Starting phenix.real_space_refine on Fri Jul 3 01:20:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zwk_74910/07_2026/9zwk_74910.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zwk_74910/07_2026/9zwk_74910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zwk_74910/07_2026/9zwk_74910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zwk_74910/07_2026/9zwk_74910.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zwk_74910/07_2026/9zwk_74910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zwk_74910/07_2026/9zwk_74910.map" } resolution = 2.34 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= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 2 5.49 5 S 61 5.16 5 C 7050 2.51 5 N 1825 2.21 5 O 2076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11017 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 5030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5030 Classifications: {'peptide': 678} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 651} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1417 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 13, 'TRANS': 174} Chain: "D" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 216 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Ad-hoc single atom residues: {' K': 2} Unusual residues: {'9Y0': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'9Y0': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 2.43, per 1000 atoms: 0.22 Number of scatterers: 11017 At special positions: 0 Unit cell: (133.92, 87.42, 130.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 61 16.00 P 2 15.00 O 2076 8.00 N 1825 7.00 C 7050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 191 " 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 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 437.5 milliseconds 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2642 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 9 sheets defined 64.9% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 Proline residue: A 22 - end of helix removed outlier: 3.569A pdb=" N LEU A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 51 removed outlier: 3.507A pdb=" N VAL A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.501A pdb=" N LEU A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 132 through 157 Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 177 through 193 Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.915A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 248 through 275 removed outlier: 3.525A pdb=" N PHE A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.125A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.993A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 4.213A pdb=" N VAL A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 355 through 368 removed outlier: 3.801A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 377 through 398 removed outlier: 3.557A pdb=" N TYR A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 422 Processing helix chain 'A' and resid 422 through 437 Processing helix chain 'A' and resid 438 through 444 removed outlier: 3.582A pdb=" N ALA A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 removed outlier: 3.978A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 509 removed outlier: 4.075A pdb=" N VAL A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) Proline residue: A 499 - end of helix removed outlier: 4.368A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 549 Proline residue: A 545 - end of helix removed outlier: 3.568A pdb=" N LEU A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'B' and resid 10 through 24 removed outlier: 3.731A pdb=" N VAL B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 16 " --> pdb=" O THR B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 33 through 56 removed outlier: 3.659A pdb=" N ILE B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 97 removed outlier: 3.989A pdb=" N GLN B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.664A pdb=" N GLN B 125 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 126 " --> pdb=" O ALA B 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 122 through 126' Processing helix chain 'B' and resid 200 through 206 removed outlier: 3.776A pdb=" N MET B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 238 Processing helix chain 'B' and resid 238 through 246 removed outlier: 3.867A pdb=" N TRP B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 264 through 284 removed outlier: 4.622A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.913A pdb=" N VAL