Starting phenix.real_space_refine on Wed Jul 30 10:30:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ytp_34091/07_2025/7ytp_34091.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ytp_34091/07_2025/7ytp_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_34091/07_2025/7ytp_34091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ytp_34091/07_2025/7ytp_34091.map" model { file = "/net/cci-nas-00/data/ceres_data/7ytp_34091/07_2025/7ytp_34091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ytp_34091/07_2025/7ytp_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-5711/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: 10.42, per 1000 atoms: 0.86 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: 3.36 Conformation dependent library (CDL) restraints added in 2.8 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: 1.90 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: 6.57 Time building geometry restraints manager: 3.95 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: 0.01 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: 65.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 39.110 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.150 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: 0.010 Load rotamer database and sin/cos tables:141.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 247.410 ------------------------------------------------------------------------------- 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 12456 Z= 0.160 Angle : 0.644 21.042 16924 Z= 0.317 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00899 ( 16) link_NAG-ASN : angle 4.48455 ( 48) link_BETA1-4 : bond 0.00361 ( 6) link_BETA1-4 : angle 1.07327 ( 18) hydrogen bonds : bond 0.31707 ( 125) hydrogen bonds : angle 7.99614 ( 240) SS BOND : bond 0.00134 ( 10) SS BOND : angle 0.74216 ( 20) covalent geometry : bond 0.00326 (12424) covalent geometry : angle 0.59824 (16838) *********************** 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 : 1.608 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: 1.4537 time to fit residues: 288.2548 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 : 1.688 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.201855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.159450 restraints weight = 12464.780| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.50 r_work: 0.3384 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 12456 Z= 0.222 Angle : 0.786 17.951 16924 Z= 0.381 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00730 ( 16) link_NAG-ASN : angle 4.55863 ( 48) link_BETA1-4 : bond 0.00993 ( 6) link_BETA1-4 : angle 1.18094 ( 18) hydrogen bonds : bond 0.04765 ( 125) hydrogen bonds : angle 6.29976 ( 240) SS BOND : bond 0.01001 ( 10) SS BOND : angle 1.18520 ( 20) covalent geometry : bond 0.00509 (12424) covalent geometry : angle 0.74777 (16838) *********************** 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 : 1.545 Fit side-chains REVERT: A 151 GLN cc_start: 0.7399 (mt0) cc_final: 0.6820 (tt0) REVERT: A 243 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.6973 (p0) REVERT: A 395 ASN cc_start: 0.7864 (m-40) cc_final: 0.6871 (p0) REVERT: A 734 GLN cc_start: 0.6522 (tt0) cc_final: 0.6312 (mt0) REVERT: A 751 TYR cc_start: 0.7419 (t80) cc_final: 0.7080 (t80) REVERT: A 820 HIS cc_start: 0.1684 (OUTLIER) cc_final: 0.0802 (m170) REVERT: B 141 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: B 378 ARG cc_start: 0.8460 (mtp85) cc_final: 0.7845 (mtp85) REVERT: B 422 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.6349 (ptt180) REVERT: B 534 ASN cc_start: 0.7353 (OUTLIER) cc_final: 0.7152 (t0) REVERT: B 537 GLU cc_start: 0.8350 (mp0) cc_final: 0.7933 (mp0) REVERT: B 699 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7838 (mtmm) REVERT: B 751 TYR cc_start: 0.7512 (t80) cc_final: 0.7269 (t80) REVERT: B 752 LEU cc_start: 0.7728 (tp) cc_final: 0.7193 (mt) REVERT: B 777 MET cc_start: 0.6077 (tpt) cc_final: 0.5763 (tpt) outliers start: 27 outliers final: 5 residues processed: 156 average time/residue: 1.4959 time to fit residues: 257.5169 Evaluate side-chains 132 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 1.967 ------------------------------------------------------------------------------- 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 534 ASN 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 121 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 