Starting phenix.real_space_refine on Wed Jun 3 19:43:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rm9_54052/06_2026/9rm9_54052.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rm9_54052/06_2026/9rm9_54052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rm9_54052/06_2026/9rm9_54052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rm9_54052/06_2026/9rm9_54052.map" model { file = "/net/cci-nas-00/data/ceres_data/9rm9_54052/06_2026/9rm9_54052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rm9_54052/06_2026/9rm9_54052.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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 Ca 5 9.91 5 Mn 1 7.51 5 S 51 5.16 5 C 5057 2.51 5 N 1416 2.21 5 O 1619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8149 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4304 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 27, 'TRANS': 538} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3573 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 434} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" 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: "G" 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {' CA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 2, ' MN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 2.10, per 1000 atoms: 0.26 Number of scatterers: 8149 At special positions: 0 Unit cell: (69.8448, 155.654, 124.723, 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) Mn 1 24.99 Ca 5 19.99 S 51 16.00 O 1619 8.00 N 1416 7.00 C 5057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 57 " distance=2.03 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 107 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 490 " distance=2.03 Simple disulfide: pdb=" SG CYS A 623 " - pdb=" SG CYS A 706 " distance=2.03 Simple disulfide: pdb=" SG CYS A 639 " - pdb=" SG CYS A 696 " distance=2.02 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 21 " distance=2.05 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 425 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 51 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.04 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 378 " distance=2.04 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 427 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 448 " distance=2.03 Simple disulfide: pdb=" SG CYS B 450 " - pdb=" SG CYS B 459 " 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 ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA E 3 " - " MAN E 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA E 3 " - " MAN E 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1204 " - " ASN A 677 " " NAG A1205 " - " ASN A 681 " " NAG B2004 " - " ASN B 232 " " NAG C 1 " - " ASN A 719 " " NAG D 1 " - " ASN A 70 " " NAG E 1 " - " ASN A 375 " " NAG F 1 " - " ASN B 190 " " NAG G 1 " - " ASN B 94 " Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 358.0 milliseconds 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1868 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 14 sheets defined 15.5% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 558 through 562 Processing helix chain 'B' and resid 10 through 18 removed outlier: 3.937A pdb=" N GLY B 18 " --> pdb=" O CYS B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.665A pdb=" N CYS B 40 " --> pdb=" O SER B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 removed outlier: 4.187A pdb=" N MET B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 120 through 139 removed outlier: 3.580A pdb=" N GLY B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 201 Processing helix chain 'B' and resid 213 through 224 removed outlier: 3.559A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.534A pdb=" N SER B 274 " --> pdb=" O TYR B 271 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN B 275 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE B 277 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 304 through 315 removed outlier: 3.710A pdb=" N GLU B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B 314 " --> pdb=" O LYS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.541A pdb=" N GLY B 439 " --> pdb=" O LEU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 447 removed outlier: 3.619A pdb=" N ILE B 447 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 11 removed outlier: 3.743A pdb=" N MET A 9 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP A 585 " --> pdb=" O GLY A 575 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY A 575 " --> pdb=" O ASP A 585 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 24 Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 80 removed outlier: 4.103A pdb=" N THR A 92 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS A 104 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N HIS A 94 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N TYR A 102 " --> pdb=" O HIS A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 342 through 343 Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 397 removed outlier: 3.735A pdb=" N ALA A 391 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLN A 401 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLN A 421 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA A 430 " --> pdb=" O MET A 418 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG A 420 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N SER A 428 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN A 422 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.511A pdb=" N HIS A 465 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N GLY A 472 " --> pdb=" O HIS A 465 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 492 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 509 through 513 removed outlier: 6.143A pdb=" N ASP A 522 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 554 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 542 through 543 removed outlier: 3.725A pdb=" N GLY A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 675 through 676 removed outlier: 3.996A pdb=" N GLY A 634 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A 703 " --> pdb=" O GLU A 632 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLU A 632 " --> pdb=" O LEU A 703 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 686 through 690 Processing sheet with id=AB2, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AB3, first strand: chain 'B' and resid 62 through 66 removed outlier: 6.631A pdb=" N VAL B 81 " --> pdb=" O GLN B 418 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU B 420 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU B 83 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AB5, first strand: chain 'B' and resid 183 through 189 removed outlier: 5.089A pdb=" N HIS B 184 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER B 148 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU B 188 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE B 144 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE B 105 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N GLY B 145 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU B 107 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N GLY B 147 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR B 109 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE B 149 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N MET B 111 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASP B 106 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL B 238 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TYR B 108 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ALA B 240 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 110 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ARG B 235 " --> pdb=" O GLN B 295 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE B 297 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 237 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA B 299 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE B 239 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N GLY B 321 " --> pdb=" O PRO B 296 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N PHE B 298 " --> pdb=" O GLY B 321 " (cutoff:3.500A) 242 hydrogen bonds defined for protein. 621 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: 1.37 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2699 1.34 - 1.47: 1942 1.47 - 1.59: 3578 1.59 - 1.72: 0 1.72 - 1.85: 67 Bond restraints: 8286 Sorted by residual: bond pdb=" C PRO A 83 " pdb=" N PRO A 84 " ideal model delta sigma weight residual 1.330 1.393 -0.063 1.19e-02 7.06e+03 2.80e+01 bond pdb=" C ASP A 449 " pdb=" N VAL A 450 " ideal model delta sigma weight residual 1.334 1.371 -0.037 1.26e-02 6.30e+03 8.43e+00 bond pdb=" C ASN A 453 " pdb=" N GLY A 454 " ideal model delta sigma weight residual 1.331 1.304 0.027 1.46e-02 4.69e+03 3.40e+00 bond pdb=" N GLN B 1 " pdb=" CA GLN B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" CB LYS B 357 " pdb=" CG LYS B 357 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.78e+00 ... (remaining 8281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 10739 1.97 - 3.94: 376 3.94 - 5.92: 95 5.92 - 7.89: 12 7.89 - 9.86: 3 Bond angle restraints: 11225 Sorted by residual: angle pdb=" N SER B 37 " pdb=" CA SER B 37 " pdb=" C SER B 37 " ideal model delta sigma weight residual 111.07 115.65 -4.58 1.07e+00 8.73e-01 1.83e+01 angle pdb=" CA GLN B 422 " pdb=" CB GLN B 422 " pdb=" CG GLN B 422 " ideal model delta sigma weight residual 114.10 122.11 -8.01 2.00e+00 2.50e-01 1.61e+01 angle pdb=" CA GLN B 400 " pdb=" CB GLN B 400 " pdb=" CG GLN B 400 " ideal model delta sigma weight residual 114.10 121.64 -7.54 2.00e+00 2.50e-01 1.42e+01 angle pdb=" CB LYS B 357 " pdb=" CG LYS B 357 " pdb=" CD LYS B 357 " ideal model delta sigma weight residual 111.30 118.93 -7.63 2.30e+00 1.89e-01 1.10e+01 angle pdb=" N PRO A 84 " pdb=" CA PRO A 84 " pdb=" C PRO A 84 " ideal model delta sigma weight residual 111.26 116.62 -5.36 1.63e+00 3.76e-01 1.08e+01 ... (remaining 11220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.03: 4873 25.03 - 50.07: 339 50.07 - 75.10: 50 75.10 - 100.13: 23 100.13 - 125.16: 18 Dihedral angle restraints: 