B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 329 through 341 removed outlier: 4.031A pdb=" N ALA B 336 " --> pdb=" O THR B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 360 removed outlier: 3.571A pdb=" N VAL B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLN B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.513A pdb=" N LEU B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 409 removed outlier: 3.582A pdb=" N ARG B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 426 removed outlier: 4.341A pdb=" N GLN B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 463 removed outlier: 3.656A pdb=" N GLN B 459 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 460 " --> pdb=" O ARG B 456 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 461 " --> pdb=" O PHE B 457 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 485 removed outlier: 4.290A pdb=" N GLU B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 507 Processing helix chain 'B' and resid 522 through 527 Processing helix chain 'B' and resid 539 through 545 removed outlier: 3.641A pdb=" N ALA B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 582 Processing helix chain 'B' and resid 582 through 595 removed outlier: 3.564A pdb=" N LYS B 586 " --> pdb=" O ASN B 582 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 599 through 606 Processing helix chain 'B' and resid 612 through 631 removed outlier: 3.557A pdb=" N ALA B 620 " --> pdb=" O ALA B 616 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 645 through 657 Processing helix chain 'B' and resid 659 through 680 Proline residue: B 665 - end of helix Processing helix chain 'C' and resid 4 through 20 Processing helix chain 'C' and resid 21 through 34 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 78 through 82 removed outlier: 4.051A pdb=" N SER C 82 " --> pdb=" O PRO C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.783A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.647A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 149 Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 168 through 172 removed outlier: 3.665A pdb=" N ILE C 171 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY C 172 " --> pdb=" O LYS C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 168 through 172' Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'D' and resid 2 through 25 Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 121 removed outlier: 3.523A pdb=" N ASP B 119 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS B 108 " --> pdb=" O ASP B 119 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 106 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG B 107 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE B 131 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP B 130 " --> pdb=" O CYS B 191 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS B 191 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 187 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL B 188 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 164 through 168 Processing sheet with id=AA5, first strand: chain 'B' and resid 318 through 324 removed outlier: 3.605A pdb=" N SER B 320 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ALA B 444 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N PHE B 322 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL B 442 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU B 440 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 385 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 468 through 470 removed outlier: 5.682A pdb=" N MET B 469 " --> pdb=" O LEU B 491 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 514 through 517 removed outlier: 8.261A pdb=" N ASP B 550 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ALA B 534 " --> pdb=" O ASP B 550 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.607A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU C 45 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N VAL C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.579A pdb=" N ILE C 132 " --> pdb=" O VAL C 176 " (cutoff:3.500A) 653 hydrogen bonds defined for protein. 