Starting phenix.real_space_refine on Fri Oct 23 10:37:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9txj_56398/10_2026/9txj_56398.cif Found real_map, /net/cci-nas-00/data/ceres_data/9txj_56398/10_2026/9txj_56398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9txj_56398/10_2026/9txj_56398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9txj_56398/10_2026/9txj_56398.map" model { file = "/net/cci-nas-00/data/ceres_data/9txj_56398/10_2026/9txj_56398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9txj_56398/10_2026/9txj_56398.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 5919 2.51 5 N 1581 2.21 5 O 1852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9386 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6080 Classifications: {'peptide': 773} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 735} Chain breaks: 2 Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1552 Classifications: {'peptide': 205} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 190} Chain breaks: 2 Chain: "E" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1642 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain: "B" 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 Time building chain proxies: 1.95, per 1000 atoms: 0.21 Number of scatterers: 9386 At special positions: 0 Unit cell: (73.75, 95, 148.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1852 8.00 N 1581 7.00 C 5919 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 717 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 197 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 193 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG B 1 " - " ASN A 207 " " NAG C 1 " - " ASN A 81 " " NAG F 1 " - " ASN A 577 " " NAG G 1 " - " ASN A 517 " Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 360.0 milliseconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2218 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 19 sheets defined 15.0% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 195 through 200 removed outlier: 4.443A pdb=" N ASP A 200 " --> pdb=" O GLN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.759A pdb=" N GLN A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 303 removed outlier: 3.971A pdb=" N GLN A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 342 Processing helix chain 'A' and resid 351 through 365 removed outlier: 3.957A pdb=" N ALA A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 407 Processing helix chain 'A' and resid 422 through 432 Processing helix chain 'A' and resid 445 through 457 removed outlier: 3.785A pdb=" N VAL A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 533 Processing helix chain 'A' and resid 542 through 560 removed outlier: 3.879A pdb=" N ARG A 546 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 582 removed outlier: 3.550A pdb=" N LEU A 571 " --> pdb=" O ASP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 850 removed outlier: 3.532A pdb=" N PHE A 848 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.901A pdb=" N SER D 90 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.025A pdb=" N ILE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 126 Processing helix chain 'E' and resid 182 through 188 removed outlier: 3.802A pdb=" N HIS E 188 " --> pdb=" O GLU E 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 206 removed outlier: 8.815A pdb=" N GLN A 173 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A 38 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASP A 175 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL A 40 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N HIS A 177 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER A 42 " --> pdb=" O HIS A 177 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N PHE A 179 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 44 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR A 36 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG A 56 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LEU A 38 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR A 54 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL A 40 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A 52 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N SER A 42 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N HIS A 50 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL A 44 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU A 147 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE A 79 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 16.790A pdb=" N PHE A 78 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 15.766A pdb=" N GLU A 97 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N THR A 80 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE A 95 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE A 82 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 74 Processing sheet with id=AA3, first strand: chain 'A' and resid 157 through 163 removed outlier: 3.874A pdb=" N LEU A 795 " --> pdb=" O MET A 792 