10 optimal weight: 0.0370 chunk 85 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 534 ASN B 167 GLN B 246 ASN B 276 ASN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.203257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.158809 restraints weight = 12620.913| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.42 r_work: 0.3423 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12456 Z= 0.101 Angle : 0.590 17.514 16924 Z= 0.286 Chirality : 0.045 0.310 2010 Planarity : 0.003 0.049 2106 Dihedral : 6.261 56.877 2080 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.31 % Favored : 94.41 % Rotamer: Outliers : 1.38 % Allowed : 12.92 % Favored : 85.70 % 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: -1.57 (0.23), residues: 1450 helix: -2.76 (0.36), residues: 150 sheet: -2.22 (0.34), residues: 272 loop : -0.37 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 793 HIS 0.002 0.000 HIS A 820 PHE 0.020 0.001 PHE B 690 TYR 0.014 0.001 TYR A 233 ARG 0.003 0.000 ARG B 750 Details of bonding type rmsd link_NAG-ASN : bond 0.00803 ( 16) link_NAG-ASN : angle 3.84132 ( 48) link_BETA1-4 : bond 0.00482 ( 6) link_BETA1-4 : angle 0.94180 ( 18) hydrogen bonds : bond 0.03153 ( 125) hydrogen bonds : angle 5.97931 ( 240) SS BOND : bond 0.00437 ( 10) SS BOND : angle 0.62246 ( 20) covalent geometry : bond 0.00213 (12424) covalent geometry : angle 0.55366 (16838) *********************** 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 147 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.517 Fit side-chains revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7354 (mt0) cc_final: 0.6767 (tt0) REVERT: A 243 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.6954 (p0) REVERT: A 395 ASN cc_start: 0.7852 (m-40) cc_final: 0.6928 (p0) REVERT: A 650 LEU cc_start: 0.8611 (mm) cc_final: 0.8216 (mt) REVERT: A 654 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: A 676 ASN cc_start: 0.7842 (m110) cc_final: 0.7550 (t0) REVERT: A 751 TYR cc_start: 0.7297 (t80) cc_final: 0.6922 (t80) REVERT: A 777 MET cc_start: 0.6126 (tpt) cc_final: 0.5900 (tpt) REVERT: B 96 PHE cc_start: 0.6926 (t80) cc_final: 0.6628 (t80) REVERT: B 138 GLN cc_start: 0.8312 (mt0) cc_final: 0.7933 (mt0) REVERT: B 141 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7695 (mt-10) REVERT: B 151 GLN cc_start: 0.6345 (mm-40) cc_final: 0.5949 (mm-40) REVERT: B 378 ARG cc_start: 0.8383 (mtp85) cc_final: 0.7627 (mtm110) REVERT: B 537 GLU cc_start: 0.8206 (mp0) cc_final: 0.7798 (mp0) REVERT: B 603 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8498 (mtp) outliers start: 19 outliers final: 6 residues processed: 138 average time/residue: 1.1701 time to fit residues: 178.4585 Evaluate side-chains 130 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 603 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 34 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.0770 chunk 143 optimal weight: 30.0000 chunk 81 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- 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 241 GLN A 734 GLN A 820 HIS B 55 HIS B 76 HIS B 138 GLN B 167 GLN B 181 GLN B 246 ASN B 276 ASN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN B 534 ASN B 820 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.192786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.146176 restraints weight = 12658.723| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.45 r_work: 0.3308 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 12456 Z= 0.263 Angle : 0.795 19.986 16924 Z= 0.388 Chirality : 0.054 0.440 2010 Planarity : 0.005 0.049 2106 Dihedral : 7.123 58.224 2080 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.97 % Favored : 92.62 % Rotamer: Outliers : 3.34 % Allowed : 12.77 % Favored : 83.89 % 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: -1.70 (0.22), residues: 1450 helix: -3.12 (0.34), residues: 150 sheet: -2.21 (0.33), residues: 272 loop : -0.44 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 793 HIS 0.009 0.002 HIS B 708 PHE 0.026 0.003 PHE A 408 TYR 0.034 0.003 TYR B 356 ARG 0.006 0.001 ARG B 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00919 ( 16) link_NAG-ASN : angle 4.39727 ( 48) link_BETA1-4 : bond 0.00475 ( 6) link_BETA1-4 : angle 1.32483 ( 18) hydrogen bonds : bond 0.04868 ( 125) hydrogen bonds : angle 6.09916 ( 240) SS BOND : bond 0.01160 ( 10) SS BOND : angle 1.76053 ( 20) covalent geometry : bond 0.00625 (12424) covalent