Starting phenix.real_space_refine on Mon Dec 30 05:02:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ytp_34091/12_2024/7ytp_34091.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ytp_34091/12_2024/7ytp_34091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ytp_34091/12_2024/7ytp_34091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ytp_34091/12_2024/7ytp_34091.map" model { file = "/net/cci-nas-00/data/ceres_data/7ytp_34091/12_2024/7ytp_34091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ytp_34091/12_2024/7ytp_34091.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 56 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 7782 2.51 5 N 2044 2.21 5 O 2298 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12178 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5907 Classifications: {'peptide': 731} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 31, 'TRANS': 697} Chain breaks: 2 Chain: "B" Number of atoms: 5907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5907 Classifications: {'peptide': 731} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 31, 'TRANS': 697} Chain breaks: 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: "D" 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: "E" 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 Chain: "H" 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 98 Unusual residues: {'JRI': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 98 Unusual residues: {'JRI': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 7.64, per 1000 atoms: 0.63 Number of scatterers: 12178 At special positions: 0 Unit cell: (100.845, 130.725, 99.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 F 2 9.00 O 2298 8.00 N 2044 7.00 C 7782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 51 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS A 263 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 787 " - pdb=" SG CYS A 814 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 51 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 189 " distance=2.03 Simple disulfide: pdb=" SG CYS B 263 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 787 " - pdb=" SG CYS B 814 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1001 " - " ASN A 66 " " NAG A1002 " - " ASN A 590 " " NAG A1003 " - " ASN A 413 " " NAG A1004 " - " ASN A 361 " " NAG A1005 " - " ASN A 679 " " NAG B1001 " - " ASN B 66 " " NAG B1002 " - " ASN B 590 " " NAG B1003 " - " ASN B 413 " " NAG B1004 " - " ASN B 361 " " NAG B1005 " - " ASN B 679 " " NAG C 1 " - " ASN A 215 " " NAG D 1 " - " ASN A 523 " " NAG E 1 " - " ASN A 69 " " NAG F 1 " - " ASN B 215 " " NAG G 1 " - " ASN B 523 " " NAG H 1 " - " ASN B 69 " Time building additional restraints: 3.47 Conformation dependent library (CDL) restraints added in 1.6 seconds 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2836 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 13 sheets defined 16.7% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 273 through 277 removed outlier: 3.501A pdb=" N ASN A 276 " --> pdb=" O CYS A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.734A pdb=" N GLY A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.510A pdb=" N LEU A 369 " --> pdb=" O PHE A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 396 removed outlier: 3.611A pdb=" N LEU A 390 " --> pdb=" O SER A 387 " (cutoff:3.500A) Proline residue: A 392 - end of helix removed outlier: 4.197A pdb=" N ASN A 395 " --> pdb=" O PRO A 392 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 396 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 3.870A pdb=" N GLN A 419 " --> pdb=" O MET A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 494 removed outlier: 4.028A pdb=" N LYS A 493 " --> pdb=" O SER A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 582 removed outlier: 4.082A pdb=" N PHE A 580 " --> pdb=" O ASN A 576 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 582 " --> pdb=" O HIS A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 593 removed outlier: 3.744A pdb=" N PHE A 591 " --> pdb=" O MET A 588 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR A 592 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A 593 " --> pdb=" O ASN A 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 588 through 593' Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.968A pdb=" N LEU A 634 " --> pdb=" O