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASP A 809 " --> pdb=" O VAL A 813 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL A 813 " --> pdb=" O ASP A 809 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 705 " --> pdb=" O LEU A 829 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU A 831 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ARG A 715 " --> pdb=" O SER A 894 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TRP A 896 " --> pdb=" O ARG A 715 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU A 899 " --> pdb=" O SER A 875 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N SER A 875 " --> pdb=" O GLU A 899 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 255 removed outlier: 3.960A pdb=" N GLU A 476 " --> pdb=" O LYS A 496 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 321 removed outlier: 6.787A pdb=" N VAL A 275 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ILE A 313 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE A 277 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N PHE A 315 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE A 279 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N SER A 378 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N PHE A 413 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE A 380 " --> pdb=" O PHE A 413 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU A 415 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A 382 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE A 417 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR A 384 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ARG A 438 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS A 414 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE A 440 " --> pdb=" O CYS A 414 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY A 416 " --> pdb=" O ILE A 440 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 481 through 486 removed outlier: 4.837A pdb=" N ASN A 481 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL A 465 " --> pdb=" O ASN A 481 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ARG A 483 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR A 463 " --> pdb=" O ARG A 483 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU A 485 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ALA A 464 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS A 512 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 727 through 732 removed outlier: 5.399A pdb=" N ASN A 728 " --> pdb=" O GLY A 741 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLY A 741 " --> pdb=" O ASN A 728 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 730 " --> pdb=" O VAL A 739 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU A 738 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL A 755 " --> pdb=" O GLU A 738 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR A 740 " --> pdb=" O ILE A 753 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE A 753 " --> pdb=" O THR A 740 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLN A 742 " --> pdb=" O SER A 751 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.733A pdb=" N GLN D 4 " --> pdb=" O LYS D 22 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL D 17 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 9 through 10 removed outlier: 6.528A pdb=" N GLU D 9 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS D 37 " --> pdb=" O TRP D 46 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TRP D 46 " --> pdb=" O LYS D 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 9 through 10 removed outlier: 6.528A pdb=" N GLU D 9 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 122 through 126 Processing sheet with id=AB3, first strand: chain 'D' and resid 122 through 126 Processing sheet with id=AB4, first strand: chain 'D' and resid 153 through 155 Processing sheet with id=AB5, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'E' and resid 53 through 54 removed outlier: 4.271A pdb=" N TYR E 50 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR E 50 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE E 33 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN E 90 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR E 96 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 53 through 54 removed outlier: 4.271A pdb=" N TYR E 50 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR E 50 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE E 33 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 113 through 117 removed outlier: 3.755A pdb=" N VAL E 132 " --> pdb=" O PHE E 117 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N TYR E 172 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AC1, first strand: chain 'E' and resid 144 through 149 404 hydrogen bonds defined for protein. 