5303 sinusoidal: 2387 harmonic: 2916 Sorted by residual: dihedral pdb=" CA SER A 82 " pdb=" C SER A 82 " pdb=" N PRO A 83 " pdb=" CA PRO A 83 " ideal model delta harmonic sigma weight residual -180.00 -122.83 -57.17 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CB CYS B 169 " pdb=" SG CYS B 169 " pdb=" SG CYS B 176 " pdb=" CB CYS B 176 " ideal model delta sinusoidal sigma weight residual 93.00 157.76 -64.76 1 1.00e+01 1.00e-02 5.51e+01 dihedral pdb=" CB CYS B 24 " pdb=" SG CYS B 24 " pdb=" SG CYS B 51 " pdb=" CB CYS B 51 " ideal model delta sinusoidal sigma weight residual 93.00 145.29 -52.29 1 1.00e+01 1.00e-02 3.73e+01 ... (remaining 5300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1171 0.087 - 0.173: 135 0.173 - 0.260: 1 0.260 - 0.346: 1 0.346 - 0.433: 1 Chirality restraints: 1309 Sorted by residual: chirality pdb=" C1 NAG A1204 " pdb=" ND2 ASN A 677 " pdb=" C2 NAG A1204 " pdb=" O5 NAG A1204 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" C1 MAN E 4 " pdb=" O3 BMA E 3 " pdb=" C2 MAN E 4 " pdb=" O5 MAN E 4 " both_signs ideal model delta sigma weight residual False 2.40 2.44 -0.04 2.00e-02 2.50e+03 3.40e+00 chirality pdb=" C1 NAG B2004 " pdb=" ND2 ASN B 232 " pdb=" C2 NAG B2004 " pdb=" O5 NAG B2004 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 1306 not shown) Planarity restraints: 1470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 86 " -0.482 9.50e-02 1.11e+02 2.16e-01 2.94e+01 pdb=" NE ARG B 86 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG B 86 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 86 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 86 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 82 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.38e+00 pdb=" C SER A 82 " 0.053 2.00e-02 2.50e+03 pdb=" O SER A 82 " -0.020 2.00e-02 2.50e+03 pdb=" N PRO A 83 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 82 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO A 83 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " -0.030 5.00e-02 4.00e+02 ... (remaining 1467 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 45 2.56 - 3.15: 6518 3.15 - 3.73: 12325 3.73 - 4.32: 17464 4.32 - 4.90: 29418 Nonbonded interactions: 65770 Sorted by model distance: nonbonded pdb="MN MN B2001 " pdb=" O HOH B2102 " model vdw 1.979 2.320 nonbonded pdb="MN MN B2001 " pdb=" O HOH B2101 " model vdw 2.008 2.320 nonbonded pdb=" OG SER B 114 " pdb="MN MN B2001 " model vdw 2.018 2.320 nonbonded pdb=" OD1 ASP A 451 " pdb="CA CA A1203 " model vdw 2.029 2.510 nonbonded pdb=" OE1 GLU A 320 " pdb="MN MN B2001 " model vdw 2.048 2.320 ... (remaining 65765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.980 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:9.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 : 0.006 0.063 8323 Z= 0.244 Angle : 0.972 13.336 11319 Z= 0.483 Chirality : 0.054 0.433 1309 Planarity : 0.008 0.216 1462 Dihedral : 19.213 125.164 3384 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.59 % Favored : 94.01 % Rotamer: Outliers : 1.04 % Allowed : 19.47 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -2.01 (0.25), residues: 1019 helix: -0.65 (0.46), residues: 100 sheet: -0.89 (0.28), residues: 313 loop : -1.74 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 86 TYR 0.011 0.002 TYR A 390 PHE 0.031 0.002 PHE B 146 TRP 0.008 0.002 TRP A 358 HIS 0.005 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.24 ( 8286) covalent geometry : angle 0.93329 / 0.47 (11225) SS BOND : bond 0.00595 / 0.30 ( 17) SS BOND : angle 1.59524 / 0.96 ( 34) hydrogen bonds : bond 0.14705 / 9.79 ( 242) hydrogen bonds : angle 7.84337 / 5.46 ( 621) link_ALPHA1-3 : bond 0.01170 / 0.57 ( 2) link_ALPHA1-3 : angle 3.03246 / 2.08 ( 6) link_ALPHA1-6 : bond 0.00882 / 0.42 ( 2) link_ALPHA1-6 : angle 1.11326 / 0.84 ( 6) link_BETA1-4 : bond 0.00344 / 0.17 ( 8) link_BETA1-4 : angle 3.23401 / 2.54 ( 24) link_NAG-ASN : bond 0.00828 / 0.42 ( 8) link_NAG-ASN : angle 4.67582 / 3.48 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.317 Fit side-chains REVERT: A 9 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8641 (ttm) REVERT: A 323 GLN cc_start: 0.7508 (pp30) cc_final: 0.7192 (pm20) REVERT: A 332 HIS cc_start: 0.8318 (OUTLIER) cc_final: 0.7812 (t70) REVERT: A 580 MET cc_start: 0.9056 (mtm) cc_final: 0.8785 (mtm) REVERT: A 608 ILE cc_start: 0.8443 (mt) cc_final: 0.8185 (mp) REVERT: A 609 MET cc_start: 0.8299 (tpp) cc_final: 0.7973 (tpp) REVERT: A 610 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7065 (mt-10) REVERT: B 73 GLN cc_start: 0.5802 (OUTLIER) cc_final: 0.5278 (tm-30) REVERT: B 106 ASP cc_start: 0.8601 (p0) cc_final: 0.8338 (p0) REVERT: B 172 LYS cc_start: 0.8678 (mppt) cc_final: 0.8146 (tmtt) REVERT: B 270 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8975 (mt) outliers start: 9 outliers final: 1 residues processed: 56 average time/residue: 0.6831 time to fit residues: 40.6319 Evaluate side-chains 45 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 270 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 20 GLN ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 