HIS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 692 through 698 removed outlier: 3.816A pdb=" N ARG A 696 " --> pdb=" O GLU A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 722 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 788 through 790 No H-bonds generated for 'chain 'A' and resid 788 through 790' Processing helix chain 'A' and resid 791 through 799 removed outlier: 3.699A pdb=" N GLN A 799 " --> pdb=" O VAL A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 removed outlier: 3.511A pdb=" N HIS A 820 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 273 through 277 removed outlier: 3.635A pdb=" N ASN B 276 " --> pdb=" O CYS B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.728A pdb=" N GLY B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 Processing helix chain 'B' and resid 363 through 369 removed outlier: 3.545A pdb=" N LEU B 369 " --> pdb=" O PHE B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 396 removed outlier: 3.678A pdb=" N LEU B 390 " --> pdb=" O SER B 387 " (cutoff:3.500A) Proline residue: B 392 - end of helix removed outlier: 4.166A pdb=" N ASN B 395 " --> pdb=" O PRO B 392 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 396 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 removed outlier: 3.842A pdb=" N GLN B 419 " --> pdb=" O MET B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 removed outlier: 4.180A pdb=" N LYS B 493 " --> pdb=" O SER B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 582 removed outlier: 4.128A pdb=" N PHE B 580 " --> pdb=" O ASN B 576 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 582 " --> pdb=" O HIS B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 593 removed outlier: 3.749A pdb=" N PHE B 591 " --> pdb=" O MET B 588 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR B 592 " --> pdb=" O LEU B 589 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 593 " --> pdb=" O ASN B 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 588 through 593' Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.960A pdb=" N LEU B 634 " --> pdb=" O HIS B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 673 removed outlier: 3.730A pdb=" N MET B 673 " --> pdb=" O PHE B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 698 removed outlier: 3.766A pdb=" N ARG B 696 " --> pdb=" O GLU B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 722 Processing helix chain 'B' and resid 768 through 773 Processing helix chain 'B' and resid 788 through 790 No H-bonds generated for 'chain 'B' and resid 788 through 790' Processing helix chain 'B' and resid 791 through 799 removed outlier: 3.705A pdb=" N GLN B 799 " --> pdb=" O VAL B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 821 removed outlier: 3.508A pdb=" N HIS B 820 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 41 removed outlier: 6.592A pdb=" N LEU A 70 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE A 94 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU A 132 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU A 153 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU A 177 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU A 209 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A 319 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU A 345 " --> pdb=" O ARG A 376 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 375 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU A 402 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU A 498 " --> pdb=" O ASN A 523 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A 522 " --> pdb=" O ASP A 548 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 547 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A 571 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU A 601 " --> pdb=" O GLU A 625 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU A 680 " --> pdb=" O ASP A 705 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 163 Processing sheet with id=AA4, first strand: chain 'A' and resid 384 through 385 Processing sheet with id=AA5, first strand: chain 'A' and resid 530 through 532 removed outlier: 6.905A pdb=" N GLN A 531 " --> pdb=" O ASP A 555 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 751 through 753 Processing sheet with id=AA7, first strand: chain 'B' and resid 37 through 41 removed outlier: 6.710A pdb=" N LEU B 70 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE B 94 