geometry : angle 0.75809 (16838) *********************** 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 172 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 126 time to evaluate : 1.452 Fit side-chains revert: symmetry clash REVERT: A 167 GLN cc_start: 0.6670 (OUTLIER) cc_final: 0.6344 (mm110) REVERT: A 195 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8371 (mt) REVERT: A 196 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7083 (tt0) REVERT: A 243 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7036 (p0) REVERT: A 275 ASN cc_start: 0.7178 (m-40) cc_final: 0.6944 (m-40) REVERT: A 551 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8368 (m-40) REVERT: A 654 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8031 (tt0) REVERT: A 665 LEU cc_start: 0.7941 (mt) cc_final: 0.7730 (mp) REVERT: A 676 ASN cc_start: 0.8313 (OUTLIER) cc_final: 0.7963 (t0) REVERT: A 734 GLN cc_start: 0.6728 (tt0) cc_final: 0.6459 (mp-120) REVERT: A 778 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6032 (tp) REVERT: B 94 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6614 (mt) REVERT: B 138 GLN cc_start: 0.8116 (mt0) cc_final: 0.7825 (mt0) REVERT: B 151 GLN cc_start: 0.6799 (mm-40) cc_final: 0.6129 (mt0) REVERT: B 378 ARG cc_start: 0.8455 (mtp85) cc_final: 0.7566 (mtp180) REVERT: B 422 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.6317 (ptt180) REVERT: B 603 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8607 (mtp) REVERT: B 777 MET cc_start: 0.6095 (tpt) cc_final: 0.5861 (tpt) outliers start: 46 outliers final: 16 residues processed: 154 average time/residue: 1.0569 time to fit residues: 180.5075 Evaluate side-chains 142 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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 195 ILE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 676 ASN 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 B residue 94 ILE Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 314 ASN 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 567 LYS Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 778 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 2 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 534 ASN B 151 GLN B 167 GLN B 276 ASN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.193019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.146544 restraints weight = 12733.524| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.44 r_work: 0.3316 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12456 Z= 0.188 Angle : 0.663 13.733 16924 Z= 0.326 Chirality : 0.049 0.314 2010 Planarity : 0.004 0.048 2106 Dihedral : 6.622 58.844 2080 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.34 % Favored : 93.24 % Rotamer: Outliers : 3.12 % Allowed : 13.86 % Favored : 83.02 % 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: -1.70 (0.22), residues: 1450 helix: -3.12 (0.34), residues: 150 sheet: -2.18 (0.33), residues: 272 loop : -0.45 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 793 HIS 0.006 0.001 HIS B 820 PHE 0.025 0.002 PHE B 690 TYR 0.016 0.002 TYR B 356 ARG 0.006 0.001 ARG B 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00630 ( 16) link_NAG-ASN : angle 3.55389 ( 48) link_BETA1-4 : bond 0.00499 ( 6) link_BETA1-4 : angle 1.04238 ( 18) hydrogen bonds : bond 0.03792 ( 125) hydrogen bonds : angle 5.90396 ( 240) SS BOND : bond 0.00740 ( 10) SS BOND : angle 1.11693 ( 20) covalent geometry : bond 0.00440 (12424) covalent geometry : angle 0.63496 (16838) *********************** 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 173 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7071 (p0) REVERT: A 360 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7973 (ttp) REVERT: A 377 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8436 (mt) REVERT: A 395 ASN cc_start: 0.7844 (m-40) cc_final: 0.6891 (p0) REVERT: A 551 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8422 (m-40) REVERT: A 665 LEU cc_start: 0.7985 (mt) cc_final: 0.7776 (mp) REVERT: A 676 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7883 (t0) REVERT: A 778 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6224 (tp) REVERT: B 94 ILE cc_start: 0.7147 (OUTLIER) cc_final: 0.6848 (mt) REVERT: B 138 GLN cc_start: 0.8041 (mt0) cc_final: 0.7723 (mt0) REVERT: B 223 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7939 (mm) REVERT: B 378 ARG cc_start: 0.8384 (mtp85) cc_final: 0.7505 (mtp180) REVERT: B 422 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.6396 (ptt180) REVERT: B 603 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8553 (mtp) outliers start: 43 outliers final: 16 residues processed: 157 average time/residue: 1.0514 time to fit residues: 183.1726 Evaluate side-chains 148 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 430 VAL 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 676 ASN 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 B residue 94 ILE Chi-restraints excluded: chain B residue 207 LYS 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 406 THR Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 781 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 202 ASN A 534 ASN A 800 HIS ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN B 265 ASN B 276 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.192235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.145774 restraints weight = 12900.900| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.47 r_work: 0.3305 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12456 Z= 0.190 Angle : 0.688 14.985 16924 Z= 0.336 Chirality : 0.049 0.308 2010 Planarity : 0.004 0.048 2106 Dihedral : 6.620 59.937 2080 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.76 % Favored : 92.83 % Rotamer: Outliers : 3.48 % Allowed : 14.80 % Favored : 81.71 % 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: -1.70 (0.22), residues: 1450 helix: -3.13 (0.34), residues: 150 sheet: -2.10 (0.33), residues: 268 loop : -0.48 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 793 HIS 0.005 0.001 HIS A 337 PHE 0.024 0.002 PHE B 690 TYR 0.015 0.002 TYR B 356 ARG 0.004 0.001 ARG B 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00736 ( 16) link_NAG-ASN : angle 4.07246 ( 48) link_BETA1-4 : bond 0.00444 ( 6) link_BETA1-4 : angle 1.15506 ( 18) hydrogen bonds : bond 0.03886 ( 125) hydrogen bonds : angle 5.89950 ( 240) SS BOND : bond 0.00824 ( 10) SS BOND : angle 1.31241 ( 20) covalent geometry : bond 0.00445 (12424) covalent geometry : angle 0.65233 (16838) *********************** 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 173 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: A 167 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.6423 (mm110) REVERT: A 175 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7813 (mm-30) REVERT: A 243 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7061 (p0) REVERT: A 275 ASN cc_start: 0.7564 (m-40) cc_final: 0.7078 (m-40) REVERT: A 360 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8123 (ttp) REVERT: A 377 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8409 (mt) REVERT: A 551 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8434 (m-40) REVERT: A 665 LEU cc_start: 0.8005 (mt) cc_final: 0.7791 (mp) REVERT: A 676 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7936 (t0) REVERT: A 778 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6419 (tp) REVERT: B 151 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6527 (mt0) REVERT: B 207 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8050 (mtmm) REVERT: B 223 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8035 (mm) REVERT: B 243 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.6675 (m-30) REVERT: B 378 ARG cc_start: 0.8481 (mtp85) cc_final: 0.7585 (mtp180) REVERT: B 603 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8691 (mtp) REVERT: B 710 GLN cc_start: 0.6516 (mm110) cc_final: 0.6278 (tt0) REVERT: B 734 GLN cc_start: 0.6337 (mt0) cc_final: 0.5675 (mp-120) outliers start: 48 outliers final: 19 residues processed: 153 average time/residue: 0.9867 time to fit residues: 167.9955 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 : 1.345 ------------------------------------------------------------------------------- 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 352 GLU Chi-restraints excluded: chain A residue 360 MET 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 430 VAL 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 676 ASN 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 151 GLN Chi-restraints excluded: chain B residue 207 LYS 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 567 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 781 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 66 optimal weight: 20.0000 chunk 117 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 70 optimal