400 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.112565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.072926 restraints weight = 15025.139| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.08 r_work: 0.3000 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8323 Z= 0.164 Angle : 0.707 15.638 11319 Z= 0.331 Chirality : 0.048 0.346 1309 Planarity : 0.004 0.053 1462 Dihedral : 11.605 100.165 1525 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.73 % Favored : 95.98 % Rotamer: Outliers : 3.00 % Allowed : 17.86 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -1.58 (0.26), residues: 1019 helix: 0.03 (0.49), residues: 107 sheet: -0.59 (0.28), residues: 325 loop : -1.55 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 399 TYR 0.018 0.001 TYR B 308 PHE 0.023 0.002 PHE A 121 TRP 0.028 0.002 TRP B 23 HIS 0.003 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 8286) covalent geometry : angle 0.65295 / 0.32 (11225) SS BOND : bond 0.00258 / 0.11 ( 17) SS BOND : angle 0.99974 / 0.65 ( 34) hydrogen bonds : bond 0.03564 / 2.27 ( 242) hydrogen bonds : angle 6.28764 / 4.33 ( 621) link_ALPHA1-3 : bond 0.00956 / 0.47 ( 2) link_ALPHA1-3 : angle 3.01118 / 2.07 ( 6) link_ALPHA1-6 : bond 0.00572 / 0.27 ( 2) link_ALPHA1-6 : angle 2.56602 / 1.70 ( 6) link_BETA1-4 : bond 0.00430 / 0.21 ( 8) link_BETA1-4 : angle 2.89051 / 2.10 ( 24) link_NAG-ASN : bond 0.00920 / 0.46 ( 8) link_NAG-ASN : angle 4.77453 / 4.06 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 43 time to evaluate : 0.339 Fit side-chains REVERT: A 9 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8730 (ttm) REVERT: A 323 GLN cc_start: 0.7402 (pp30) cc_final: 0.7084 (pm20) REVERT: A 608 ILE cc_start: 0.8163 (mt) cc_final: 0.7839 (mp) REVERT: A 609 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7761 (tpp) REVERT: A 610 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6873 (mt-10) REVERT: B 9 SER cc_start: 0.4647 (OUTLIER) cc_final: 0.4359 (m) REVERT: B 73 GLN cc_start: 0.5823 (OUTLIER) cc_final: 0.5341 (tm-30) REVERT: B 172 LYS cc_start: 0.8762 (mppt) cc_final: 0.8181 (ttpt) REVERT: B 270 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8781 (mt) outliers start: 26 outliers final: 8 residues processed: 65 average time/residue: 0.6099 time to fit residues: 42.2500 Evaluate side-chains 50 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 270 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.111445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.071623 restraints weight = 15002.710| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.08 r_work: 0.2972 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8323 Z= 0.171 Angle : 0.672 13.087 11319 Z= 0.318 Chirality : 0.048 0.335 1309 Planarity : 0.004 0.053 1462 Dihedral : 9.227 98.968 1524 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.22 % Favored : 95.58 % Rotamer: Outliers : 3.34 % Allowed : 18.20 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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 (0.26), residues: 1019 helix: 0.26 (0.50), residues: 108 sheet: -0.47 (0.28), residues: 325 loop : -1.35 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 647 TYR 0.014 0.001 TYR B 308 PHE 0.020 0.002 PHE A 121 TRP 0.027 0.002 TRP B 23 HIS 0.003 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 8286) covalent geometry : angle 0.62329 / 0.31 (11225) SS BOND : bond 0.00223 / 0.11 ( 17) SS BOND : angle 0.86795 / 0.54 ( 34) hydrogen bonds : bond 0.03577 / 2.32 ( 242) hydrogen bonds : angle 6.03946 / 4.14 ( 621) link_ALPHA1-3 : bond 0.01066 / 0.52 ( 2) link_ALPHA1-3 : angle 2.63992 / 1.93 ( 6) link_ALPHA1-6 : bond 0.01015 / 0.49 ( 2) link_ALPHA1-6 : angle 2.33147 / 1.59 ( 6) link_BETA1-4 : bond 0.00389 / 0.19 ( 8) link_BETA1-4 : angle 2.72099 / 1.96 ( 24) link_NAG-ASN : bond 0.00776 / 0.39 ( 8) link_NAG-ASN : angle 4.44415 / 3.66 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 39 time to evaluate : 0.273 Fit side-chains REVERT: A 9 MET cc_start: 0.8946 (ttm) cc_final: 0.8690 (ttm) REVERT: A 323 GLN cc_start: 0.7367 (pp30) cc_final: 0.7069 (pm20) REVERT: A 608 ILE cc_start: 0.8214 (mt) cc_final: 0.7905 (mp) REVERT: A 610 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6937 (mt-10) REVERT: A 647 ARG cc_start: 0.8090 (mmm160) cc_final: 0.7885 (mmm160) REVERT: A 739 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8251 (pt0) REVERT: B 73 GLN cc_start: 0.5675 (OUTLIER) cc_final: 0.5184 (tm-30) REVERT: B 172 LYS cc_start: 0.8798 (mppt) cc_final: 0.8324 (ttpt) REVERT: B 360 TYR cc_start: 0.7131 (m-80) cc_final: 0.6874 (m-80) REVERT: B 377 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7699 (t0) outliers start: 29 outliers final: 9 residues processed: 65 average time/residue: 0.5116 time to fit residues: 35.8453 Evaluate side-chains 47 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 377 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 37 optimal weight: 0.0000 chunk 82 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 0.0370 chunk 86 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 13 optimal weight: 0.0570 chunk 92 