.015 0.001 TYR A 385 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00034 ( 1) link_NAG-ASN : angle 3.22631 ( 3) link_BETA1-4 : bond 0.00233 ( 1) link_BETA1-4 : angle 1.45811 ( 3) hydrogen bonds : bond 0.05762 ( 179) hydrogen bonds : angle 4.19850 ( 501) metal coordination : bond 0.00313 ( 2) SS BOND : bond 0.00377 ( 7) SS BOND : angle 1.30876 ( 14) covalent geometry : bond 0.00257 ( 6641) covalent geometry : angle 0.50007 ( 9023) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.709 Fit side-chains REVERT: A 89 GLN cc_start: 0.5876 (mp10) cc_final: 0.5465 (mp10) REVERT: A 323 MET cc_start: 0.8409 (mmp) cc_final: 0.8101 (mmp) REVERT: A 383 MET cc_start: 0.8411 (mtp) cc_final: 0.8147 (mtm) REVERT: B 465 GLU cc_start: 0.7875 (tt0) cc_final: 0.7263 (tm-30) outliers start: 18 outliers final: 16 residues processed: 82 average time/residue: 1.2022 time to fit residues: 103.8613 Evaluate side-chains 82 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 66 optimal weight: 0.0040 chunk 74 optimal weight: 0.9980 chunk 4 optimal weight: 0.0970 chunk 41 optimal weight: 0.0070 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 0.0010 chunk 43 optimal weight: 2.9990 overall best weight: 0.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.169965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.141301 restraints weight = 7085.950| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.80 r_work: 0.3553 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6652 Z= 0.080 Angle : 0.417 4.791 9043 Z= 0.213 Chirality : 0.040 0.124 935 Planarity : 0.004 0.036 1172 Dihedral : 3.869 32.967 912 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.59 % Allowed : 14.49 % Favored : 83.91 % 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: -0.76 (0.29), residues: 784 helix: 0.17 (0.29), residues: 342 sheet: 1.22 (0.99), residues: 36 loop : -1.26 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.002 0.001 HIS A 241 PHE 0.011 0.001 PHE B 377 TYR 0.009 0.001 TYR B 351 ARG 0.001 0.000 ARG A 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 1) link_NAG-ASN : angle 2.34214 ( 3) link_BETA1-4 : bond 0.00553 ( 1) link_BETA1-4 : angle 1.08149 ( 3) hydrogen bonds : bond 0.03658 ( 179) hydrogen bonds : angle 3.96473 ( 501) metal coordination : bond 0.00130 ( 2) SS BOND : bond 0.00181 ( 7) SS BOND : angle 0.74369 ( 14) covalent geometry : bond 0.00164 ( 6641) covalent geometry : angle 0.41371 ( 9023) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5504.20 seconds wall clock time: 97 minutes 4.16 seconds (5824.16 seconds total)