1080 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: 1.76 Time building geometry restraints manager: 1.01 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: 3018 1.34 - 1.46: 1917 1.46 - 1.58: 4594 1.58 - 1.70: 1 1.70 - 1.82: 57 Bond restraints: 9587 Sorted by residual: bond pdb=" N VAL A 327 " pdb=" CA VAL A 327 " ideal model delta sigma weight residual 1.462 1.494 -0.033 8.70e-03 1.32e+04 1.40e+01 bond pdb=" N ARG A 323 " pdb=" CA ARG A 323 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.18e-02 7.18e+03 8.49e+00 bond pdb=" N GLN A 321 " pdb=" CA GLN A 321 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.21e-02 6.83e+03 7.18e+00 bond pdb=" N LEU A 326 " pdb=" CA LEU A 326 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.34e-02 5.57e+03 6.30e+00 bond pdb=" N SER A 325 " pdb=" CA SER A 325 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.33e-02 5.65e+03 5.75e+00 ... (remaining 9582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 12638 1.90 - 3.80: 289 3.80 - 5.70: 73 5.70 - 7.61: 11 7.61 - 9.51: 6 Bond angle restraints: 13017 Sorted by residual: angle pdb=" CA GLU D 81 " pdb=" CB GLU D 81 " pdb=" CG GLU D 81 " ideal model delta sigma weight residual 114.10 123.61 -9.51 2.00e+00 2.50e-01 2.26e+01 angle pdb=" CA GLU E 81 " pdb=" CB GLU E 81 " pdb=" CG GLU E 81 " ideal model delta sigma weight residual 114.10 122.42 -8.32 2.00e+00 2.50e-01 1.73e+01 angle pdb=" CA MET A 609 " pdb=" CB MET A 609 " pdb=" CG MET A 609 " ideal model delta sigma weight residual 114.10 120.89 -6.79 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CA VAL A 327 " pdb=" C VAL A 327 " pdb=" N PRO A 328 " ideal model delta sigma weight residual 117.33 120.75 -3.42 1.01e+00 9.80e-01 1.15e+01 angle pdb=" C VAL D 113 " pdb=" N SER D 114 " pdb=" CA SER D 114 " ideal model delta sigma weight residual 121.54 127.97 -6.43 1.91e+00 2.74e-01 1.13e+01 ... (remaining 13012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5276 17.95 - 35.89: 438 35.89 - 53.84: 117 53.84 - 71.79: 35 71.79 - 89.73: 16 Dihedral angle restraints: 5882 sinusoidal: 2440 harmonic: 3442 Sorted by residual: dihedral pdb=" CB CYS A 717 " pdb=" SG CYS A 717 " pdb=" SG CYS A 895 " pdb=" CB CYS A 895 " ideal model delta sinusoidal sigma weight residual -86.00 -163.17 77.17 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CA MET A 799 " pdb=" C MET A 799 " pdb=" N ASP A 800 " pdb=" CA ASP A 800 " ideal model delta harmonic sigma weight residual 180.00 -160.23 -19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 88 " pdb=" CB CYS E 88 " ideal model delta sinusoidal sigma weight residual 93.00 61.34 31.66 1 1.00e+01 1.00e-02 1.43e+01 ... (remaining 5879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1029 0.041 - 0.082: 304 0.082 - 0.123: 124 0.123 - 0.164: 28 0.164 - 0.205: 3 Chirality restraints: 1488 Sorted by residual: chirality pdb=" CA VAL A 327 " pdb=" N VAL A 327 " pdb=" C VAL A 327 " pdb=" CB VAL A 327 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 81 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CA ILE E 116 " pdb=" N ILE E 116 " pdb=" C ILE E 116 " pdb=" CB ILE E 116 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 1485 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 323 " 0.450 9.50e-02 1.11e+02 2.02e-01 2.50e+01 pdb=" NE ARG A 323 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 323 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 323 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 323 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 586 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO A 587 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 587 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 587 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 124 " 0.032 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO D 125 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 125 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 125 " 0.027 5.00e-02 4.00e+02 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.04: 5154 3.04 - 3.50: 9182 3.50 - 3.97: 13535 3.97 - 4.43: 15437 4.43 - 4.90: 26434 Nonbonded interactions: 69742 Sorted by model distance: nonbonded pdb=" O VAL D 113 " pdb=" OG SER D 114 " model vdw 2.572 3.040 nonbonded pdb=" C SER E 74 " pdb=" OG SER E 74 " model vdw 2.620 2.616 nonbonded pdb=" N THR A 586 " pdb=" O THR A 586 " model vdw 2.621 2.496 nonbonded pdb=" O LEU E 178 " pdb=" CB LEU E 178 " model vdw 2.622 2.752 nonbonded pdb=" O SER A 407 " pdb=" OG SER A 407 " model vdw 2.625 3.040 ... (remaining 69737 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 'B' selection = chain 'C' selection = 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: 0.660 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: 0.030 Set scattering table: 0.030 Process input model: 9.760 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9600 Z= 0.209 Angle : 0.794 11.211 13051 Z= 0.410 Chirality : 0.048 0.205 1488 Planarity : 0.007 0.202 1670 Dihedral : 15.590 89.733 3649 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 0.