weight: 50.0000 chunk 124 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 202 ASN A 534 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.191519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.130552 restraints weight = 12732.392| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.61 r_work: 0.3268 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12456 Z= 0.156 Angle : 0.643 12.991 16924 Z= 0.315 Chirality : 0.047 0.310 2010 Planarity : 0.004 0.047 2106 Dihedral : 6.434 58.908 2080 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.34 % Favored : 93.31 % Rotamer: Outliers : 3.12 % Allowed : 15.89 % Favored : 80.99 % 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: -1.58 (0.22), residues: 1450 helix: -2.91 (0.38), residues: 126 sheet: -2.08 (0.33), residues: 268 loop : -0.48 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 793 HIS 0.004 0.001 HIS A 337 PHE 0.022 0.002 PHE B 690 TYR 0.013 0.002 TYR A 233 ARG 0.003 0.000 ARG B 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00631 ( 16) link_NAG-ASN : angle 3.42828 ( 48) link_BETA1-4 : bond 0.00451 ( 6) link_BETA1-4 : angle 1.07123 ( 18) hydrogen bonds : bond 0.03443 ( 125) hydrogen bonds : angle 5.81285 ( 240) SS BOND : bond 0.00697 ( 10) SS BOND : angle 1.08341 ( 20) covalent geometry : bond 0.00364 (12424) covalent geometry : angle 0.61601 (16838) *********************** 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 171 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 GLN cc_start: 0.6693 (OUTLIER) cc_final: 0.6427 (mm110) REVERT: A 196 GLU cc_start: 0.7504 (tt0) cc_final: 0.7150 (tt0) REVERT: A 243 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7110 (p0) REVERT: A 275 ASN cc_start: 0.7648 (m-40) cc_final: 0.7206 (m-40) REVERT: A 377 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8447 (mt) REVERT: A 395 ASN cc_start: 0.8021 (OUTLIER) cc_final: 0.7675 (t0) REVERT: A 676 ASN cc_start: 0.8179 (OUTLIER) cc_final: 0.7915 (t0) REVERT: A 778 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6232 (tp) REVERT: B 130 LYS cc_start: 0.7329 (tppp) cc_final: 0.7126 (tppp) REVERT: B 151 GLN cc_start: 0.7286 (mt0) cc_final: 0.6636 (mm-40) REVERT: B 175 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: B 378 ARG cc_start: 0.8489 (mtp85) cc_final: 0.7655 (mtp180) REVERT: B 422 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.6446 (ptt180) REVERT: B 603 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8668 (mtp) REVERT: B 710 GLN cc_start: 0.6551 (mm110) cc_final: 0.6326 (tt0) REVERT: B 734 GLN cc_start: 0.6329 (mt0) cc_final: 0.5633 (mp-120) REVERT: B 777 MET cc_start: 0.5296 (tmm) cc_final: 0.5041 (tmm) outliers start: 43 outliers final: 21 residues processed: 154 average time/residue: 0.9634 time to fit residues: 165.3862 Evaluate side-chains 154 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 395 ASN Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 752 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 175 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 778 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 18 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 202 ASN A 300 ASN A 534 ASN ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.189708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139904 restraints weight = 12829.450| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.35 r_work: 0.3287 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12456 Z= 0.227 Angle : 0.723 13.349 16924 Z= 0.354 Chirality : 0.050 0.304 2010 Planarity : 0.004 0.047 2106 Dihedral : 6.790 59.742 2080 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.76 % Favored : 92.83 % Rotamer: Outliers : 2.98 % Allowed : 16.40 % Favored : 80.62 % 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: -1.53 (0.22), residues: 1450 helix: -2.65 (0.41), residues: 108 sheet: -2.09 (0.32), residues: 268 loop : -0.51 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 793 HIS 0.006 0.001 HIS A 337 PHE 0.022 0.003 PHE A 506 TYR 0.015 0.003 TYR A 233 ARG 0.005 0.001 ARG B 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00656 ( 16) link_NAG-ASN : angle 3.70992 ( 48) link_BETA1-4 : bond 0.00405 ( 6) link_BETA1-4 : angle 1.27489 ( 18) hydrogen bonds : bond 0.04261 ( 125) hydrogen bonds : angle 5.89074 ( 240) SS BOND : bond 0.00962 ( 10) SS BOND : angle 1.46599 ( 20) covalent geometry : bond 0.00534 (12424) covalent geometry : angle 0.69457 (16838) *********************** 