Starting phenix.real_space_refine on Tue Mar 3 17:58:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w8s_32358/03_2026/7w8s_32358.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w8s_32358/03_2026/7w8s_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_32358/03_2026/7w8s_32358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w8s_32358/03_2026/7w8s_32358.map" model { file = "/net/cci-nas-00/data/ceres_data/7w8s_32358/03_2026/7w8s_32358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w8s_32358/03_2026/7w8s_32358.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.35, per 1000 atoms: 0.21 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: 0.68 Conformation dependent library (CDL) restraints added in 251.0 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: 0.13 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: 0.77 Time building geometry restraints manager: 0.84 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: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.770 Find NCS groups from input model: 0.020 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:9.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.060 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.002 0.000 ARG B 509 TYR 0.021 0.001 TYR A 385 PHE 0.014 0.001 PHE B 453 TRP 0.009 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6641) covalent geometry : angle 0.59743 ( 9023) SS BOND : bond 0.00194 ( 7) SS BOND : angle 1.07353 ( 14) hydrogen bonds : bond 0.42099 ( 179) hydrogen bonds : angle 9.04772 ( 501) metal coordination : bond 0.19699 ( 2) link_BETA1-4 : bond 0.00509 ( 1) link_BETA1-4 : angle 1.26074 ( 3) link_NAG-ASN : bond 0.00186 ( 1) link_NAG-ASN : angle 3.16573 ( 3) *********************** 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 : 0.234 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: 0.8282 (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: 0.7696 (ttmt) cc_final: 0.6962 (tttp) outliers start: 24 outliers final: 5 residues processed: 124 average time/residue: 0.5615 time to fit residues: 72.7659 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 : 0.241 ------------------------------------------------------------------------------- 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 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 322 ASN A 420 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.164152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.135509 restraints weight = 6932.724| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.77 r_work: 0.3492 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6652 Z= 0.156 Angle : 0.605 6.667 9043 Z= 0.318 Chirality : 0.044 0.130 935 Planarity : 0.006 0.043 1172 Dihedral : 5.067 31.461 914 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.61 % Allowed : 9.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.25), residues: 784 helix: -2.79 (0.21), residues: 343 sheet: 1.62 (0.99), residues: 36 loop : -1.68 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 509 TYR 0.021 0.002 TYR A 385 PHE 0.019 0.002 PHE A 28 TRP 0.012 0.001 TRP A 163 HIS 0.009 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6641) covalent geometry : angle 0.59688 ( 9023) SS BOND : bond 0.00580 ( 7) SS BOND : angle 1.68831 ( 14) hydrogen bonds : bond 0.08664 ( 179) hydrogen bonds : angle 4.96047 ( 501) metal coordination : bond 0.00521 ( 2) link_BETA1-4 : bond 0.00356 ( 1) link_BETA1-4 : angle 1.94104 ( 3) link_NAG-ASN : bond 0.00153 ( 1) link_NAG-ASN : angle 3.73745 ( 3) *********************** 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 99 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.197 Fit side-chains REVERT: A 89 GLN cc_start: 0.5969 (mp10) cc_final: 0.5563 (mp10) REVERT: A 323 MET cc_start: 0.8484 (mmp) cc_final: 0.8202 (mmt) REVERT: A 383 MET cc_start: 0.8448 (mtp) cc_final: 0.8159 (mtm) REVERT: A 580 ASP cc_start: 0.7980 (t0) cc_final: 0.7591 (t0) outliers start: 18 outliers final: 10 residues processed: 94 average time/residue: 0.5123 time to fit residues: 50.6542 Evaluate side-chains 81 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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 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 37 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 31 optimal weight: 0.0000 chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.165953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.137367 restraints weight = 6913.206| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.77 r_work: 0.3504 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6652 Z= 0.111 Angle : 0.488 5.161 9043 Z= 0.256 Chirality : 0.041 0.136 935 Planarity : 0.004 0.040 1172 Dihedral : 4.564 31.099 913 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.61 % Allowed : 10.00 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.27), residues: 784 helix: -1.76 (0.25), residues: 339 sheet: 1.45 (1.01), residues: 36 loop : -1.56 (0.26), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 273 TYR 0.013 0.001 TYR A 385 PHE 0.014 0.001 PHE A 28 TRP 0.011 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 6641) covalent geometry : angle 0.48120 ( 9023) SS BOND : bond 0.00341 ( 7) SS BOND : angle 1.48530 ( 14) hydrogen bonds : bond 0.06293 ( 179) hydrogen bonds : angle 4.50872 ( 501) metal coordination : bond 0.00217 ( 2) link_BETA1-4 : bond 0.00287 ( 1) link_BETA1-4 : angle 1.33621 ( 3) link_NAG-ASN : bond 0.00154 ( 1) link_NAG-ASN : angle 3.03044 ( 3) *********************** 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 99 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.266 Fit side-chains REVERT: A 89 GLN cc_start: 0.5831 (mp10) cc_final: 0.5446 (mp10) REVERT: A 171 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: A 323 MET cc_start: 0.8382 (mmp) cc_final: 0.8039 (mmt) REVERT: A 383 MET cc_start: 0.8353 (mtp) cc_final: 0.8117 (mtm) REVERT: A 580 ASP cc_start: 0.7810 (t0) cc_final: 0.7554 (m-30) REVERT: A 586 ASN cc_start: 0.7116 (m-40) cc_final: 0.6859 (t0) REVERT: B 395 VAL cc_start: 0.7332 (OUTLIER) cc_final: 0.7100 (t) REVERT: B 465 GLU cc_start: 0.7915 (tt0) cc_final: 0.7207 (tm-30) outliers start: 18 outliers final: 9 residues processed: 92 average time/residue: 0.5576 time to fit residues: 53.7494 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 : 0.319 ------------------------------------------------------------------------------- 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 483 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 28 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 24 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 0.0050 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.167857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.139302 restraints weight = 7032.163| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.78 r_work: 0.3529 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2211 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= 0.091 Angle : 0.443 4.751 9043 Z= 0.230 Chirality : 0.040 0.132 935 Planarity : 0.004 0.037 1172 Dihedral : 4.226 31.833 913 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.90 % Allowed : 10.87 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.28), residues: 784 helix: -1.07 (0.27), residues: 345 sheet: 1.41 (1.00), residues: 36 loop : -1.39 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 548 TYR 0.011 0.001 TYR B 396 PHE 0.010 0.001 PHE A 28 TRP 0.010 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00190 ( 6641) covalent geometry : angle 0.43681 ( 9023) SS BOND : bond 0.00334 ( 7) SS BOND : angle 1.34429 ( 14) hydrogen bonds : bond 0.04846 ( 179) hydrogen bonds : angle 4.17061 ( 501) metal coordination : bond 0.00186 ( 2) link_BETA1-4 : bond 0.00356 ( 1) link_BETA1-4 : angle 1.17576 ( 3) link_NAG-ASN : bond 0.00159 ( 1) link_NAG-ASN : angle 2.73010 ( 3) *********************** 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 96 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.229 Fit side-chains REVERT: A 89 GLN cc_start: 0.5733 (mp10) cc_final: 0.5320 (mp10) REVERT: A 233 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7176 (pt) REVERT: A 323 MET cc_start: 0.8363 (mmp) cc_final: 0.7985 (mmp) REVERT: A 383 MET cc_start: 0.8330 (mtp) cc_final: 0.8040 (mtm) REVERT: A 586 ASN cc_start: 0.7178 (m-40) cc_final: 0.6956 (t0) REVERT: B 465 GLU cc_start: 0.7932 (tt0) cc_final: 0.7347 (tm-30) REVERT: B 513 LEU cc_start: 0.7928 (mt) cc_final: 0.7680 (mp) outliers start: 20 outliers final: 10 residues processed: 90 average time/residue: 0.5446 time to fit residues: 51.4811 Evaluate side-chains 83 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 233 ILE 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 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 49 optimal weight: 0.0670 chunk 4 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 71 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.165924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.137139 restraints weight = 7017.261| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.78 r_work: 0.3510 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2251 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= 0.105 Angle : 0.477 4.809 9043 Z= 0.248 Chirality : 0.041 0.131 935 Planarity : 0.004 0.037 1172 Dihedral : 4.296 35.271 913 