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.19 % Allowed : 12.07 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.24), residues: 1174 helix: 0.74 (0.41), residues: 153 sheet: 0.57 (0.24), residues: 484 loop : -1.10 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 775 TYR 0.020 0.001 TYR D 49 PHE 0.024 0.002 PHE A 186 TRP 0.008 0.001 TRP A 322 HIS 0.006 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.21 ( 9587) covalent geometry : angle 0.78072 / 0.41 (13017) SS BOND : bond 0.00557 / 0.44 ( 5) SS BOND : angle 1.58900 / 1.06 ( 10) hydrogen bonds : bond 0.12303 / 8.55 ( 378) hydrogen bonds : angle 5.67231 / 3.95 ( 1080) link_BETA1-4 : bond 0.00966 / 0.59 ( 4) link_BETA1-4 : angle 4.49557 / 2.55 ( 12) link_NAG-ASN : bond 0.00480 / 0.30 ( 4) link_NAG-ASN : angle 1.59686 / 0.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.9415 (mmm) cc_final: 0.8842 (mmm) REVERT: A 134 VAL cc_start: 0.7937 (t) cc_final: 0.7642 (p) REVERT: A 150 LEU cc_start: 0.9501 (mt) cc_final: 0.9118 (mp) REVERT: A 194 MET cc_start: 0.9017 (mmm) cc_final: 0.8745 (mmm) REVERT: A 285 MET cc_start: 0.9184 (mmm) cc_final: 0.8946 (mmm) REVERT: A 544 MET cc_start: 0.8520 (mmm) cc_final: 0.8299 (mmm) REVERT: A 551 LEU cc_start: 0.9495 (tp) cc_final: 0.9288 (tt) REVERT: A 792 MET cc_start: 0.8590 (mmm) cc_final: 0.8377 (mmm) REVERT: D 47 ILE cc_start: 0.9289 (mm) cc_final: 0.9039 (mt) REVERT: E 81 GLU cc_start: 0.9364 (pm20) cc_final: 0.9148 (pm20) REVERT: E 174 MET cc_start: 0.8533 (ttt) cc_final: 0.8214 (ttt) outliers start: 2 outliers final: 1 residues processed: 75 average time/residue: 0.0793 time to fit residues: 9.0700 Evaluate side-chains 46 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 143 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 117] chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.0370 chunk 97 optimal weight: 0.0970 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** 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 = 0.3209 r_free = 0.3209 target = 0.051598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.034625 restraints weight = 41985.827| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 5.50 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9600 Z= 0.102 Angle : 0.581 7.878 13051 Z= 0.283 Chirality : 0.044 0.238 1488 Planarity : 0.004 0.046 1670 Dihedral : 9.079 85.902 1444 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.54 % Allowed : 13.32 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.24), residues: 1174 helix: 1.12 (0.42), residues: 160 sheet: 0.88 (0.24), residues: 472 loop : -0.96 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 210 TYR 0.012 0.001 TYR D 49 PHE 0.010 0.001 PHE A 142 TRP 0.006 0.001 TRP E 35 HIS 0.002 0.001 HIS A 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 9587) covalent geometry : angle 0.57023 / 0.28 (13017) SS BOND : bond 0.00505 / 0.36 ( 5) SS BOND : angle 1.52555 / 0.91 ( 10) hydrogen bonds : bond 0.03343 / 2.30 ( 378) hydrogen bonds : angle 4.96020 / 3.52 ( 1080) link_BETA1-4 : bond 0.00472 / 0.31 ( 4) link_BETA1-4 : angle 3.16003 / 1.72 ( 12) link_NAG-ASN : bond 0.00284 / 0.18 ( 4) link_NAG-ASN : angle 1.56356 / 0.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.9475 (mmm) cc_final: 0.8838 (mmm) REVERT: A 134 VAL cc_start: 0.7878 (t) cc_final: 0.7583 (p) REVERT: A 150 LEU cc_start: 0.9439 (mt) cc_final: 0.9081 (mp) REVERT: A 285 MET cc_start: 0.9179 (mmm) cc_final: 0.8962 (mmm) REVERT: A 544 MET cc_start: 0.8408 (mmm) cc_final: 0.8187 (mmm) REVERT: A 551 LEU cc_start: 0.9486 (tp) cc_final: 0.9249 (tt) REVERT: D 30 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8179 (t) REVERT: D 179 MET cc_start: 0.7894 (tmm) cc_final: 0.7684 (tmm) REVERT: E 4 MET cc_start: 0.8172 (mtp) cc_final: 0.7929 (mtp) REVERT: E 174 MET cc_start: 0.8216 (ttt) cc_final: 0.7985 (ttt) outliers start: 16 outliers final: 10 residues processed: 62 average time/residue: 0.0771 time to fit residues: 7.6559 Evaluate side-chains 54 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 170 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [107, 26, 47, 58, 54, 29, 67, 16, 97, 23, 105] chunk 107 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 554 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.050096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.033306 restraints weight = 42195.820| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 5.50 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9600 Z= 0.174 Angle : 0.608 8.381 13051 Z= 0.299 Chirality : 0.043 0.229 1488 Planarity : 0.005 0.113 1670 Dihedral : 8.635 77.652 1444 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.03 % Allowed : 14.86 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1174 helix: 1.53 (0.42), residues: 160 sheet: 1.09 (0.24), residues: 486 loop : -0.90 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG E 210 TYR 0.012 0.002 TYR D 49 PHE 0.011 0.001 PHE E 62 TRP 0.007 0.001 TRP E 35 HIS 0.004 0.001 HIS A 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 9587) covalent geometry : angle 0.59960 / 0.30 (13017) SS BOND : bond 0.00446 / 0.34 ( 5) SS BOND : angle 1.51937 / 0.94 ( 10) hydrogen bonds : bond 0.03752 / 2.58 ( 378) hydrogen bonds : angle 4.80002 / 3.40 ( 1080) link_BETA1-4 : bond 0.00589 / 0.36 ( 4) link_BETA1-4 : angle 2.69299 / 1.49 ( 12) link_NAG-ASN : bond 0.00862 / 0.55 ( 4) link_NAG-ASN : angle 1.55428 / 0.