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU B 132 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU B 153 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU B 209 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU B 230 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU B 319 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU B 345 " --> pdb=" O ARG B 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 79 through 80 Processing sheet with id=AA9, first strand: chain 'B' and resid 162 through 163 Processing sheet with id=AB1, first strand: chain 'B' and resid 384 through 385 Processing sheet with id=AB2, first strand: chain 'B' and resid 401 through 403 removed outlier: 7.018A pdb=" N LEU B 498 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 522 " --> pdb=" O ASP B 548 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU B 547 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU B 571 " --> pdb=" O MET B 602 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 601 " --> pdb=" O GLU B 625 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU B 680 " --> pdb=" O ASP B 705 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 530 through 532 Processing sheet with id=AB4, first strand: chain 'B' and resid 751 through 753 125 hydrogen bonds defined for protein. 240 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: 4.09 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1960 1.28 - 1.42: 2937 1.42 - 1.55: 7453 1.55 - 1.68: 2 1.68 - 1.82: 72 Bond restraints: 12424 Sorted by residual: bond pdb=" C1 NAG A1005 " pdb=" O5 NAG A1005 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.68e+00 bond pdb=" CB PRO B 148 " pdb=" CG PRO B 148 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.70e+00 bond pdb=" CG PRO B 148 " pdb=" CD PRO B 148 " ideal model delta sigma weight residual 1.503 1.437 0.066 3.40e-02 8.65e+02 3.75e+00 bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.91e+00 bond pdb=" C1 NAG A1001 " pdb=" O5 NAG A1001 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.76e+00 ... (remaining 12419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 16368 1.56 - 3.11: 400 3.11 - 4.67: 51 4.67 - 6.22: 14 6.22 - 7.78: 5 Bond angle restraints: 16838 Sorted by residual: angle pdb=" N PRO B 148 " pdb=" CD PRO B 148 " pdb=" CG PRO B 148 " ideal model delta sigma weight residual 103.20 96.59 6.61 1.50e+00 4.44e-01 1.94e+01 angle pdb=" CA PRO B 148 " pdb=" N PRO B 148 " pdb=" CD PRO B 148 " ideal model delta sigma weight residual 112.00 106.05 5.95 1.40e+00 5.10e-01 1.81e+01 angle pdb=" N GLY A 686 " pdb=" CA GLY A 686 " pdb=" C GLY A 686 " ideal model delta sigma weight residual 116.01 109.88 6.13 1.64e+00 3.72e-01 1.40e+01 angle pdb=" C SER B 429 " pdb=" N VAL B 430 " pdb=" CA VAL B 430 " ideal model delta sigma weight residual 121.97 128.07 -6.10 1.80e+00 3.09e-01 1.15e+01 angle pdb=" CA GLY A 686 " pdb=" C GLY A 686 " pdb=" N LEU A 687 " ideal model delta sigma weight residual 118.67 115.38 3.29 9.80e-01 1.04e+00 1.13e+01 ... (remaining 16833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 7243 17.80 - 35.61: 534 35.61 - 53.41: 95 53.41 - 71.21: 34 71.21 - 89.02: 10 Dihedral angle restraints: 7916 sinusoidal: 3582 harmonic: 4334 Sorted by residual: dihedral pdb=" CB CYS B 263 " pdb=" SG CYS B 263 " pdb=" SG CYS B 270 " pdb=" CB CYS B 270 " ideal model delta sinusoidal sigma weight residual -86.00 -175.02 89.02 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS A 263 " pdb=" SG CYS A 263 " pdb=" SG CYS A 270 " pdb=" CB CYS A 270 " ideal model delta sinusoidal sigma weight residual -86.00 -173.93 87.93 1 1.00e+01 1.00e-02 9.25e+01 dihedral pdb=" CB CYS A 491 " pdb=" SG CYS A 491 " pdb=" SG CYS A 521 " pdb=" CB CYS A 521 " ideal model delta sinusoidal sigma weight residual 93.00 37.04 55.96 1 1.00e+01 1.00e-02 4.23e+01 ... (remaining 7913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1717 0.060 - 0.120: 266 0.120 - 0.180: 24 0.180 - 0.240: 1 0.240 - 0.301: 2 Chirality restraints: 2010 Sorted by residual: chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 66 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 66 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 69 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2007 not shown) Planarity restraints: 2122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 JRI B1006 " 0.130 2.00e-02 2.50e+03 1.08e-01 1.46e+02 pdb=" C5 JRI B1006 " 