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.19 % Allowed : 11.16 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.28), residues: 784 helix: -0.72 (0.28), residues: 345 sheet: 1.51 (0.99), residues: 36 loop : -1.44 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 273 TYR 0.014 0.001 TYR A 385 PHE 0.014 0.001 PHE A 28 TRP 0.010 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 6641) covalent geometry : angle 0.47063 ( 9023) SS BOND : bond 0.00392 ( 7) SS BOND : angle 1.24386 ( 14) hydrogen bonds : bond 0.05390 ( 179) hydrogen bonds : angle 4.16040 ( 501) metal coordination : bond 0.00237 ( 2) link_BETA1-4 : bond 0.00234 ( 1) link_BETA1-4 : angle 1.29209 ( 3) link_NAG-ASN : bond 0.00050 ( 1) link_NAG-ASN : angle 3.10949 ( 3) *********************** 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 93 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.253 Fit side-chains REVERT: A 89 GLN cc_start: 0.5829 (mp10) cc_final: 0.5428 (mp10) REVERT: A 383 MET cc_start: 0.8358 (mtp) cc_final: 0.8071 (mtm) REVERT: B 465 GLU cc_start: 0.7892 (tt0) cc_final: 0.7304 (tm-30) outliers start: 22 outliers final: 14 residues processed: 87 average time/residue: 0.5400 time to fit residues: 49.3587 Evaluate side-chains 84 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 121 ASN 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 456 LEU Chi-restraints excluded: chain A residue 496 THR 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 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 32 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 45 optimal weight: 0.0570 chunk 58 optimal weight: 0.0000 chunk 29 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 0.5302 ------------------------------------------------------------------------------- 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 A 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.167266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.138393 restraints weight = 7014.190| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.80 r_work: 0.3518 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2368 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 : 0.452 5.083 9043 Z= 0.234 Chirality : 0.041 0.129 935 Planarity : 0.004 0.036 1172 Dihedral : 4.259 43.818 913 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.32 % Allowed : 12.75 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.29), residues: 784 helix: -0.35 (0.28), residues: 344 sheet: 1.57 (1.00), residues: 36 loop : -1.44 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 273 TYR 0.011 0.001 TYR A 385 PHE 0.011 0.001 PHE A 28 TRP 0.010 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 6641) covalent geometry : angle 0.44628 ( 9023) SS BOND : bond 0.00322 ( 7) SS BOND : angle 1.09958 ( 14) hydrogen bonds : bond 0.04750 ( 179) hydrogen bonds : angle 4.07857 ( 501) metal coordination : bond 0.00189 ( 2) link_BETA1-4 : bond 0.00277 ( 1) link_BETA1-4 : angle 1.20227 ( 3) link_NAG-ASN : bond 0.00113 ( 1) link_NAG-ASN : angle 2.98330 ( 3) *********************** 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 86 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.262 Fit side-chains REVERT: A 89 GLN cc_start: 0.5799 (mp10) cc_final: 0.5381 (mp10) REVERT: A 323 MET cc_start: 0.8345 (mmp) cc_final: 0.8003 (mmt) REVERT: A 383 MET cc_start: 0.8315 (mtp) cc_final: 0.8033 (mtm) REVERT: B 465 GLU cc_start: 0.7922 (tt0) cc_final: 0.7300 (tm-30) REVERT: B 513 LEU cc_start: 0.7861 (mt) cc_final: 0.7605 (mp) outliers start: 16 outliers final: 14 residues processed: 83 average time/residue: 0.5529 time to fit residues: 48.2951 Evaluate side-chains 83 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 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 B residue 362 VAL 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 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 58 optimal weight: 0.0470 chunk 68 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.5280 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.167264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.138398 restraints weight = 7014.648| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.80 r_work: 0.3515 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2416 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= 0.092 Angle : 0.451 4.868 9043 Z= 0.232 Chirality : 0.040 0.130 935 Planarity : 0.004 0.036 1172 Dihedral : 4.361 56.221 913 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.04 % Allowed : 12.90 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.29), residues: 784 helix: -0.13 (0.29), residues: 343 sheet: 1.50 (1.00), residues: 36 