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.9440 (mmm) cc_final: 0.8650 (mmm) REVERT: A 134 VAL cc_start: 0.8283 (t) cc_final: 0.7984 (p) REVERT: A 285 MET cc_start: 0.9271 (mmm) cc_final: 0.8983 (mmm) REVERT: A 428 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8881 (ttpp) REVERT: A 544 MET cc_start: 0.8772 (mmm) cc_final: 0.8451 (mmm) REVERT: D 33 MET cc_start: 0.9142 (mmm) cc_final: 0.8847 (mmm) REVERT: D 80 MET cc_start: 0.8422 (ttm) cc_final: 0.7101 (mtp) REVERT: D 81 GLU cc_start: 0.8073 (tp30) cc_final: 0.7804 (tp30) REVERT: D 179 MET cc_start: 0.8092 (tmm) cc_final: 0.7743 (tmm) REVERT: E 174 MET cc_start: 0.8236 (ttt) cc_final: 0.7978 (ttt) outliers start: 21 outliers final: 11 residues processed: 60 average time/residue: 0.0767 time to fit residues: 7.1442 Evaluate side-chains 49 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 170 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [101, 79, 68, 69, 47, 115, 21, 92, 106, 24, 3] chunk 101 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 92 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 HIS E 165 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.047963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.031304 restraints weight = 44363.045| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 5.56 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 9600 Z= 0.294 Angle : 0.694 7.407 13051 Z= 0.346 Chirality : 0.044 0.241 1488 Planarity : 0.004 0.048 1670 Dihedral : 8.393 69.254 1442 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.90 % Allowed : 15.06 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.25), residues: 1174 helix: 1.14 (0.40), residues: 167 sheet: 0.84 (0.24), residues: 490 loop : -0.98 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 187 TYR 0.019 0.002 TYR A 157 PHE 0.012 0.002 PHE A 453 TRP 0.006 0.001 TRP A 763 HIS 0.010 0.001 HIS E 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.29 ( 9587) covalent geometry : angle 0.68645 / 0.34 (13017) SS BOND : bond 0.00611 / 0.49 ( 5) SS BOND : angle 1.72868 / 1.06 ( 10) hydrogen bonds : bond 0.04341 / 3.00 ( 378) hydrogen bonds : angle 5.12958 / 3.63 ( 1080) link_BETA1-4 : bond 0.00488 / 0.29 ( 4) link_BETA1-4 : angle 2.61206 / 1.31 ( 12) link_NAG-ASN : bond 0.01325 / 0.84 ( 4) link_NAG-ASN : angle 1.85300 / 0.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 34 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 125 MET cc_start: 0.9320 (mmm) cc_final: 0.8591 (mmm) REVERT: A 271 MET cc_start: 0.9240 (mtt) cc_final: 0.9024 (mtm) REVERT: A 285 MET cc_start: 0.9377 (mmm) cc_final: 0.8957 (mmm) REVERT: A 428 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8826 (ttpp) REVERT: A 544 MET cc_start: 0.9025 (mmm) cc_final: 0.8667 (mmm) REVERT: A 699 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8511 (tt) REVERT: D 33 MET cc_start: 0.9016 (mmm) cc_final: 0.8210 (mmp) REVERT: D 179 MET cc_start: 0.8224 (tmm) cc_final: 0.7922 (tmm) REVERT: E 174 MET cc_start: 0.8230 (ttt) cc_final: 0.7991 (ttt) outliers start: 30 outliers final: 12 residues processed: 62 average time/residue: 0.0722 time to fit residues: 7.2206 Evaluate side-chains 46 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 170 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [63, 57, 91, 67, 47, 78, 3, 64, 101, 56, 96] chunk 63 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.048202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.031595 restraints weight = 44181.741| |-----------------------------------------------------------------------------| r_work (start): 0.2614 rms_B_bonded: 5.58 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9600 Z= 0.214 Angle : 0.613 8.075 13051 Z= 0.305 Chirality : 0.043 0.233 1488 Planarity : 0.004 0.046 1670 Dihedral : 7.849 58.859 1442 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.51 % Allowed : 16.22 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.25), residues: 1174 helix: 1.29 (0.41), residues: 167 sheet: 0.80 (0.24), residues: 492 loop : -0.95 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 210 TYR 0.015 0.002 TYR D 49 PHE 0.012 0.001 PHE E 73 TRP 0.006 0.001 TRP A 896 HIS 0.004 0.001 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 ( 9587) covalent geometry : angle 0.60539 / 0.30 (13017) SS BOND : bond 0.00550 / 0.44 ( 5) SS BOND : angle 1.54470 / 0.96 ( 10) hydrogen bonds : bond 0.03779 / 2.59 ( 378) hydrogen bonds : angle 4.96296 / 3.53 ( 1080) link_BETA1-4 : bond 0.00625 / 0.38 ( 4) link_BETA1-4 : angle 2.74057 / 1.43 ( 12) link_NAG-ASN : bond 0.00771 / 0.49 ( 4) link_NAG-ASN : angle 1.19358 / 0.