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 165 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7050 (p0) REVERT: A 275 ASN cc_start: 0.7567 (m-40) cc_final: 0.7223 (m110) REVERT: A 377 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8443 (mt) REVERT: A 676 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.7968 (t0) REVERT: A 711 LEU cc_start: 0.7237 (mt) cc_final: 0.7022 (mt) REVERT: A 734 GLN cc_start: 0.6804 (tt0) cc_final: 0.6289 (tm-30) REVERT: A 778 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6526 (tp) REVERT: B 130 LYS cc_start: 0.7378 (tppp) cc_final: 0.6998 (tppp) REVERT: B 243 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6877 (m-30) REVERT: B 422 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.6333 (ptt180) REVERT: B 603 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8677 (mtp) REVERT: B 734 GLN cc_start: 0.6703 (mt0) cc_final: 0.5891 (mp-120) REVERT: B 751 TYR cc_start: 0.7659 (t80) cc_final: 0.7229 (t80) REVERT: B 781 HIS cc_start: 0.6387 (OUTLIER) cc_final: 0.5926 (p90) outliers start: 41 outliers final: 21 residues processed: 150 average time/residue: 1.0327 time to fit residues: 171.5588 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 : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 422 ARG Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 752 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 217 THR Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 781 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 135 optimal weight: 30.0000 chunk 60 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.190913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.128089 restraints weight = 12715.195| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.44 r_work: 0.3278 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12456 Z= 0.173 Angle : 0.661 11.821 16924 Z= 0.325 Chirality : 0.048 0.305 2010 Planarity : 0.004 0.047 2106 Dihedral : 6.519 58.861 2080 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.62 % Favored : 93.03 % Rotamer: Outliers : 2.54 % Allowed : 17.34 % Favored : 80.12 % 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: -1.51 (0.22), residues: 1450 helix: -2.61 (0.42), residues: 108 sheet: -2.09 (0.33), residues: 268 loop : -0.50 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 793 HIS 0.004 0.001 HIS A 337 PHE 0.023 0.002 PHE B 690 TYR 0.014 0.002 TYR A 233 ARG 0.003 0.000 ARG B 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00726 ( 16) link_NAG-ASN : angle 3.51005 ( 48) link_BETA1-4 : bond 0.00433 ( 6) link_BETA1-4 : angle 1.13460 ( 18) hydrogen bonds : bond 0.03631 ( 125) hydrogen bonds : angle 5.90844 ( 240) SS BOND : bond 0.00744 ( 10) SS BOND : angle 1.13584 ( 20) covalent geometry : bond 0.00404 (12424) covalent geometry : angle 0.63297 (16838) *********************** 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 158 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7082 (p0) REVERT: A 275 ASN cc_start: 0.7640 (m-40) cc_final: 0.7309 (m-40) REVERT: A 377 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8401 (mt) REVERT: A 676 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7973 (t0) REVERT: A 734 GLN cc_start: 0.6954 (tt0) cc_final: 0.6405 (tm-30) REVERT: B 243 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6851 (m-30) REVERT: B 311 LYS cc_start: 0.8533 (tttm) cc_final: 0.8131 (ttmp) REVERT: B 422 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.6432 (ptt180) REVERT: B 603 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8645 (mtp) REVERT: B 710 GLN cc_start: 0.7198 (tt0) cc_final: 0.6943 (tt0) REVERT: B 734 GLN cc_start: 0.6678 (mt0) cc_final: 0.5852 (mp10) outliers start: 35 outliers final: 20 residues processed: 146 average time/residue: 1.0326 time to fit residues: 167.0234 Evaluate side-chains 147 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 430 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 752 LEU 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 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 422 ARG Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 778 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 52 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 5 optimal weight: 20.0000 chunk 3 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN B 151 GLN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.191168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.132898 