loop : -1.39 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 509 TYR 0.011 0.001 TYR A 385 PHE 0.011 0.001 PHE A 28 TRP 0.010 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 6641) covalent geometry : angle 0.44554 ( 9023) SS BOND : bond 0.00310 ( 7) SS BOND : angle 1.08465 ( 14) hydrogen bonds : bond 0.04667 ( 179) hydrogen bonds : angle 4.02559 ( 501) metal coordination : bond 0.00182 ( 2) link_BETA1-4 : bond 0.00326 ( 1) link_BETA1-4 : angle 1.18960 ( 3) link_NAG-ASN : bond 0.00093 ( 1) link_NAG-ASN : angle 2.91196 ( 3) *********************** 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 92 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.237 Fit side-chains REVERT: A 89 GLN cc_start: 0.5794 (mp10) cc_final: 0.5372 (mp10) REVERT: A 160 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: A 189 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7471 (tp30) REVERT: A 323 MET cc_start: 0.8335 (mmp) cc_final: 0.7974 (mmp) REVERT: A 383 MET cc_start: 0.8329 (mtp) cc_final: 0.8028 (mtm) REVERT: A 518 ARG cc_start: 0.8184 (tmm160) cc_final: 0.7870 (ttp-110) REVERT: B 465 GLU cc_start: 0.7912 (tt0) cc_final: 0.7282 (tm-30) REVERT: B 513 LEU cc_start: 0.7853 (mt) cc_final: 0.7612 (mp) outliers start: 21 outliers final: 14 residues processed: 89 average time/residue: 0.5832 time to fit residues: 54.3590 Evaluate side-chains 86 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 160 GLU 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 343 VAL Chi-restraints excluded: chain A residue 347 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 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 5 optimal weight: 0.4980 chunk 47 optimal weight: 0.0050 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 0.0060 overall best weight: 0.3010 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.169435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140689 restraints weight = 6983.468| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.80 r_work: 0.3545 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6652 Z= 0.079 Angle : 0.419 4.868 9043 Z= 0.214 Chirality : 0.040 0.133 935 Planarity : 0.004 0.035 1172 Dihedral : 4.081 53.029 912 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.29), residues: 784 helix: 0.06 (0.29), residues: 350 sheet: 1.48 (1.00), residues: 36 loop : -1.24 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 273 TYR 0.009 0.001 TYR B 351 PHE 0.008 0.001 PHE B 377 TRP 0.009 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00164 ( 6641) covalent geometry : angle 0.41452 ( 9023) SS BOND : bond 0.00211 ( 7) SS BOND : angle 0.85114 ( 14) hydrogen bonds : bond 0.03878 ( 179) hydrogen bonds : angle 3.93952 ( 501) metal coordination : bond 0.00116 ( 2) link_BETA1-4 : bond 0.00374 ( 1) link_BETA1-4 : angle 1.03156 ( 3) link_NAG-ASN : bond 0.00158 ( 1) link_NAG-ASN : angle 2.60010 ( 3) *********************** 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: 18 poor density : 72 time to evaluate : 0.226 Fit side-chains REVERT: A 89 GLN cc_start: 0.5736 (mp10) cc_final: 0.5316 (mp10) REVERT: A 189 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7483 (tp30) REVERT: A 383 MET cc_start: 0.8327 (mtp) cc_final: 0.8029 (mtm) REVERT: B 465 GLU cc_start: 0.7905 (tt0) cc_final: 0.7228 (tm-30) REVERT: B 513 LEU cc_start: 0.7849 (mt) cc_final: 0.7613 (mp) outliers start: 18 outliers final: 13 residues processed: 86 average time/residue: 0.5694 time to fit residues: 51.3727 Evaluate side-chains 80 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 190 MET Chi-restraints excluded: chain A residue 203 TRP 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 B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.166468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.137437 restraints weight = 7085.063| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.81 r_work: 0.3505 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2476 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= 0.104 Angle : 0.469 4.835 9043 Z= 0.242 Chirality : 0.041 0.130 935 Planarity : 0.004 0.036 1172 Dihedral : 4.156 44.561 912 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.75 % Allowed : 13.19 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.29), residues: 784 helix: 0.00 (0.29), residues: 350 sheet: 1.40 (1.00), residues: 36 loop : -1.31 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 509 TYR 0.013 0.001 TYR A 385 PHE 0.013 0.001 PHE A 28 TRP 0.010 0.001 TRP A 163 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 6641) covalent geometry : angle 0.46382 ( 9023) SS BOND : bond 0.00279 ( 7) SS BOND : angle 0.92261 ( 14) hydrogen bonds : bond 