1884 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: 1.91 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2410 1.33 - 1.46: 2514 1.46 - 1.58: 6074 1.58 - 1.71: 4 1.71 - 1.84: 110 Bond restraints: 11112 Sorted by residual: bond pdb=" CG PRO B 11 " pdb=" CD PRO B 11 " ideal model delta sigma weight residual 1.503 1.540 -0.037 3.40e-02 8.65e+02 1.20e+00 bond pdb=" CG ARG B 475 " pdb=" CD ARG B 475 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" CB GLN B 211 " pdb=" CG GLN B 211 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.35e-01 bond pdb=" N GLY A 377 " pdb=" CA GLY A 377 " ideal model delta sigma weight residual 1.449 1.462 -0.013 1.45e-02 4.76e+03 7.80e-01 bond pdb=" CG GLN B 211 " pdb=" CD GLN B 211 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.51e-01 ... (remaining 11107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 14815 1.36 - 2.71: 206 2.71 - 4.07: 53 4.07 - 5.42: 21 5.42 - 6.78: 6 Bond angle restraints: 15101 Sorted by residual: angle pdb=" N VAL A 496 " pdb=" CA VAL A 496 " pdb=" C VAL A 496 " ideal model delta sigma weight residual 112.96 108.19 4.77 1.00e+00 1.00e+00 2.28e+01 angle pdb=" CG ARG B 475 " pdb=" CD ARG B 475 " pdb=" NE ARG B 475 " ideal model delta sigma weight residual 112.00 118.78 -6.78 2.20e+00 2.07e-01 9.49e+00 angle pdb=" CA ARG B 475 " pdb=" CB ARG B 475 " pdb=" CG ARG B 475 " ideal model delta sigma weight residual 114.10 120.16 -6.06 2.00e+00 2.50e-01 9.19e+00 angle pdb=" CA LYS B 308 " pdb=" CB LYS B 308 " pdb=" CG LYS B 308 " ideal model delta sigma weight residual 114.10 119.11 -5.01 2.00e+00 2.50e-01 6.27e+00 angle pdb=" CA CYS B 191 " pdb=" CB CYS B 191 " pdb=" SG CYS B 191 " ideal model delta sigma weight residual 114.40 120.01 -5.61 2.30e+00 1.89e-01 5.95e+00 ... (remaining 15096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.70: 6093 23.70 - 47.40: 436 47.40 - 71.10: 86 71.10 - 94.81: 18 94.81 - 118.51: 2 Dihedral angle restraints: 6635 sinusoidal: 2523 harmonic: 4112 Sorted by residual: dihedral pdb=" CA ILE B 189 " pdb=" C ILE B 189 " pdb=" N GLU B 190 " pdb=" CA GLU B 190 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C23 9Y0 A 602 " pdb=" C21 9Y0 A 602 " pdb=" C22 9Y0 A 602 " pdb=" O6 9Y0 A 602 " ideal model delta sinusoidal sigma weight residual 0.61 119.12 -118.51 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" CA LEU B 183 " pdb=" C LEU B 183 " pdb=" N SER B 184 " pdb=" CA SER B 184 " ideal model delta harmonic sigma weight residual 180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 6632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1211 0.028 - 0.056: 376 0.056 - 0.085: 131 0.085 - 0.113: 81 0.113 - 0.141: 13 Chirality restraints: 1812 Sorted by residual: chirality pdb=" CA PRO B 11 " pdb=" N PRO B 11 " pdb=" C PRO B 11 " pdb=" CB PRO B 11 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA VAL C 116 " pdb=" N VAL C 116 " pdb=" C VAL C 116 " pdb=" CB VAL C 116 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 1809 not shown) Planarity restraints: 1910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 10 " -0.037 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO B 11 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 11 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 11 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 215 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO B 216 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 216 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 216 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 143 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C ASP B 143 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP B 143 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY B 144 " 0.010 2.00e-02 2.50e+03 ... (remaining 1907 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.78: 2519 2.78 - 3.37: 12708 3.37 - 3.96: 22382 3.96 - 4.55: 31056 4.55 - 5.14: 44492 Nonbonded interactions: 113157 Sorted by model distance: nonbonded pdb=" OD1 ASN A 467 " pdb=" OG SER A 469 " model vdw 2.193 3.040 nonbonded pdb=" OG1 THR C 72 " pdb=" O MET C 75 " model vdw 2.304 3.040 nonbonded pdb=" O PRO C 35 " pdb=" ND2 ASN C 39 " model vdw 2.315 3.120 nonbonded pdb=" OG SER B 341 " pdb=" NZ LYS B 395 " model vdw 2.317 3.120 nonbonded pdb=" O LYS A 323 " pdb=" NH1 ARG C 68 " model vdw 2.317 3.120 ... (remaining 113152 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: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.300 Find NCS groups from input model: 0.050 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:7.