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.113017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.074520 restraints weight = 15305.572| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.00 r_work: 0.3016 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8323 Z= 0.108 Angle : 0.619 12.546 11319 Z= 0.291 Chirality : 0.046 0.341 1309 Planarity : 0.003 0.047 1462 Dihedral : 8.573 100.341 1521 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.88 % Allowed : 19.35 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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 (0.26), residues: 1019 helix: 0.58 (0.51), residues: 108 sheet: -0.31 (0.28), residues: 322 loop : -1.29 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 399 TYR 0.012 0.001 TYR B 308 PHE 0.016 0.001 PHE A 121 TRP 0.025 0.002 TRP B 23 HIS 0.002 0.000 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 8286) covalent geometry : angle 0.56885 / 0.28 (11225) SS BOND : bond 0.00195 / 0.09 ( 17) SS BOND : angle 0.74324 / 0.46 ( 34) hydrogen bonds : bond 0.02958 / 1.87 ( 242) hydrogen bonds : angle 5.88866 / 4.02 ( 621) link_ALPHA1-3 : bond 0.01187 / 0.57 ( 2) link_ALPHA1-3 : angle 2.66828 / 1.88 ( 6) link_ALPHA1-6 : bond 0.01324 / 0.63 ( 2) link_ALPHA1-6 : angle 2.16957 / 1.46 ( 6) link_BETA1-4 : bond 0.00439 / 0.20 ( 8) link_BETA1-4 : angle 2.70636 / 1.93 ( 24) link_NAG-ASN : bond 0.00799 / 0.40 ( 8) link_NAG-ASN : angle 4.27988 / 3.51 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 37 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 80 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8312 (p) REVERT: A 323 GLN cc_start: 0.7346 (pp30) cc_final: 0.7015 (pm20) REVERT: A 580 MET cc_start: 0.9150 (mtm) cc_final: 0.8735 (mtm) REVERT: A 608 ILE cc_start: 0.8140 (mt) cc_final: 0.7854 (mp) REVERT: A 610 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6883 (mt-10) REVERT: A 647 ARG cc_start: 0.8139 (mmm160) cc_final: 0.7782 (mmm160) REVERT: B 9 SER cc_start: 0.5013 (OUTLIER) cc_final: 0.4747 (m) REVERT: B 48 MET cc_start: 0.6685 (pmm) cc_final: 0.6449 (pmm) REVERT: B 73 GLN cc_start: 0.5647 (OUTLIER) cc_final: 0.5222 (tm-30) REVERT: B 172 LYS cc_start: 0.8838 (mppt) cc_final: 0.8362 (ttpt) REVERT: B 270 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8842 (mt) REVERT: B 360 TYR cc_start: 0.7085 (m-80) cc_final: 0.6818 (m-80) REVERT: B 377 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7747 (t0) outliers start: 25 outliers final: 9 residues processed: 60 average time/residue: 0.4891 time to fit residues: 31.8172 Evaluate side-chains 49 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 420 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 chunk 55 optimal weight: 0.0970 chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.110400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.071883 restraints weight = 15126.349| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.98 r_work: 0.2953 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8323 Z= 0.187 Angle : 0.645 12.763 11319 Z= 0.308 Chirality : 0.048 0.332 1309 Planarity : 0.004 0.048 1462 Dihedral : 8.233 103.643 1521 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.57 % Allowed : 18.89 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -1.09 (0.26), residues: 1019 helix: 0.56 (0.51), residues: 108 sheet: -0.29 (0.28), residues: 328 loop : -1.24 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 717 TYR 0.014 0.001 TYR B 308 PHE 0.018 0.002 PHE A 121 TRP 0.020 0.002 TRP B 23 HIS 0.003 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 ( 8286) covalent geometry : angle 0.59868 / 0.30 (11225) SS BOND : bond 0.00208 / 0.11 ( 17) SS BOND : angle 0.77448 / 0.49 ( 34) hydrogen bonds : bond 0.03358 / 2.17 ( 242) hydrogen bonds : angle 5.91841 / 4.04 ( 621) link_ALPHA1-3 : bond 0.01152 / 0.56 ( 2) link_ALPHA1-3 : angle 2.43504 / 1.75 ( 6) link_ALPHA1-6 : bond 0.01263 / 0.60 ( 2) link_ALPHA1-6 : angle 1.76546 / 1.21 ( 6) link_BETA1-4 : bond 0.00370 / 0.18 ( 8) link_BETA1-4 : angle 2.67466 / 1.89 ( 24) link_NAG-ASN : bond 0.00768 / 0.38 ( 8) link_NAG-ASN : angle 4.28847 / 3.55 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 35 time to evaluate : 0.341 Fit side-chains REVERT: A 80 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8249 (p) REVERT: A 323 GLN cc_start: 0.7382 (pp30) cc_final: 0.7011 (pm20) REVERT: A 608 ILE cc_start: 0.8190 (mt) cc_final: 0.7916 (mp) REVERT: A 610 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6867 (mt-10) REVERT: A 647 ARG cc_start: 0.8146 (mmm160) cc_final: 0.7924 (mmp80) REVERT: B 9 SER cc_start: 0.5057 (OUTLIER) cc_final: 0.4805 (m) REVERT: B 48 MET cc_start: 0.6541 (pmm) cc_final: 0.6294 (pmm) REVERT: B 65 THR cc_start: 0.7231 (OUTLIER) cc_final: 0.6895 (t) REVERT: B 73 GLN cc_start: 0.5228 (OUTLIER) cc_final: 0.4835 (tm-30) REVERT: B 172 LYS cc_start: 0.8891 (mppt) cc_final: 0.8374 (ttpt) REVERT: B 360 TYR cc_start: 0.7231 (m-80) cc_final: 0.6985 (m-80) REVERT: B 377 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7772 (t0) outliers start: 31 outliers final: 10 residues processed: 64 average time/residue: 0.4476 time to fit