restraints weight = 12797.505| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.58 r_work: 0.3225 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12456 Z= 0.163 Angle : 0.666 14.038 16924 Z= 0.325 Chirality : 0.049 0.346 2010 Planarity : 0.004 0.047 2106 Dihedral : 6.437 58.533 2080 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.03 % Favored : 92.62 % Rotamer: Outliers : 2.47 % Allowed : 17.92 % Favored : 79.61 % 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: -1.49 (0.22), residues: 1450 helix: -2.66 (0.39), residues: 120 sheet: -2.08 (0.32), residues: 268 loop : -0.44 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 793 HIS 0.004 0.001 HIS A 337 PHE 0.024 0.002 PHE B 690 TYR 0.013 0.002 TYR A 233 ARG 0.003 0.000 ARG B 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00765 ( 16) link_NAG-ASN : angle 4.01211 ( 48) link_BETA1-4 : bond 0.00407 ( 6) link_BETA1-4 : angle 1.12915 ( 18) hydrogen bonds : bond 0.03646 ( 125) hydrogen bonds : angle 5.89495 ( 240) SS BOND : bond 0.00707 ( 10) SS BOND : angle 1.11409 ( 20) covalent geometry : bond 0.00379 (12424) covalent geometry : angle 0.63018 (16838) ********************** 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 160 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7114 (p0) REVERT: A 275 ASN cc_start: 0.7640 (m-40) cc_final: 0.7299 (m-40) REVERT: A 360 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8128 (ttp) REVERT: A 377 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8375 (mt) REVERT: A 676 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7994 (t0) REVERT: A 690 PHE cc_start: 0.7389 (t80) cc_final: 0.7030 (t80) REVERT: A 734 GLN cc_start: 0.7046 (tt0) cc_final: 0.6520 (tm-30) REVERT: A 777 MET cc_start: 0.5655 (tmm) cc_final: 0.5269 (tmm) REVERT: B 197 LYS cc_start: 0.7224 (tptt) cc_final: 0.6753 (tppt) REVERT: B 243 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6915 (m-30) REVERT: B 275 ASN cc_start: 0.7803 (m-40) cc_final: 0.7470 (m-40) REVERT: B 422 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.6491 (ptt180) REVERT: B 710 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.7234 (tt0) REVERT: B 734 GLN cc_start: 0.6627 (mt0) cc_final: 0.5816 (mp10) outliers start: 34 outliers final: 22 residues processed: 144 average time/residue: 1.0972 time to fit residues: 175.5177 Evaluate side-chains 153 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 360 MET 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 430 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 752 LEU 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 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 314 ASN Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 710 GLN Chi-restraints excluded: chain B residue 778 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 97 optimal weight: 0.1980 chunk 16 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 96 optimal weight: 0.0270 chunk 9 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN B 151 GLN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.191336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128695 restraints weight = 12726.039| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.60 r_work: 0.3237 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.206 12456 Z= 0.240 Angle : 0.908 59.200 16924 Z= 0.498 Chirality : 0.049 0.515 2010 Planarity : 0.004 0.046 2106 Dihedral : 6.430 58.499 2080 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.90 % Favored : 92.76 % Rotamer: Outliers : 2.54 % Allowed : 17.92 % Favored : 79.54 % Cbeta Deviations : 0.07 % 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: -1.50 (0.22), residues: 1450 helix: -2.66 (0.39), residues: 120 sheet: -2.08 (0.32), residues: 268 loop : -0.45 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 793 HIS 0.003 0.001 HIS B 298 PHE 0.023 0.002 PHE B 690 TYR 0.013 0.002 TYR A 233 ARG 0.002 0.000 ARG B 376 Details of bonding type rmsd link_NAG-ASN : bond 0.01071 ( 16) link_NAG-ASN : angle 3.93850 ( 48) link_BETA1-4 : bond 0.00471 ( 6) link_BETA1-4 : angle 1.15240 ( 18) hydrogen bonds : bond 0.03608 ( 125) hydrogen bonds : angle 5.89936 ( 240) SS BOND : bond 0.00657 ( 10) SS BOND : angle 1.12007 ( 20) covalent geometry : bond 0.00489 (12424) covalent geometry : angle 0.88396 (16838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10226.22 seconds wall clock time: 180 minutes 41.73 seconds (10841.73 seconds total)