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 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 : 0.002 0.039 11113 Z= 0.084 Angle : 0.468 6.776 15103 Z= 0.243 Chirality : 0.036 0.141 1812 Planarity : 0.004 0.055 1910 Dihedral : 17.083 118.507 3990 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.62 % Allowed : 19.89 % Favored : 79.49 % 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: 0.83 (0.22), residues: 1444 helix: 1.42 (0.18), residues: 836 sheet: -0.11 (0.72), residues: 64 loop : -0.69 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 55 TYR 0.012 0.001 TYR A 381 PHE 0.019 0.001 PHE B 360 TRP 0.007 0.001 TRP A 176 HIS 0.003 0.000 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00178 / 0.08 (11112) covalent geometry : angle 0.46586 / 0.24 (15101) SS BOND : bond 0.00230 / 0.12 ( 1) SS BOND : angle 3.43417 / 1.96 ( 2) hydrogen bonds : bond 0.23649 / 15.90 ( 653) hydrogen bonds : angle 6.81330 / 4.94 ( 1884) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.421 Fit side-chains REVERT: B 8 LEU cc_start: 0.7864 (mp) cc_final: 0.7652 (mp) outliers start: 7 outliers final: 7 residues processed: 131 average time/residue: 0.5968 time to fit residues: 84.4748 Evaluate side-chains 128 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 31 TRP Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 562 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0070 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 30.0000 chunk 55 optimal weight: 5.9990 overall best weight: 1.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN A 513 GLN B 30 GLN B 93 GLN ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS C 157 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.177537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.092150 restraints weight = 11133.524| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.66 r_work: 0.2934 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11113 Z= 0.226 Angle : 0.628 7.177 15103 Z= 0.331 Chirality : 0.046 0.162 1812 Planarity : 0.005 0.052 1910 Dihedral : 10.567 96.716 1617 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.38 % Allowed : 16.20 % Favored : 81.43 % 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: 0.93 (0.22), residues: 1444 helix: 1.50 (0.17), residues: 845 sheet: -0.08 (0.67), residues: 63 loop : -0.69 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 475 TYR 0.026 0.002 TYR A 381 PHE 0.020 0.002 PHE A 79 TRP 0.010 0.002 TRP C 139 HIS 0.006 0.001 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.23 (11112) covalent geometry : angle 0.62714 / 0.33 (15101) SS BOND : bond 0.00574 / 0.30 ( 1) SS BOND : angle 1.97594 / 1.12 ( 2) hydrogen bonds : bond 0.06351 / 4.32 ( 653) hydrogen bonds : angle 4.72744 / 3.45 ( 1884) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 357 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8391 (mp) REVERT: A 445 MET cc_start: 0.9207 (mtt) cc_final: 0.8880 (mtt) REVERT: B 279 MET cc_start: 0.7614 (mmp) cc_final: 0.7390 (mmm) REVERT: B 504 ARG cc_start: 0.6324 (mmt90) cc_final: 0.5593 (tpp-160) REVERT: B 515 MET cc_start: 0.2550 (ttt) cc_final: 0.2296 (tpt) REVERT: B 659 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8045 (tm) outliers start: 27 outliers final: 9 residues processed: 147 average time/residue: 0.5779 time to fit residues: 92.1645 Evaluate side-chains 130 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 113 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 75 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 26 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 133 optimal weight: 0.8980 chunk 88 optimal weight: 20.0000 chunk 20 optimal weight: 0.5980 chunk 67 optimal weight: 0.3980 chunk 95 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 154 GLN C 157 GLN C 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.180339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.096025 restraints weight = 11312.541| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.65 r_work: 0.2971 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11113 Z= 0.121 Angle : 0.505 5.979 15103 Z= 0.263 Chirality : 0.040 0.157 1812 Planarity : 0.004 0.045 1910 Dihedral : 9.979 131.191 1607 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.46 % Allowed : 16.46 % Favored : 81.07 % 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: 1.14 (0.22), residues: 1444 helix: 1.74 (0.18), residues: 851 sheet: -0.15 (0.65), residues: 63 loop : -0.74 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 55 TYR 0.020 0.001 TYR A 381 PHE 0.013 0.001 PHE B 360 TRP 0.010 0.001 TRP B 71 HIS 0.006 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (11112) covalent geometry : angle 0.50448 / 0.26 (15101) SS BOND : bond 0.00414 / 0.22 ( 1) SS BOND : angle 1.30431 / 0.74 ( 2) hydrogen bonds : bond 0.04858 / 3.33 ( 653) hydrogen bonds : angle 4.27293 / 3.11 ( 1884) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 357 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8399 (mp) REVERT: A 445 MET