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 33 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 47 ARG cc_start: 0.9444 (OUTLIER) cc_final: 0.8589 (mpt-90) REVERT: A 125 MET cc_start: 0.9297 (mmm) cc_final: 0.8553 (mmm) REVERT: A 285 MET cc_start: 0.9381 (mmm) cc_final: 0.8990 (mmm) REVERT: A 428 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8749 (ttpp) REVERT: A 544 MET cc_start: 0.9035 (mmm) cc_final: 0.8677 (mmm) REVERT: A 699 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8506 (tt) REVERT: D 33 MET cc_start: 0.9064 (mmm) cc_final: 0.8742 (mmm) REVERT: D 45 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8273 (tt0) REVERT: D 92 VAL cc_start: 0.7979 (OUTLIER) cc_final: 0.7698 (p) REVERT: D 179 MET cc_start: 0.8228 (tmm) cc_final: 0.7610 (tmm) REVERT: E 11 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8445 (mm) REVERT: E 174 MET cc_start: 0.8262 (ttt) cc_final: 0.7965 (ttt) outliers start: 26 outliers final: 16 residues processed: 58 average time/residue: 0.0793 time to fit residues: 7.3255 Evaluate side-chains 54 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 33 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 170 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [58, 70, 86, 110, 80, 24, 73, 68, 52, 69, 38] chunk 58 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.048279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.031879 restraints weight = 44192.807| |-----------------------------------------------------------------------------| r_work (start): 0.2604 rms_B_bonded: 5.55 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9600 Z= 0.210 Angle : 0.617 8.348 13051 Z= 0.304 Chirality : 0.043 0.188 1488 Planarity : 0.004 0.047 1670 Dihedral : 7.378 59.226 1442 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.70 % Allowed : 16.22 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.25), residues: 1174 helix: 1.38 (0.42), residues: 167 sheet: 0.74 (0.24), residues: 495 loop : -1.06 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 371 TYR 0.016 0.002 TYR D 49 PHE 0.011 0.001 PHE A 453 TRP 0.005 0.001 TRP A 896 HIS 0.005 0.001 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 ( 9587) covalent geometry : angle 0.60843 / 0.30 (13017) SS BOND : bond 0.00550 / 0.44 ( 5) SS BOND : angle 1.57271 / 1.02 ( 10) hydrogen bonds : bond 0.03779 / 2.60 ( 378) hydrogen bonds : angle 4.93998 / 3.52 ( 1080) link_BETA1-4 : bond 0.00537 / 0.33 ( 4) link_BETA1-4 : angle 2.95872 / 1.54 ( 12) link_NAG-ASN : bond 0.00827 / 0.52 ( 4) link_NAG-ASN : angle 1.16362 / 0.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 33 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.9305 (mmm) cc_final: 0.8547 (mmm) REVERT: A 285 MET cc_start: 0.9400 (mmm) cc_final: 0.9026 (mmm) REVERT: A 428 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8764 (ttpp) REVERT: A 544 MET cc_start: 0.9141 (mmm) cc_final: 0.8678 (mmm) REVERT: A 699 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8485 (tt) REVERT: D 33 MET cc_start: 0.9057 (mmm) cc_final: 0.8710 (mmm) REVERT: D 45 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8272 (tt0) REVERT: D 179 MET cc_start: 0.8303 (tmm) cc_final: 0.7689 (tmm) REVERT: E 11 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8488 (mm) REVERT: E 174 MET cc_start: 0.8318 (ttt) cc_final: 0.8010 (ttt) outliers start: 28 outliers final: 16 residues processed: 61 average time/residue: 0.0783 time to fit residues: 7.3056 Evaluate side-chains 50 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 31 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 170 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [95, 69, 103, 113, 6, 108, 56, 45, 16, 106, 72] chunk 95 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 106 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.048371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.031842 restraints weight = 43404.344| |-----------------------------------------------------------------------------| r_work (start): 0.2621 rms_B_bonded: 5.56 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9600 Z= 0.152 Angle : 0.590 8.765 13051 Z= 0.290 Chirality : 0.043 0.171 1488 Planarity : 0.004 0.048 1670 Dihedral : 7.064 57.930 1442 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.70 % Allowed : 16.70 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.25), residues: 1174 helix: 1.57 (0.42), residues: 167 sheet: 0.81 (0.24), residues: 495 loop : -1.00 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 210 TYR 0.016 0.001 TYR D 49 PHE 0.012 0.001 PHE E 73 TRP 0.006 0.001 TRP E 35 HIS 0.003 0.001 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 9587) covalent geometry : angle 0.58141 / 0.29 (13017) SS BOND : bond 0.00479 / 0.38 ( 5) SS BOND : angle 1.35180 / 0.85 ( 10) hydrogen bonds : bond 0.03428 / 2.36 ( 378) hydrogen bonds : angle 4.78505 / 3.41 ( 1080) link_BETA1-4 : bond 0.00681 / 0.42 ( 4) link_BETA1-4 : angle 3.08156 / 1.59 ( 12) link_NAG-ASN : bond 0.00408 / 0.27 ( 4) link_NAG-ASN : angle 0.98005 / 0.