0.102 2.00e-02 2.50e+03 pdb=" C9 JRI B1006 " -0.048 2.00e-02 2.50e+03 pdb=" N2 JRI B1006 " -0.168 2.00e-02 2.50e+03 pdb=" O2 JRI B1006 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 JRI A1006 " -0.123 2.00e-02 2.50e+03 1.02e-01 1.29e+02 pdb=" C5 JRI A1006 " -0.096 2.00e-02 2.50e+03 pdb=" C9 JRI A1006 " 0.046 2.00e-02 2.50e+03 pdb=" N2 JRI A1006 " 0.158 2.00e-02 2.50e+03 pdb=" O2 JRI A1006 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 147 " -0.075 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO B 148 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO B 148 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 148 " -0.059 5.00e-02 4.00e+02 ... (remaining 2119 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 430 2.72 - 3.27: 12223 3.27 - 3.81: 19471 3.81 - 4.36: 26440 4.36 - 4.90: 43062 Nonbonded interactions: 101626 Sorted by model distance: nonbonded pdb=" OE1 GLU A 93 " pdb=" OG SER A 131 " model vdw 2.179 3.040 nonbonded pdb=" O SER B 429 " pdb=" N ASN B 431 " model vdw 2.199 3.120 nonbonded pdb=" OG1 THR B 290 " pdb=" OE1 GLU B 291 " model vdw 2.223 3.040 nonbonded pdb=" O LEU A 223 " pdb=" ND2 ASN A 247 " model vdw 2.237 3.120 nonbonded pdb=" N LEU A 72 " pdb=" O ASP A 95 " model vdw 2.244 3.120 ... (remaining 101621 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.410 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 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:11.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 : 0.003 0.119 12424 Z= 0.194 Angle : 0.598 7.776 16838 Z= 0.307 Chirality : 0.045 0.301 2010 Planarity : 0.005 0.110 2106 Dihedral : 13.078 87.343 5050 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.76 % Favored : 94.97 % Rotamer: Outliers : 0.15 % Allowed : 0.15 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.23), residues: 1450 helix: -2.84 (0.40), residues: 126 sheet: -2.11 (0.35), residues: 282 loop : -0.35 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 692 HIS 0.004 0.000 HIS B 46 PHE 0.019 0.001 PHE A 690 TYR 0.012 0.001 TYR A 184 ARG 0.003 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 180 time to evaluate : 1.306 Fit side-chains REVERT: A 141 GLU cc_start: 0.6521 (mt-10) cc_final: 0.6111 (mm-30) REVERT: A 395 ASN cc_start: 0.6825 (m-40) cc_final: 0.6395 (p0) REVERT: A 734 GLN cc_start: 0.6108 (tt0) cc_final: 0.5905 (mt0) REVERT: B 537 GLU cc_start: 0.7648 (mp0) cc_final: 0.7396 (mp0) outliers start: 2 outliers final: 0 residues processed: 180 average time/residue: 1.1372 time to fit residues: 224.7271 Evaluate side-chains 133 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 132 optimal weight: 0.3980 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 187 ASN A 202 ASN A 534 ASN A 820 HIS B 265 ASN B 337 HIS B 344 GLN B 354 GLN B 515 HIS B 534 ASN B 708 HIS B 709 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 12424 Z= 0.331 Angle : 0.748 9.159 16838 Z= 0.372 Chirality : 0.052 0.373 2010 Planarity : 0.005 0.056 2106 Dihedral : 7.230 59.900 2080 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.69 % Favored : 92.90 % Rotamer: Outliers : 1.96 % Allowed : 9.72 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.23), residues: 1450 helix: -3.17 (0.31), residues: 162 sheet: -2.28 (0.34), residues: 272 loop : -0.40 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 692 HIS 0.004 0.001 HIS A 90 PHE 0.029 0.003 PHE A 408 TYR 0.044 0.003 TYR B 356 ARG 0.009 0.001 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 1.482 Fit side-chains REVERT: A 151 GLN cc_start: 0.7415 (mt0) cc_final: 0.7017 (tt0) REVERT: A 243 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6606 (p0) REVERT: A 395 ASN cc_start: 0.6943 (m-40) cc_final: 0.6456 (p0) REVERT: A 751 TYR cc_start: 0.7334 (t80) cc_final: 0.7001 (t80) REVERT: A 820 HIS cc_start: 0.1516 (OUTLIER) cc_final: 0.0764 (m170) REVERT: B 141 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7292 (mt-10) REVERT: B 378 ARG cc_start: 0.7580 (mtp85) cc_final: 0.7008 (mtp85) REVERT: B 422 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.5998 (ptt180) REVERT: B 537 GLU cc_start: 0.8065 (mp0) cc_final: 0.7701 (mp0) REVERT: B 699 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7763 (mtmm) REVERT: B 752 LEU cc_start: 0.7764 (tp) cc_final: 0.7312 (mt) REVERT: B 777 MET cc_start: 0.6030 (tpt) cc_final: 0.5780 (tpt) outliers start: 27 outliers final: 5 residues processed: 156 average