cc_start: 0.9116 (mtt) cc_final: 0.8806 (mtt) REVERT: B 20 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7521 (tp30) REVERT: B 504 ARG cc_start: 0.6346 (mmt90) cc_final: 0.5597 (tpp-160) REVERT: B 515 MET cc_start: 0.2627 (OUTLIER) cc_final: 0.2377 (tpt) REVERT: B 659 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7831 (tm) REVERT: C 50 ARG cc_start: 0.8853 (mmm160) cc_final: 0.8623 (mmm160) outliers start: 28 outliers final: 15 residues processed: 138 average time/residue: 0.5374 time to fit residues: 80.3535 Evaluate side-chains 135 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 31 TRP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 528 GLN Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 113 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 81 optimal weight: 1.9990 chunk 103 optimal weight: 0.0470 chunk 124 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 chunk 83 optimal weight: 20.0000 chunk 113 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 154 GLN C 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.180630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.096769 restraints weight = 11372.881| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.65 r_work: 0.2976 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11113 Z= 0.115 Angle : 0.497 6.525 15103 Z= 0.257 Chirality : 0.039 0.132 1812 Planarity : 0.004 0.046 1910 Dihedral : 9.632 133.952 1607 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.73 % Allowed : 16.55 % Favored : 80.72 % 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: 1.27 (0.22), residues: 1444 helix: 1.84 (0.18), residues: 853 sheet: 0.05 (0.66), residues: 63 loop : -0.71 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 55 TYR 0.020 0.001 TYR A 381 PHE 0.011 0.001 PHE A 494 TRP 0.010 0.001 TRP B 71 HIS 0.005 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (11112) covalent geometry : angle 0.49690 / 0.26 (15101) SS BOND : bond 0.00418 / 0.22 ( 1) SS BOND : angle 0.99411 / 0.56 ( 2) hydrogen bonds : bond 0.04553 / 3.13 ( 653) hydrogen bonds : angle 4.14331 / 3.02 ( 1884) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 357 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8373 (mp) REVERT: A 445 MET cc_start: 0.9129 (mtt) cc_final: 0.8835 (mtt) REVERT: B 20 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7522 (tp30) REVERT: B 206 MET cc_start: 0.5787 (ptp) cc_final: 0.4360 (pp-130) REVERT: B 279 MET cc_start: 0.7506 (mmp) cc_final: 0.7236 (mmm) REVERT: B 504 ARG cc_start: 0.6238 (mmt90) cc_final: 0.5591 (tpp-160) REVERT: B 515 MET cc_start: 0.2663 (OUTLIER) cc_final: 0.2456 (tpt) REVERT: B 659 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7886 (tm) REVERT: C 50 ARG cc_start: 0.8853 (mmm160) cc_final: 0.8624 (mmm160) REVERT: C 75 MET cc_start: 0.7963 (ptm) cc_final: 0.7759 (ptt) outliers start: 31 outliers final: 16 residues processed: 144 average time/residue: 0.5528 time to fit residues: 86.2782 Evaluate side-chains 139 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 31 TRP Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 528 GLN Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 113 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 121 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 119 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 154 GLN C 157 GLN C 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.179561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.095721 restraints weight = 11265.666| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.64 r_work: 0.2964 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11113 Z= 0.125 Angle : 0.505 6.018 15103 Z= 0.263 Chirality : 0.040 0.266 1812 Planarity : 0.004 0.047 1910 Dihedral : 9.625 142.160 1607 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.73 % Allowed : 16.99 % Favored : 80.28 % 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: 1.27 (0.22), residues: 1444 helix: 1.79 (0.17), residues: 861 sheet: 0.37 (0.64), residues: 62 loop : -0.71 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 55 TYR 0.022 0.001 TYR A 381 PHE 0.013 0.001 PHE A 494 TRP 0.010 0.001 TRP B 71 HIS 0.005 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (11112) covalent geometry : angle 0.50455 / 0.26 (15101) SS BOND : bond 0.00414 / 0.22 ( 1) SS BOND : angle 0.83015 / 0.47 ( 2) hydrogen bonds : bond 0.04708 / 3.24 ( 653) hydrogen bonds : angle 4.12361 / 3.01 ( 1884) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 48 ARG cc_start: 0.7855 (ttp80) cc_final: 0.7630 (mtp180) REVERT: A 357 