residues: 31.0297 Evaluate side-chains 49 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 377 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 94 HIS ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.110730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.072315 restraints weight = 14951.045| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.95 r_work: 0.2964 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8323 Z= 0.151 Angle : 0.634 16.096 11319 Z= 0.300 Chirality : 0.047 0.335 1309 Planarity : 0.003 0.047 1462 Dihedral : 8.140 103.968 1521 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.69 % Allowed : 18.78 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -1.02 (0.26), residues: 1019 helix: 0.64 (0.51), residues: 108 sheet: -0.28 (0.28), residues: 331 loop : -1.18 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 485 TYR 0.013 0.001 TYR B 308 PHE 0.018 0.001 PHE A 121 TRP 0.022 0.002 TRP B 23 HIS 0.003 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 8286) covalent geometry : angle 0.57913 / 0.29 (11225) SS BOND : bond 0.00198 / 0.10 ( 17) SS BOND : angle 0.75207 / 0.47 ( 34) hydrogen bonds : bond 0.03169 / 2.03 ( 242) hydrogen bonds : angle 5.89026 / 4.01 ( 621) link_ALPHA1-3 : bond 0.01146 / 0.55 ( 2) link_ALPHA1-3 : angle 2.37636 / 1.71 ( 6) link_ALPHA1-6 : bond 0.01328 / 0.63 ( 2) link_ALPHA1-6 : angle 1.61504 / 1.12 ( 6) link_BETA1-4 : bond 0.00370 / 0.18 ( 8) link_BETA1-4 : angle 2.62356 / 1.84 ( 24) link_NAG-ASN : bond 0.00701 / 0.35 ( 8) link_NAG-ASN : angle 4.77772 / 4.22 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 37 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 80 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8171 (p) REVERT: A 323 GLN cc_start: 0.7379 (pp30) cc_final: 0.6989 (pm20) REVERT: A 415 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.8922 (tt) REVERT: A 580 MET cc_start: 0.9160 (mtm) cc_final: 0.8756 (mtm) REVERT: A 608 ILE cc_start: 0.8162 (mt) cc_final: 0.7857 (mp) REVERT: A 609 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7005 (mmt) REVERT: A 610 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6847 (mt-10) REVERT: A 647 ARG cc_start: 0.8170 (mmm160) cc_final: 0.7913 (mmm160) REVERT: B 9 SER cc_start: 0.5070 (OUTLIER) cc_final: 0.4832 (m) REVERT: B 65 THR cc_start: 0.7315 (OUTLIER) cc_final: 0.6976 (t) REVERT: B 73 GLN cc_start: 0.5156 (OUTLIER) cc_final: 0.4787 (tm-30) REVERT: B 360 TYR cc_start: 0.7201 (m-80) cc_final: 0.6830 (m-80) REVERT: B 377 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7749 (t0) REVERT: B 407 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6885 (ptp90) outliers start: 32 outliers final: 11 residues processed: 67 average time/residue: 0.4723 time to fit residues: 34.3296 Evaluate side-chains 55 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 36 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 407 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 8 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 11 optimal weight: 0.0470 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.110157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.071677 restraints weight = 15112.480| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.98 r_work: 0.2957 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8323 Z= 0.171 Angle : 0.638 14.168 11319 Z= 0.306 Chirality : 0.047 0.334 1309 Planarity : 0.003 0.048 1462 Dihedral : 8.108 104.951 1521 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.15 % Allowed : 18.32 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -0.95 (0.26), residues: 1019 helix: 0.63 (0.51), residues: 108 sheet: -0.28 (0.28), residues: 343 loop : -1.10 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 39 TYR 0.012 0.001 TYR B 308 PHE 0.019 0.001 PHE A 121 TRP 0.025 0.002 TRP B 23 HIS 0.003 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 8286) covalent geometry : angle 0.58904 / 0.30 (11225) SS BOND : bond 0.00204 / 0.11 ( 17) SS BOND : angle 0.92918 / 0.57 ( 34) hydrogen bonds : bond 0.03214 / 2.06 ( 242) hydrogen bonds : angle 5.92561 / 4.04 ( 621) link_ALPHA1-3 : bond 0.01173 / 0.57 ( 2) link_ALPHA1-3 : angle 2.32082 / 1.67 ( 6) link_ALPHA1-6 : bond 0.01209 / 0.58 ( 2) link_ALPHA1-6 : angle 1.53061 / 1.06 ( 6) link_BETA1-4 : bond 0.00367 / 0.19 ( 8) link_BETA1-4 : angle 2.60021 / 1.82 ( 24) link_NAG-ASN : bond 0.00675 / 0.34 ( 8) link_NAG-ASN : angle 4.45692 / 3.84 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 35 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 80 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8108 (p) REVERT: A 323 GLN cc_start: 0.7412 (pp30) cc_final: 0.7007 (pm20) REVERT: A 415 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.8906 (tt) REVERT: A 580 MET cc_start: 0.9169 (mtm) cc_final: 0.8764 (mtm) REVERT: A 608 ILE cc_start: 0.8142 (mt) cc_final: 0.7807 (mp) REVERT: A 609 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.6911 (mmt) REVERT: A 610 GLU cc_start: 0.7396 (mt-10) cc_final: 0.6795 (mt-10) REVERT: A 647 ARG cc_start: 0.8179 (mmm160) cc_final: 0.7909 (mmm160) REVERT: B 65 THR cc_start: 0.7380 (OUTLIER) cc_final: 0.7022 (t) REVERT: B 360 TYR cc_start: 0.7246 (m-80) cc_final: 0.7004 (m-80) REVERT: B 377 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7738 (t0) REVERT: B 407 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6875 (ptp90) outliers start: 36 outliers final: 16 residues processed: 69 average time/residue: 0.4862 time to fit residues: 36.3059 Evaluate side-chains 57 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 35 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 407 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 61 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.109801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.071443 restraints weight = 15062.070| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.96 r_work: 0.2951 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8323 Z= 0.178 Angle : 0.641 13.550 11319 Z= 0.307 Chirality : 0.048 0.334 1309 Planarity : 0.004 0.048 1462 Dihedral : 8.100 105.443 1521 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.57 % Allowed : 18.43 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -0.92 (0.26), residues: 1019 helix: 0.60 (0.52), residues: 108 sheet: -0.25 (0.28), residues: 343 loop : -1.07 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 717 TYR 0.012 0.001 TYR B 308 PHE 0.020 0.002 PHE A 121 TRP 0.025 0.002 TRP B 23 HIS 0.003 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 8286) covalent geometry : angle 0.59440 / 0.30 (11225) SS BOND : bond 0.00254 / 0.13 ( 17) SS BOND : angle 0.91466 / 0.58 ( 34) hydrogen bonds : bond 0.03313 / 2.14 ( 242) hydrogen bonds : angle 5.89353 / 4.01 ( 621) link_ALPHA1-3 : bond 0.01208 / 0.58 ( 2) link_ALPHA1-3 : angle 2.30692 / 1.65 ( 6) link_ALPHA1-6 : bond 0.01205 / 0.58 ( 2) link_ALPHA1-6 : angle 1.50910 / 1.04 ( 6) link_BETA1-4 : bond 0.00355 / 0.18 ( 8) link_BETA1-4 : angle 2.55736 / 1.78 ( 24) link_NAG-ASN : bond 0.00712 / 0.36 ( 8) link_NAG-ASN : angle 4.35257 / 3.70 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 34 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 80 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8094 (p) REVERT: A 323 GLN cc_start: 0.7421 (pp30) cc_final: 0.7009 (pm20) REVERT: A 415 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.8911 (tt) REVERT: A 580 MET cc_start: 0.9176 (mtm) cc_final: 0.8794 (mtm) REVERT: A 608 ILE cc_start: 0.8141 (mt) cc_final: 0.7819 (mp) REVERT: A 609 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.6846 (mmt) REVERT: A 610 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6821 (mt-10) REVERT: A 647 ARG cc_start: 0.8214 (mmm160) cc_final: 0.7945 (mmp80) REVERT: B 65 THR cc_start: 0.7473 (OUTLIER) cc_final: 0.7118 (t) REVERT: B 73 GLN cc_start: 0.5113 (OUTLIER) cc_final: 0.4744 (tm-30) REVERT: B 360 TYR cc_start: 0.7332 (m-80) cc_final: 0.7093 (m-80) REVERT: B 377 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7767 (t0) REVERT: B 407 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6810 (ptp90) outliers start: 31 outliers final: 15 residues processed: 63 average time/residue: 0.5097 time to fit residues: 34.5917 Evaluate side-chains 55 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 33 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 407 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 59 optimal weight: 0.0770 chunk 57 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 0.0980 overall best weight: 0.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.113176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.075652 restraints weight = 15125.273| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.95 r_work: 0.3015 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8323 Z= 0.103 Angle : 0.608 13.138 11319 Z= 0.290 Chirality : 0.046 0.337 1309 Planarity : 0.003 0.046 1462 Dihedral : 7.902 104.777 1521 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.11 % Allowed : 19.12 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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 (0.26), residues: 1019 helix: 0.89 (0.52), residues: 108 sheet: -0.16 (0.28), residues: 342 loop : -1.01 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 717 TYR 0.010 0.001 TYR B 308 PHE 0.016 0.001 PHE A 121 TRP 0.040 0.002 TRP B 23 HIS 0.002 0.000 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 8286) covalent geometry : angle 0.56252 / 0.28 (11225) SS BOND : bond 0.00203 / 0.09 ( 17) SS BOND : angle 0.87719 / 0.55 ( 34) hydrogen bonds : bond 0.02858 / 1.79 ( 242) hydrogen bonds : angle 5.76203 / 3.92 ( 621) link_ALPHA1-3 : bond 0.01257 / 0.61 ( 2) link_ALPHA1-3 : angle 2.13044 / 1.54 ( 6) link_ALPHA1-6 : bond 0.01172 / 0.56 ( 2) link_ALPHA1-6 : angle 1.45802 / 1.02 ( 6) link_BETA1-4 : bond 0.00405 / 0.19 ( 8) link_BETA1-4 : angle 2.47510 / 1.73 ( 24) link_NAG-ASN : bond 0.00715 / 0.36 ( 8) link_NAG-ASN : angle 4.19339 / 3.54 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 37 time to evaluate : 0.350 Fit side-chains REVERT: A 80 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8144 (p) REVERT: A 323 GLN cc_start: 0.7257 (pp30) cc_final: 0.6872 (pm20) REVERT: A 580 MET