time/residue: 1.1270 time to fit residues: 193.7521 Evaluate side-chains 132 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 699 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 ASN A 241 GLN A 534 ASN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS B 246 ASN B 276 ASN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12424 Z= 0.270 Angle : 0.630 9.555 16838 Z= 0.317 Chirality : 0.048 0.310 2010 Planarity : 0.004 0.051 2106 Dihedral : 6.545 58.251 2080 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.93 % Favored : 93.72 % Rotamer: Outliers : 2.10 % Allowed : 12.41 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.23), residues: 1450 helix: -3.09 (0.33), residues: 162 sheet: -2.24 (0.33), residues: 272 loop : -0.37 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 793 HIS 0.030 0.002 HIS A 820 PHE 0.019 0.002 PHE B 382 TYR 0.023 0.002 TYR B 356 ARG 0.004 0.001 ARG B 750 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.367 Fit side-chains revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6636 (p0) REVERT: A 395 ASN cc_start: 0.7108 (m-40) cc_final: 0.6628 (p0) REVERT: A 734 GLN cc_start: 0.6436 (mt0) cc_final: 0.5917 (mp-120) REVERT: A 778 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6062 (tp) REVERT: B 378 ARG cc_start: 0.7644 (mtp85) cc_final: 0.7066 (mtm180) REVERT: B 537 GLU cc_start: 0.7962 (mp0) cc_final: 0.7682 (mp0) outliers start: 29 outliers final: 9 residues processed: 147 average time/residue: 1.0887 time to fit residues: 176.9075 Evaluate side-chains 128 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 187 ASN A 202 ASN A 534 ASN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN B 534 ASN ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 820 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 12424 Z= 0.381 Angle : 0.735 10.006 16838 Z= 0.369 Chirality : 0.052 0.314 2010 Planarity : 0.005 0.051 2106 Dihedral : 7.072 58.635 2080 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.76 % Favored : 92.83 % Rotamer: Outliers : 3.48 % Allowed : 13.57 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.22), residues: 1450 helix: -3.23 (0.33), residues: 150 sheet: -2.23 (0.32), residues: 272 loop : -0.48 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 793 HIS 0.011 0.002 HIS A 820 PHE 0.028 0.003 PHE B 690 TYR 0.029 0.003 TYR B 356 ARG 0.006 0.001 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 127 time to evaluate : 1.491 Fit side-chains revert: symmetry clash REVERT: A 167 GLN cc_start: 0.6610 (OUTLIER) cc_final: 0.6369 (mm110) REVERT: A 243 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6707 (p0) REVERT: A 377 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7587 (mt) REVERT: A 422 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.6008 (ptt180) REVERT: A 551 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.8117 (m-40) REVERT: A 654 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7504 (tt0) REVERT: A 665 LEU cc_start: 0.7834 (mt) cc_final: 0.7616 (mp) REVERT: A 734 GLN cc_start: 0.6596 (mt0) cc_final: 0.6091 (mp-120) REVERT: B 94 ILE cc_start: 0.7212 (OUTLIER) cc_final: 0.6840 (mt) REVERT: B 141 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: B 223 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7935 (mm) REVERT: B 378 ARG cc_start: 0.7692 (mtp85) cc_final: 0.6780 (mtp180) REVERT: B 537 GLU cc_start: 0.8033 (mp0) cc_final: 0.7713 (mp0) REVERT: B 603 MET cc_start: 0.8755 (mtp) cc_final: 0.8481 (mtp) outliers start: 48 outliers final: 14 residues processed: 156 average time/residue: 1.1223 time to fit residues: 192.7381 Evaluate side-chains 141 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 300 ASN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 HIS B 167 GLN B 265 ASN B 276 ASN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12424 Z= 0.299 Angle : 0.653 9.825 16838 Z= 0.329 Chirality : 0.049 0.308 2010 Planarity : 0.004 0.050 2106 Dihedral : 6.775 59.906 2080 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.00 % Favored : 93.66 % Rotamer: Outliers : 2.76 % Allowed : 15.38 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.22), residues: 1450 helix: -3.21 (0.33), residues: 150 sheet: -2.13 (0.33), residues: 268 loop : -0.51 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 793 HIS 0.006 0.001 HIS B 708 PHE 0.024 0.002 PHE B 690 TYR 0.015 0.002 TYR A 233 ARG 0.003 0.001 