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8389 (mp) REVERT: B 206 MET cc_start: 0.5633 (ptp) cc_final: 0.4291 (pp-130) REVERT: B 279 MET cc_start: 0.7547 (mmp) cc_final: 0.7303 (mmm) REVERT: B 504 ARG cc_start: 0.6233 (mmt90) cc_final: 0.5575 (tpp-160) REVERT: B 659 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7923 (tm) REVERT: C 75 MET cc_start: 0.7995 (ptm) cc_final: 0.7787 (ptt) outliers start: 31 outliers final: 20 residues processed: 142 average time/residue: 0.5703 time to fit residues: 88.0647 Evaluate side-chains 141 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 31 TRP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 528 GLN Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 133 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 5 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 108 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 154 GLN C 157 GLN C 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.177963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.092262 restraints weight = 11198.995| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.68 r_work: 0.2939 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11113 Z= 0.155 Angle : 0.534 6.340 15103 Z= 0.278 Chirality : 0.042 0.184 1812 Planarity : 0.004 0.048 1910 Dihedral : 9.664 142.084 1607 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.55 % Allowed : 17.52 % Favored : 79.93 % 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: 1.19 (0.22), residues: 1444 helix: 1.73 (0.17), residues: 852 sheet: 0.30 (0.66), residues: 56 loop : -0.69 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 55 TYR 0.024 0.002 TYR A 381 PHE 0.016 0.001 PHE A 494 TRP 0.010 0.001 TRP B 71 HIS 0.006 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (11112) covalent geometry : angle 0.53381 / 0.28 (15101) SS BOND : bond 0.00451 / 0.24 ( 1) SS BOND : angle 0.69249 / 0.39 ( 2) hydrogen bonds : bond 0.05183 / 3.56 ( 653) hydrogen bonds : angle 4.20724 / 3.07 ( 1884) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7810 (mtp180) REVERT: A 357 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8369 (mp) REVERT: B 155 GLU cc_start: -0.1262 (OUTLIER) cc_final: -0.1782 (tp30) REVERT: B 206 MET cc_start: 0.5403 (ptp) cc_final: 0.4163 (pp-130) REVERT: B 279 MET cc_start: 0.7711 (mmp) cc_final: 0.7472 (mmm) REVERT: B 504 ARG cc_start: 0.6155 (mmt90) cc_final: 0.5515 (tpp-160) REVERT: B 659 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8074 (tm) outliers start: 29 outliers final: 19 residues processed: 139 average time/residue: 0.5696 time to fit residues: 86.1955 Evaluate side-chains 135 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 31 TRP Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 528 GLN Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 133 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 55 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 129 optimal weight: 0.3980 chunk 139 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 49 optimal weight: 0.0170 chunk 29 optimal weight: 1.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.179842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.093775 restraints weight = 11186.367| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.72 r_work: 0.2973 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11113 Z= 0.115 Angle : 0.498 10.294 15103 Z= 0.257 Chirality : 0.040 0.142 1812 Planarity : 0.004 0.048 1910 Dihedral : 9.320 145.350 1607 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.55 % Allowed : 17.52 % Favored : 79.93 % 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: 1.32 (0.22), residues: 1444 helix: 1.86 (0.17), residues: 852 sheet: 0.38 (0.67), residues: 56 loop : -0.67 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 55 TYR 0.020 0.001 TYR A 381 PHE 0.011 0.001 PHE A 494 TRP 0.010 0.001 TRP B 71 HIS 0.006 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (11112) covalent geometry : angle 0.49765 / 0.26 (15101) SS BOND : bond 0.00373 / 0.20 ( 1) SS BOND : angle 0.63249 / 0.35 ( 2) hydrogen bonds : bond 0.04434 / 3.06 ( 653) hydrogen bonds : angle 4.05130 / 2.95 ( 1884) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7967 (ttm170) cc_final: 0.7587 (ttp-110) REVERT: A 48 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7706 (mtp180) REVERT: A 155 PHE cc_start: 0.8741 (m-80) cc_final: 0.8522 (m-80) REVERT: A 357 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8393 (mp) REVERT: B 155 GLU cc_start: -0.1311 (OUTLIER) cc_final: -0.1817 (tp30) REVERT: B 206 MET cc_start: 0.5423 (ptp) cc_final: 0.4114 (pp-130) REVERT: B 279 MET cc_start: 0.7688 (mmp) cc_final: 0.7453 (mmm) REVERT: B 504 ARG cc_start: 0.6144 (mmt90) cc_final: 0.5530 (tpp-160) REVERT: B 659 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8075 (tm) outliers start: 29 outliers final: 20 residues processed: 140 average time/residue: 0.6151 time to fit residues: 93.2336 Evaluate side-chains 139 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 31 TRP Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 528 GLN Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 113 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 91 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 chunk 125 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 60 optimal weight: 0.2980 chunk 72 optimal weight: 9.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 157 GLN C 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.180582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.094736 restraints weight = 11175.568| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.73 r_work: 0.2990 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11113 Z= 0.108 Angle : 0.487 9.762 15103 Z= 0.251 Chirality : 0.039 0.135 1812 Planarity : 0.004 0.048 1910 Dihedral : 9.018 142.551 1607 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.11 % Allowed : 17.96 % Favored : 79.93 % 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: 1.51 (0.22), residues: 1444 helix: 2.03 (0.17), residues: 848 sheet: 0.36 (0.67), residues: 56 loop : -0.59 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 55 TYR 0.020 0.001 TYR A 381 PHE 0.010 0.001 PHE A 494 TRP 0.010 0.001 TRP B 71 HIS 0.007 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (11112) covalent geometry : angle 0.48739 / 0.25 (15101) SS BOND : bond 0.00361 / 0.19 ( 1) SS BOND : angle 0.56817 / 0.32 ( 2) hydrogen bonds : bond 0.04259 / 2.94 ( 653) hydrogen bonds : angle 3.98467 / 2.90 ( 1884) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7969 (ttm170) cc_final: 0.7600 (ttp-110) REVERT: A 48 ARG cc_start: 0.7904 (ttp80) cc_final: 0.7679 (mtp180) REVERT: A 357 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8414 (mp) REVERT: A 414 MET cc_start: 0.8620 (mmp) cc_final: 0.8345 (mmp) REVERT: A 511 LYS cc_start: 0.8707 (ttpp) cc_final: 0.8408 (tttp) REVERT: B 155 GLU cc_start: -0.1181 (OUTLIER) cc_final: -0.1703 (tp30) REVERT: B 206 MET cc_start: 0.5434 (ptp) cc_final: 0.4156 (pp-130) REVERT: B 504 ARG cc_start: 0.6166 (mmt90) cc_final: 0.5512 (tpp-160) REVERT: B 515 MET cc_start: 0.3829 (mmm) cc_final: 0.3581 (mmm) REVERT: B 659 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8078 (tm) REVERT: C 156 THR cc_start: 0.8568 (m) cc_final: 0.8298 (p) outliers start: 24 outliers final: 15 residues processed: 137 average time/residue: 0.5803 time to fit residues: 86.1484 Evaluate side-chains 136 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 31 TRP Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 113 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 21 optimal weight: 0.4980 chunk 113 optimal weight: 0.7980 chunk 136 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.178977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.092536 restraints weight = 11029.309| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.73 r_work: 0.2953 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11113 Z= 0.136 Angle : 0.518 9.480 15103 Z= 0.267 Chirality : 0.040 0.138 1812 Planarity : 0.004 0.048 1910 Dihedral : 9.092 139.262 1607 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.20 % Allowed : 17.87 % Favored : 79.93 % 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: 1.39 (0.22), residues: 1444 helix: 1.90 (0.17), residues: 846 sheet: 0.37 (0.67), residues: 56 loop : -0.57 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 55 TYR 0.024 0.002 TYR A 381 PHE 0.013 0.001 PHE A 494 TRP 0.010 0.001 TRP B 71 HIS 0.008 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (11112) covalent geometry : angle 0.51842 / 0.27 (15101) SS BOND : bond 0.00398 / 0.21 ( 1) SS BOND : angle 0.56382 / 0.31 ( 2) hydrogen bonds : bond 0.04818 / 3.32 ( 653) hydrogen bonds : angle 4.08080 / 2.97 ( 1884) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7990 (ttm170) cc_final: 0.7614 (ttp-110) REVERT: A 48 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7735 (mtp180) REVERT: A 357 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8375 (mp) REVERT: B 155 GLU cc_start: -0.1306 (OUTLIER) cc_final: -0.1798 (tp30) REVERT: B 206 MET cc_start: 0.5414 (ptp) cc_final: 0.4160 (pp-130) REVERT: B 279 MET cc_start: 0.7704 (mmp) cc_final: 