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 32 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.9309 (mmm) cc_final: 0.8524 (mmm) REVERT: A 285 MET cc_start: 0.9395 (mmm) cc_final: 0.9032 (mmm) REVERT: A 428 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8750 (ttpp) REVERT: A 544 MET cc_start: 0.9101 (mmm) cc_final: 0.8618 (mmm) REVERT: A 699 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8386 (tt) REVERT: D 33 MET cc_start: 0.9049 (mmm) cc_final: 0.8752 (mmm) REVERT: D 45 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8267 (tt0) REVERT: D 98 ASP cc_start: 0.8826 (t0) cc_final: 0.8389 (t0) REVERT: D 179 MET cc_start: 0.8244 (tmm) cc_final: 0.7579 (tmm) REVERT: E 11 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8628 (mm) REVERT: E 174 MET cc_start: 0.8308 (ttt) cc_final: 0.8012 (ttt) outliers start: 28 outliers final: 19 residues processed: 58 average time/residue: 0.0712 time to fit residues: 6.5968 Evaluate side-chains 54 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 32 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 170 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [65, 111, 20, 105, 54, 48, 12, 100, 95, 101, 62] chunk 65 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 101 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.048997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.032444 restraints weight = 43032.933| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 5.56 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9600 Z= 0.116 Angle : 0.571 9.254 13051 Z= 0.278 Chirality : 0.042 0.180 1488 Planarity : 0.004 0.048 1670 Dihedral : 6.667 58.467 1442 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.41 % Allowed : 16.70 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.25), residues: 1174 helix: 1.91 (0.43), residues: 161 sheet: 0.97 (0.24), residues: 494 loop : -0.87 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 775 TYR 0.015 0.001 TYR D 49 PHE 0.012 0.001 PHE E 73 TRP 0.005 0.001 TRP A 896 HIS 0.002 0.000 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 9587) covalent geometry : angle 0.56189 / 0.28 (13017) SS BOND : bond 0.00437 / 0.35 ( 5) SS BOND : angle 1.10870 / 0.71 ( 10) hydrogen bonds : bond 0.03103 / 2.18 ( 378) hydrogen bonds : angle 4.63126 / 3.30 ( 1080) link_BETA1-4 : bond 0.00768 / 0.47 ( 4) link_BETA1-4 : angle 3.24267 / 1.67 ( 12) link_NAG-ASN : bond 0.00226 / 0.15 ( 4) link_NAG-ASN : angle 0.98411 / 0.52 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 35 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 125 MET cc_start: 0.9297 (mmm) cc_final: 0.8488 (mmm) REVERT: A 169 VAL cc_start: 0.9410 (t) cc_final: 0.9070 (p) REVERT: A 203 THR cc_start: 0.7838 (OUTLIER) cc_final: 0.7637 (p) REVERT: A 285 MET cc_start: 0.9355 (mmm) cc_final: 0.8996 (mmm) REVERT: A 428 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8687 (ttpp) REVERT: A 544 MET cc_start: 0.9124 (mmm) cc_final: 0.8582 (mmm) REVERT: A 699 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8411 (tt) REVERT: D 33 MET cc_start: 0.9001 (mmm) cc_final: 0.8716 (mmm) REVERT: D 45 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8193 (tt0) REVERT: D 98 ASP cc_start: 0.8767 (t0) cc_final: 0.8323 (t0) REVERT: D 179 MET cc_start: 0.8215 (tmm) cc_final: 0.7544 (tmm) REVERT: E 11 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8593 (mm) REVERT: E 174 MET cc_start: 0.8337 (ttt) cc_final: 0.8058 (ttt) outliers start: 25 outliers final: 16 residues processed: 58 average time/residue: 0.0761 time to fit residues: 6.9958 Evaluate side-chains 52 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 32 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 170 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [106, 90, 10, 32, 38, 0, 21, 3, 97, 91, 33] chunk 106 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 0.0060 chunk 38 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.048317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.031495 restraints weight = 43116.175| |-----------------------------------------------------------------------------| r_work (start): 0.2521 rms_B_bonded: 5.53 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9600 Z= 0.163 Angle : 0.599 9.707 13051 Z= 0.292 Chirality : 0.043 0.182 1488 Planarity : 0.004 0.048 1670 Dihedral : 6.605 57.481 1442 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.22 % Allowed : 17.18 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.25), residues: 1174 helix: 1.73 (0.42), residues: 167 sheet: 0.94 (0.24), residues: 497 loop : -0.91 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 210 TYR 0.015 0.001 TYR D 49 PHE 0.011 0.001 PHE E 73 TRP 0.009 0.001 TRP D 190 HIS 0.003 0.001 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 9587) covalent geometry : angle 0.58993 / 0.29 (13017) SS BOND : bond 0.00428 / 0.34 ( 5) SS BOND : angle 1.42993 / 0.92 ( 10) hydrogen bonds : bond 0.03326 / 2.32 ( 378) hydrogen bonds : angle 4.66397 / 3.33 ( 1080) link_BETA1-4 : bond 0.00722 / 0.44 ( 4) link_BETA1-4 : angle 3.20634 / 1.66 ( 12) link_NAG-ASN : bond 0.00473 / 0.30 ( 4) link_NAG-ASN : angle 1.09960 / 0.