0.05003 ( 179) hydrogen bonds : angle 3.99654 ( 501) metal coordination : bond 0.00245 ( 2) link_BETA1-4 : bond 0.00301 ( 1) link_BETA1-4 : angle 1.25090 ( 3) link_NAG-ASN : bond 0.00025 ( 1) link_NAG-ASN : angle 3.09119 ( 3) *********************** 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 87 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.245 Fit side-chains REVERT: A 89 GLN cc_start: 0.5802 (mp10) cc_final: 0.5389 (mp10) REVERT: A 160 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: A 189 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7476 (tp30) REVERT: A 323 MET cc_start: 0.8335 (mmp) cc_final: 0.7975 (mmp) REVERT: A 383 MET cc_start: 0.8356 (mtp) cc_final: 0.8051 (mtm) REVERT: B 465 GLU cc_start: 0.7881 (tt0) cc_final: 0.7211 (tm-30) REVERT: B 513 LEU cc_start: 0.7861 (mt) cc_final: 0.7627 (mp) outliers start: 19 outliers final: 16 residues processed: 83 average time/residue: 0.5326 time to fit residues: 46.4564 Evaluate side-chains 85 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 229 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 552 GLN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 66 optimal weight: 0.0050 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.163302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.134097 restraints weight = 6956.395| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.79 r_work: 0.3421 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6652 Z= 0.150 Angle : 0.564 6.436 9043 Z= 0.294 Chirality : 0.044 0.131 935 Planarity : 0.004 0.037 1172 Dihedral : 4.516 37.380 912 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.19 % Allowed : 13.33 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.28), residues: 784 helix: -0.22 (0.28), residues: 336 sheet: 1.37 (0.98), residues: 36 loop : -1.47 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 518 TYR 0.019 0.002 TYR A 385 PHE 0.018 0.002 PHE A 28 TRP 0.009 0.001 TRP A 163 HIS 0.009 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6641) covalent geometry : angle 0.55714 ( 9023) SS BOND : bond 0.00431 ( 7) SS BOND : angle 1.31168 ( 14) hydrogen bonds : bond 0.06672 ( 179) hydrogen bonds : angle 4.23331 ( 501) metal coordination : bond 0.00399 ( 2) link_BETA1-4 : bond 0.00186 ( 1) link_BETA1-4 : angle 1.65878 ( 3) link_NAG-ASN : bond 0.00147 ( 1) link_NAG-ASN : angle 3.67259 ( 3) ********************** 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 90 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.252 Fit side-chains REVERT: A 89 GLN cc_start: 0.5967 (mp10) cc_final: 0.5757 (mp10) REVERT: A 160 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8344 (tt0) REVERT: A 189 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7584 (tp30) REVERT: A 323 MET cc_start: 0.8452 (mmp) cc_final: 0.8110 (mmt) REVERT: A 383 MET cc_start: 0.8468 (mtp) cc_final: 0.8211 (mtm) REVERT: B 465 GLU cc_start: 0.7944 (tt0) cc_final: 0.7374 (tm-30) outliers start: 22 outliers final: 14 residues processed: 85 average time/residue: 0.5712 time to fit residues: 50.9095 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 : 0.280 ------------------------------------------------------------------------------- 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 160 GLU Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 229 THR 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 B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.164990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.135899 restraints weight = 7043.488| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.81 r_work: 0.3495 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6652 Z= 0.115 Angle : 0.495 5.553 9043 Z= 0.258 Chirality : 0.042 0.127 935 Planarity : 0.004 0.037 1172 Dihedral : 4.322 30.768 912 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.90 % Allowed : 13.48 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.28), residues: 784 helix: -0.08 (0.29), residues: 336 sheet: 1.33 (0.96), residues: 36 loop : -1.41 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.015 0.001 TYR A 385 PHE 0.014 0.001 PHE A 28 TRP 0.009 0.001 TRP A 163 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 6641) covalent geometry : angle 0.48990 ( 9023) SS BOND : bond 0.00312 ( 7) SS BOND : angle 1.00115 ( 14) hydrogen bonds : bond 0.05618 ( 179) hydrogen bonds : angle 4.11562 ( 501) metal coordination : bond 0.00283 ( 2) link_BETA1-4 : bond 0.00268 ( 1) link_BETA1-4 : angle 1.46338 ( 3) link_NAG-ASN : bond 0.00018 ( 1) link_NAG-ASN : angle 3.27146 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2266.59 seconds wall clock time: 39 minutes 11.02 seconds (2351.02 seconds total)