0.7493 (mmm) REVERT: B 456 ARG cc_start: 0.3771 (OUTLIER) cc_final: 0.3507 (mmm160) REVERT: B 469 MET cc_start: 0.4685 (ttp) cc_final: 0.4395 (tmm) REVERT: B 504 ARG cc_start: 0.6225 (mmt90) cc_final: 0.5545 (tpp-160) REVERT: B 659 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8108 (tm) REVERT: C 187 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6941 (mppt) outliers start: 25 outliers final: 16 residues processed: 138 average time/residue: 0.6143 time to fit residues: 91.7733 Evaluate side-chains 134 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 31 TRP Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 456 ARG Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 187 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 105 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 114 optimal weight: 0.0370 chunk 66 optimal weight: 10.0000 chunk 116 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 358 GLN C 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.180070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.094171 restraints weight = 11185.210| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.67 r_work: 0.2979 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11113 Z= 0.115 Angle : 0.512 10.426 15103 Z= 0.261 Chirality : 0.039 0.138 1812 Planarity : 0.004 0.048 1910 Dihedral : 8.978 139.449 1607 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.94 % Allowed : 18.49 % Favored : 79.58 % 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: 1.46 (0.22), residues: 1444 helix: 1.95 (0.17), residues: 846 sheet: 0.48 (0.67), residues: 56 loop : -0.55 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 55 TYR 0.020 0.001 TYR A 381 PHE 0.011 0.001 PHE A 494 TRP 0.010 0.001 TRP B 71 HIS 0.008 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (11112) covalent geometry : angle 0.51185 / 0.26 (15101) SS BOND : bond 0.00262 / 0.14 ( 1) SS BOND : angle 0.50258 / 0.28 ( 2) hydrogen bonds : bond 0.04408 / 3.04 ( 653) hydrogen bonds : angle 3.99919 / 2.92 ( 1884) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7590 (ttp-110) REVERT: A 48 ARG cc_start: 0.7927 (ttp80) cc_final: 0.7700 (mtp180) REVERT: A 357 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8389 (mp) REVERT: A 511 LYS cc_start: 0.8722 (ttpp) cc_final: 0.8413 (tttp) REVERT: B 155 GLU cc_start: -0.1225 (OUTLIER) cc_final: -0.1722 (tp30) REVERT: B 206 MET cc_start: 0.5384 (ptp) cc_final: 0.4134 (pp-130) REVERT: B 456 ARG cc_start: 0.3745 (OUTLIER) cc_final: 0.3481 (mmm160) REVERT: B 469 MET cc_start: 0.4521 (ttp) cc_final: 0.4311 (tmm) REVERT: B 504 ARG cc_start: 0.6172 (mmt90) cc_final: 0.5476 (tpp-160) REVERT: B 659 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8107 (tm) REVERT: C 187 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6923 (mppt) outliers start: 22 outliers final: 16 residues processed: 134 average time/residue: 0.6089 time to fit residues: 88.3393 Evaluate side-chains 137 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 31 TRP Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 456 ARG Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 187 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 70 optimal weight: 4.9990 chunk 68 optimal weight: 0.0030 chunk 53 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 51 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 358 GLN C 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.178578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.092725 restraints weight = 11146.808| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.70 r_work: 0.2949 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11113 Z= 0.141 Angle : 0.529 8.652 15103 Z= 0.272 Chirality : 0.041 0.140 1812 Planarity : 0.004 0.048 1910 Dihedral : 9.057 135.107 1607 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.11 % Allowed : 18.13 % Favored : 79.75 % 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: 1.40 (0.22), residues: 1444 helix: 1.89 (0.17), residues: 846 sheet: 0.56 (0.68), residues: 56 loop : -0.56 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 55 TYR 0.023 0.002 TYR A 381 PHE 0.014 0.001 PHE A 494 TRP 0.010 0.001 TRP B 71 HIS 0.009 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (11112) covalent geometry : angle 0.52900 / 0.27 (15101) SS BOND : bond 0.00287 / 0.15 ( 1) SS BOND : angle 0.45052 / 0.24 ( 2) hydrogen bonds : bond 0.04871 / 3.35 ( 653) hydrogen bonds : angle 4.07925 / 2.98 ( 1884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5991.87 seconds wall clock time: 102 minutes 26.94 seconds (6146.94 seconds total)