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 GLN cc_start: 0.6608 (OUTLIER) cc_final: 0.6341 (mm110) REVERT: A 243 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6695 (p0) REVERT: A 275 ASN cc_start: 0.7369 (m-40) cc_final: 0.6938 (m-40) REVERT: A 551 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.8086 (m-40) REVERT: A 654 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: A 665 LEU cc_start: 0.7837 (mt) cc_final: 0.7621 (mp) REVERT: A 734 GLN cc_start: 0.6728 (mt0) cc_final: 0.6096 (mp-120) REVERT: B 130 LYS cc_start: 0.7489 (tppp) cc_final: 0.7022 (tppp) REVERT: B 141 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7441 (mt-10) REVERT: B 151 GLN cc_start: 0.6873 (mt0) cc_final: 0.6158 (mt0) REVERT: B 243 ASP cc_start: 0.6760 (OUTLIER) cc_final: 0.6402 (m-30) REVERT: B 378 ARG cc_start: 0.7661 (mtp85) cc_final: 0.6757 (mtp180) REVERT: B 537 GLU cc_start: 0.8034 (mp0) cc_final: 0.7688 (mp0) REVERT: B 603 MET cc_start: 0.8740 (mtp) cc_final: 0.8466 (mtp) outliers start: 38 outliers final: 16 residues processed: 149 average time/residue: 1.0541 time to fit residues: 175.2753 Evaluate side-chains 146 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 141 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 HIS A 820 HIS B 55 HIS B 151 GLN B 276 ASN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12424 Z= 0.319 Angle : 0.668 9.906 16838 Z= 0.337 Chirality : 0.050 0.361 2010 Planarity : 0.004 0.050 2106 Dihedral : 6.764 59.647 2080 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.69 % Favored : 92.90 % Rotamer: Outliers : 3.63 % Allowed : 15.60 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.22), residues: 1450 helix: -2.96 (0.36), residues: 132 sheet: -2.08 (0.33), residues: 268 loop : -0.51 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 793 HIS 0.020 0.001 HIS A 820 PHE 0.023 0.002 PHE B 690 TYR 0.015 0.002 TYR A 233 ARG 0.004 0.001 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 124 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 GLN cc_start: 0.6660 (OUTLIER) cc_final: 0.6402 (mm110) REVERT: A 243 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6704 (p0) REVERT: A 275 ASN cc_start: 0.7285 (m-40) cc_final: 0.6870 (m-40) REVERT: A 377 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7577 (mt) REVERT: A 422 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.5966 (ptt180) REVERT: A 551 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.8099 (m-40) REVERT: A 665 LEU cc_start: 0.7847 (mt) cc_final: 0.7633 (mp) REVERT: A 734 GLN cc_start: 0.6759 (mt0) cc_final: 0.6109 (mp-120) REVERT: A 778 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6225 (tt) REVERT: B 141 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7448 (mt-10) REVERT: B 223 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8054 (mm) REVERT: B 243 ASP cc_start: 0.6797 (OUTLIER) cc_final: 0.6441 (m-30) REVERT: B 378 ARG cc_start: 0.7693 (mtp85) cc_final: 0.6786 (mtp180) REVERT: B 603 MET cc_start: 0.8767 (mtp) cc_final: 0.8511 (mtp) REVERT: B 676 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7309 (t0) REVERT: B 734 GLN cc_start: 0.6320 (mt0) cc_final: 0.5771 (mp-120) outliers start: 50 outliers final: 19 residues processed: 157 average time/residue: 1.0477 time to fit residues: 182.5500 Evaluate side-chains 149 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 HIS B 55 HIS ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12424 Z= 0.198 Angle : 0.600 9.851 16838 Z= 0.304 Chirality : 0.047 0.309 2010 Planarity : 0.004 0.049 2106 Dihedral : 6.362 58.319 2080 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.14 % Favored : 93.59 % Rotamer: Outliers : 3.05 % Allowed : 16.98 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.22), residues: 1450 helix: -2.59 (0.40), residues: 120 sheet: -2.06 (0.33), residues: 268 loop : -0.46 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 793 HIS 0.012 0.001 HIS A 820 PHE 0.022 0.002 PHE B 690 TYR 0.013 0.002 TYR A 233 ARG 0.003 0.000 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: A 167 GLN cc_start: 0.6658 (OUTLIER) cc_final: 0.6382 (mm110) REVERT: A 243 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6698 (p0) REVERT: A 275 ASN cc_start: 0.7363 (m-40) cc_final: 0.6973 (m-40) REVERT: A 422 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.6039 (ptt180) REVERT: A 551 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7949 (m-40) REVERT: A 654 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: A 734 GLN cc_start: 0.6678 (mt0) cc_final: 0.6024 (mp-120) REVERT: B 130 LYS cc_start: 0.7250 (tppp) cc_final: 0.6948 (tppp) REVERT: B 141 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7362 (mt-10) REVERT: B 151 GLN cc_start: 0.6824 (mt0) cc_final: 0.6030 (mt0) REVERT: B 243 ASP cc_start: 0.6776 (OUTLIER) cc_final: 0.6432 (m-30) REVERT: B 378 ARG cc_start: 0.7580 (mtp85) cc_final: 0.6697 (mtp180) REVERT: B 603 MET cc_start: 0.8760 (mtp) cc_final: 0.8463 (mtp) REVERT: B 710 GLN cc_start: 0.6779 (tt0) cc_final: 0.6541 (tt0) REVERT: B 734 GLN cc_start: 0.6416 (mt0) cc_final: 0.5765 (mp10) outliers start: 42 outliers final: 20 residues processed: 157 average time/residue: 1.0604 time to fit residues: 184.0124 Evaluate side-chains 152 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 HIS A 823 GLN B 151 GLN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12424 Z= 0.249 Angle : 0.625 9.749 16838 Z= 0.316 Chirality : 0.048 0.308 2010 Planarity : 0.004 0.050 2106 Dihedral : 6.427 59.003 2080 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.48 % Favored : 93.17 % Rotamer: Outliers : 2.98 % Allowed : 17.13 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.22), residues: 1450 helix: -2.52 (0.43), residues: 108 sheet: -2.04 (0.33), residues: 268 loop : -0.45 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 793 HIS 0.013 0.001 HIS A 820 PHE 0.022 0.002 PHE B 690 TYR 0.014 0.002 TYR A 233 ARG 0.003 0.000 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: A 167 GLN cc_start: 0.6662 (OUTLIER) cc_final: 0.6420 (mm110) REVERT: A 243 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6698 (p0) REVERT: A 275 ASN cc_start: 0.7357 (m-40) cc_final: 0.6966 (m-40) REVERT: A 422 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.6039 (ptt180) REVERT: A 551 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7969 (m-40) REVERT: A 654 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7497 (tt0) REVERT: A 710 GLN cc_start: 0.7175 (tt0) cc_final: 0.6728 (tt0) REVERT: A 734 GLN cc_start: 0.6712 (mt0) cc_final: 0.6048 (mp-120) REVERT: A 778 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6356 (tt) REVERT: B 130 LYS cc_start: 0.7264 (tppp) cc_final: 0.6960 (tppp) REVERT: B 141 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7389 (mt-10) REVERT: B 151 GLN cc_start: 0.6991 (mt0) cc_final: 0.6434 (mt0) REVERT: B 243 ASP cc_start: 0.6772 (OUTLIER) cc_final: 0.6421 (m-30) REVERT: B 378 ARG cc_start: 0.7617 (mtp85) cc_final: 0.6736 (mtp180) REVERT: B 603 MET cc_start: 0.8788 (mtp) cc_final: 0.8525 (mtp) REVERT: B 710 GLN cc_start: 0.6735 (tt0) cc_final: 0.6498 (tt0) REVERT: B 734 GLN cc_start: 0.6432 (mt0) cc_final: 0.5792 (mp-120) REVERT: B 777 MET cc_start: 0.6504 (OUTLIER) cc_final: 0.5932 (tpt) REVERT: B 782 HIS cc_start: 0.5518 (m90) cc_final: 0.5176 (m90) outliers start: 41 outliers final: 22 residues processed: 147 average time/residue: 1.0886 time to fit residues: 176.6138 Evaluate side-chains 154 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 777 MET Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 78 optimal weight: 0.0470 chunk 57 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 40 optimal weight: 0.0770 chunk 118 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 HIS A 823 GLN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12424 Z= 0.176 Angle : 0.591 9.862 16838 Z= 0.299 Chirality : 0.048 0.413 2010 Planarity : 0.004 0.049 2106 Dihedral : 6.192 57.704 2080 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.00 % Favored : 93.72 % Rotamer: Outliers : 2.54 % Allowed : 17.56 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.22), residues: 1450 helix: -2.40 (0.44), residues: 108 sheet: -2.02 (0.33), residues: 268 loop : -0.39 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 793 HIS 0.015 0.001 HIS A 820 PHE 0.022 0.002 PHE B 690 TYR 0.012 0.002 TYR A 233 ARG 0.002 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 1.460 Fit side-chains revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7315 (mt-10) REVERT: A 167 GLN cc_start: 0.6734 (OUTLIER) cc_final: 0.6509 (mm110) REVERT: A 175 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7451 (mm-30) REVERT: A 243 ASP cc_start: 0.7163 (OUTLIER) cc_final: 0.6698 (p0) REVERT: A 275 ASN cc_start: 0.7274 (m-40) cc_final: 0.6935 (m-40) REVERT: A 422 