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 32 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 125 MET cc_start: 0.9364 (mmm) cc_final: 0.8632 (mmm) REVERT: A 169 VAL cc_start: 0.9493 (t) cc_final: 0.9173 (p) REVERT: A 285 MET cc_start: 0.9428 (mmm) cc_final: 0.9202 (mmm) REVERT: A 428 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8792 (ttpp) REVERT: A 544 MET cc_start: 0.9208 (mmm) cc_final: 0.8741 (mmm) REVERT: A 699 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8555 (tt) REVERT: D 33 MET cc_start: 0.9090 (mmm) cc_final: 0.8807 (mmm) REVERT: D 45 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8370 (tt0) REVERT: D 98 ASP cc_start: 0.8990 (t0) cc_final: 0.8534 (t0) REVERT: D 179 MET cc_start: 0.8372 (tmm) cc_final: 0.7674 (tmm) REVERT: E 174 MET cc_start: 0.8415 (ttt) cc_final: 0.8082 (ttt) outliers start: 23 outliers final: 17 residues processed: 54 average time/residue: 0.0753 time to fit residues: 6.4511 Evaluate side-chains 51 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 32 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 170 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [115, 14, 26, 1, 15, 57, 105, 53, 103, 66, 45] chunk 115 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.0040 chunk 1 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 overall best weight: 2.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.048478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.031622 restraints weight = 42941.351| |-----------------------------------------------------------------------------| r_work (start): 0.2528 rms_B_bonded: 5.51 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9600 Z= 0.150 Angle : 0.602 9.859 13051 Z= 0.291 Chirality : 0.043 0.224 1488 Planarity : 0.004 0.047 1670 Dihedral : 6.485 57.867 1442 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.83 % Allowed : 17.57 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1174 helix: 1.75 (0.42), residues: 167 sheet: 0.97 (0.24), residues: 497 loop : -0.93 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 210 TYR 0.015 0.001 TYR D 49 PHE 0.012 0.001 PHE E 73 TRP 0.005 0.001 TRP A 896 HIS 0.003 0.001 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 9587) covalent geometry : angle 0.59194 / 0.29 (13017) SS BOND : bond 0.00409 / 0.33 ( 5) SS BOND : angle 1.36727 / 0.88 ( 10) hydrogen bonds : bond 0.03273 / 2.28 ( 378) hydrogen bonds : angle 4.63367 / 3.30 ( 1080) link_BETA1-4 : bond 0.00783 / 0.48 ( 4) link_BETA1-4 : angle 3.25485 / 1.68 ( 12) link_NAG-ASN : bond 0.00372 / 0.24 ( 4) link_NAG-ASN : angle 1.16538 / 0.62 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 33 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 125 MET cc_start: 0.9364 (mmm) cc_final: 0.8681 (mmm) REVERT: A 169 VAL cc_start: 0.9499 (t) cc_final: 0.9183 (p) REVERT: A 285 MET cc_start: 0.9429 (mmm) cc_final: 0.9205 (mmm) REVERT: A 428 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8800 (ttpp) REVERT: A 544 MET cc_start: 0.9248 (mmm) cc_final: 0.8779 (mmm) REVERT: A 699 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8532 (tt) REVERT: A 799 MET cc_start: 0.9026 (ttt) cc_final: 0.8263 (tmm) REVERT: D 33 MET cc_start: 0.9102 (mmm) cc_final: 0.8827 (mmm) REVERT: D 45 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8384 (tt0) REVERT: D 98 ASP cc_start: 0.9017 (t0) cc_final: 0.8603 (t0) REVERT: D 179 MET cc_start: 0.8395 (tmm) cc_final: 0.7690 (tmm) REVERT: E 3 GLN cc_start: 0.9538 (pt0) cc_final: 0.8980 (pm20) REVERT: E 174 MET cc_start: 0.8419 (ttt) cc_final: 0.8083 (ttt) outliers start: 19 outliers final: 16 residues processed: 51 average time/residue: 0.0811 time to fit residues: 6.5243 Evaluate side-chains 51 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 33 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 170 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [44, 90, 47, 103, 51, 26, 17, 31, 30, 68, 29] chunk 44 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.047644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.030786 restraints weight = 43228.267| |-----------------------------------------------------------------------------| r_work (start): 0.2501 rms_B_bonded: 5.48 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9600 Z= 0.214 Angle : 0.639 10.204 13051 Z= 0.310 Chirality : 0.043 0.202 1488 Planarity : 0.004 0.047 1670 Dihedral : 6.558 56.528 1442 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.93 % Allowed : 17.37 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.25), residues: 1174 helix: 1.71 (0.42), residues: 167 sheet: 0.82 (0.24), residues: 495 loop : -1.00 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 210 TYR 0.016 0.001 TYR D 49 PHE 0.012 0.001 PHE A 453 TRP 0.010 0.001 TRP E 35 HIS 0.005 0.001 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 ( 9587) covalent geometry : angle 0.62971 / 0.31 (13017) SS BOND : bond 0.00561 / 0.45 ( 5) SS BOND : angle 1.34319 / 0.84 ( 10) hydrogen bonds : bond 0.03746 / 2.61 ( 378) hydrogen bonds : angle 4.76890 / 3.40 ( 1080) link_BETA1-4 : bond 0.00700 / 0.43 ( 4) link_BETA1-4 : angle 3.18674 / 1.66 ( 12) link_NAG-ASN : bond 0.00708 / 0.45 ( 4) link_NAG-ASN : angle 1.49804 / 0.80 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1553.53 seconds wall clock time: 27 minutes 32.92 seconds (1652.92 seconds total)