cc_start: 0.9139 (mtm) cc_final: 0.8753 (mtm) REVERT: A 608 ILE cc_start: 0.8139 (mt) cc_final: 0.7805 (mp) REVERT: A 610 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6820 (mt-10) REVERT: A 647 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7971 (mmp80) REVERT: B 73 GLN cc_start: 0.4968 (OUTLIER) cc_final: 0.4633 (tm-30) REVERT: B 172 LYS cc_start: 0.9024 (mppt) cc_final: 0.8508 (ttpp) REVERT: B 360 TYR cc_start: 0.7202 (m-80) cc_final: 0.6888 (m-80) REVERT: B 407 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6816 (ptp90) outliers start: 27 outliers final: 14 residues processed: 61 average time/residue: 0.5175 time to fit residues: 34.0267 Evaluate side-chains 51 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 34 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 407 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 93 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 0.0470 chunk 55 optimal weight: 0.9990 chunk 96 optimal weight: 0.0670 chunk 8 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.112554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.075107 restraints weight = 15071.473| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.93 r_work: 0.3001 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8323 Z= 0.120 Angle : 0.614 13.055 11319 Z= 0.291 Chirality : 0.046 0.334 1309 Planarity : 0.003 0.046 1462 Dihedral : 7.880 104.633 1521 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.30 % Allowed : 20.05 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -0.73 (0.26), residues: 1019 helix: 0.94 (0.53), residues: 108 sheet: -0.12 (0.28), residues: 343 loop : -0.99 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 717 TYR 0.012 0.001 TYR B 308 PHE 0.014 0.001 PHE A 121 TRP 0.041 0.002 TRP B 23 HIS 0.003 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 8286) covalent geometry : angle 0.56964 / 0.28 (11225) SS BOND : bond 0.00192 / 0.09 ( 17) SS BOND : angle 0.82741 / 0.53 ( 34) hydrogen bonds : bond 0.02902 / 1.83 ( 242) hydrogen bonds : angle 5.69238 / 3.87 ( 621) link_ALPHA1-3 : bond 0.01248 / 0.60 ( 2) link_ALPHA1-3 : angle 2.14275 / 1.54 ( 6) link_ALPHA1-6 : bond 0.01139 / 0.54 ( 2) link_ALPHA1-6 : angle 1.44973 / 1.01 ( 6) link_BETA1-4 : bond 0.00342 / 0.16 ( 8) link_BETA1-4 : angle 2.46146 / 1.71 ( 24) link_NAG-ASN : bond 0.00712 / 0.36 ( 8) link_NAG-ASN : angle 4.14077 / 3.51 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 32 time to evaluate : 0.321 Fit side-chains REVERT: A 80 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8156 (p) REVERT: A 323 GLN cc_start: 0.7264 (pp30) cc_final: 0.6875 (pm20) REVERT: A 580 MET cc_start: 0.9134 (mtm) cc_final: 0.8757 (mtm) REVERT: A 608 ILE cc_start: 0.8139 (mt) cc_final: 0.7790 (mp) REVERT: A 610 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6765 (mt-10) REVERT: A 647 ARG cc_start: 0.8288 (mmm160) cc_final: 0.7999 (mmp80) REVERT: B 73 GLN cc_start: 0.5009 (OUTLIER) cc_final: 0.4667 (tm-30) REVERT: B 172 LYS cc_start: 0.9022 (mppt) cc_final: 0.8505 (ttpp) REVERT: B 360 TYR cc_start: 0.7272 (m-80) cc_final: 0.7061 (m-80) REVERT: B 407 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6924 (ptp90) outliers start: 20 outliers final: 16 residues processed: 52 average time/residue: 0.5523 time to fit residues: 30.9661 Evaluate side-chains 51 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 32 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 407 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 66 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 0.0070 chunk 54 optimal weight: 0.0980 chunk 70 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.110886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.071323 restraints weight = 14362.602| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.97 r_work: 0.2952 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8323 Z= 0.110 Angle : 0.600 13.007 11319 Z= 0.284 Chirality : 0.046 0.332 1309 Planarity : 0.003 0.045 1462 Dihedral : 7.760 103.901 1521 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.19 % Allowed : 20.16 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -0.62 (0.26), residues: 1019 helix: 1.02 (0.53), residues: 108 sheet: -0.06 (0.28), residues: 336 loop : -0.89 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 717 TYR 0.011 0.001 TYR B 308 PHE 0.013 0.001 PHE A 121 TRP 0.043 0.002 TRP B 23 HIS 0.003 0.000 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8286) covalent geometry : angle 0.55611 / 0.27 (11225) SS BOND : bond 0.00191 / 0.10 ( 17) SS BOND : angle 0.81653 / 0.53 ( 34) hydrogen bonds : bond 0.02827 / 1.77 ( 242) hydrogen bonds : angle 5.61657 / 3.82 ( 621) link_ALPHA1-3 : bond 0.01241 / 0.60 ( 2) link_ALPHA1-3 : angle 2.10815 / 1.50 ( 6) link_ALPHA1-6 : bond 0.01054 / 0.50 ( 2) link_ALPHA1-6 : angle 1.43193 / 1.00 ( 6) link_BETA1-4 : bond 0.00365 / 0.17 ( 8) link_BETA1-4 : angle 2.39027 / 1.66 ( 24) link_NAG-ASN : bond 0.00726 / 0.36 ( 8) link_NAG-ASN : angle 4.08183 / 3.45 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3711.37 seconds wall clock time: 63 minutes 48.62 seconds (3828.62 seconds total)