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.6096 (ptt180) REVERT: A 551 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7932 (m-40) REVERT: A 710 GLN cc_start: 0.7129 (tt0) cc_final: 0.6702 (tt0) REVERT: A 734 GLN cc_start: 0.6664 (mt0) cc_final: 0.6028 (mp-120) REVERT: B 130 LYS cc_start: 0.7414 (tppp) cc_final: 0.7021 (tppp) REVERT: B 141 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7369 (mt-10) REVERT: B 151 GLN cc_start: 0.6963 (mt0) cc_final: 0.6422 (mt0) REVERT: B 243 ASP cc_start: 0.6736 (OUTLIER) cc_final: 0.6405 (m-30) REVERT: B 603 MET cc_start: 0.8784 (mtp) cc_final: 0.8515 (mtp) REVERT: B 710 GLN cc_start: 0.6711 (tt0) cc_final: 0.6481 (tt0) REVERT: B 734 GLN cc_start: 0.6385 (mt0) cc_final: 0.5762 (mp-120) REVERT: B 777 MET cc_start: 0.6317 (OUTLIER) cc_final: 0.5769 (tpt) REVERT: B 782 HIS cc_start: 0.5473 (m90) cc_final: 0.5175 (m90) outliers start: 35 outliers final: 15 residues processed: 146 average time/residue: 1.1417 time to fit residues: 184.4884 Evaluate side-chains 145 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 777 MET Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 96 optimal weight: 0.0470 chunk 145 optimal weight: 0.0470 chunk 133 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 overall best weight: 2.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 HIS B 300 ASN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12424 Z= 0.250 Angle : 0.624 9.702 16838 Z= 0.314 Chirality : 0.048 0.306 2010 Planarity : 0.004 0.049 2106 Dihedral : 6.308 58.781 2080 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.41 % Favored : 93.24 % Rotamer: Outliers : 2.03 % Allowed : 18.29 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.22), residues: 1450 helix: -2.41 (0.44), residues: 108 sheet: -1.99 (0.33), residues: 268 loop : -0.40 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 793 HIS 0.014 0.001 HIS A 820 PHE 0.023 0.002 PHE A 690 TYR 0.013 0.002 TYR A 233 ARG 0.002 0.000 ARG B 376 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 1.546 Fit side-chains revert: symmetry clash REVERT: A 167 GLN cc_start: 0.6789 (OUTLIER) cc_final: 0.6552 (mm110) REVERT: A 243 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6702 (p0) REVERT: A 275 ASN cc_start: 0.7286 (m-40) cc_final: 0.6978 (m-40) REVERT: A 422 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.6042 (ptt180) REVERT: A 551 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7964 (m-40) REVERT: A 710 GLN cc_start: 0.7105 (tt0) cc_final: 0.6661 (tt0) REVERT: A 734 GLN cc_start: 0.6848 (mt0) cc_final: 0.6127 (mp-120) REVERT: B 130 LYS cc_start: 0.7413 (tppp) cc_final: 0.7015 (tppp) REVERT: B 141 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: B 151 GLN cc_start: 0.7002 (mt0) cc_final: 0.6447 (mt0) REVERT: B 275 ASN cc_start: 0.7477 (m-40) cc_final: 0.7124 (m-40) REVERT: B 603 MET cc_start: 0.8779 (mtp) cc_final: 0.8529 (mtp) REVERT: B 710 GLN cc_start: 0.6828 (tt0) cc_final: 0.6608 (tt0) REVERT: B 734 GLN cc_start: 0.6455 (mt0) cc_final: 0.5801 (mp-120) REVERT: B 782 HIS cc_start: 0.5371 (m90) cc_final: 0.5113 (m90) outliers start: 28 outliers final: 19 residues processed: 141 average time/residue: 1.0888 time to fit residues: 169.8731 Evaluate side-chains 146 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 116 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 HIS ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 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 = 0.4133 r_free = 0.4133 target = 0.192043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.131441 restraints weight = 12718.486| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.60 r_work: 0.3210 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12424 Z= 0.193 Angle : 0.595 9.608 16838 Z= 0.300 Chirality : 0.047 0.305 2010 Planarity : 0.004 0.049 2106 Dihedral : 6.155 58.029 2080 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.14 % Favored : 93.59 % Rotamer: Outliers : 1.96 % Allowed : 18.43 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.22), residues: 1450 helix: -2.44 (0.41), residues: 120 sheet: -1.96 (0.33), residues: 268 loop : -0.36 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 793 HIS 0.005 0.001 HIS A 820 PHE 0.025 0.002 PHE A 690 TYR 0.012 0.002 TYR B 233 ARG 0.002 0.000 ARG B 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3778.78 seconds wall clock time: 68 minutes 51.20 seconds (4131.20 seconds total)