Starting phenix.real_space_refine on Sat Aug 23 13:09:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ytp_34091/08_2025/7ytp_34091.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ytp_34091/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ytp_34091/08_2025/7ytp_34091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ytp_34091/08_2025/7ytp_34091.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ytp_34091/08_2025/7ytp_34091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ytp_34091/08_2025/7ytp_34091.map" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.01, per 1000 atoms: 0.25 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: 1.03 Conformation dependent library (CDL) restraints added in 559.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.49 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: 2.07 Time building geometry restraints manager: 1.39 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.370 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.960 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 121 TYR 0.012 0.001 TYR A 184 PHE 0.019 0.001 PHE A 690 TRP 0.010 0.001 TRP A 692 HIS 0.004 0.000 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00326 (12424) covalent geometry : angle 0.59824 (16838) SS BOND : bond 0.00134 ( 10) SS BOND : angle 0.74216 ( 20) hydrogen bonds : bond 0.31707 ( 125) hydrogen bonds : angle 7.99614 ( 240) link_BETA1-4 : bond 0.00361 ( 6) link_BETA1-4 : angle 1.07327 ( 18) link_NAG-ASN : bond 0.00899 ( 16) link_NAG-ASN : angle 4.48455 ( 48) *********************** 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 : 0.467 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: 0.5460 time to fit residues: 107.5619 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 : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- 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 76 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.198986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.153578 restraints weight = 12429.780| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.48 r_work: 0.3346 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 12456 Z= 0.264 Angle : 0.804 16.039 16924 Z= 0.394 Chirality : 0.052 0.316 2010 Planarity : 0.005 0.066 2106 Dihedral : 7.262 59.231 2080 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.69 % Favored : 92.90 % Rotamer: Outliers : 1.74 % Allowed : 10.01 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.23), residues: 1450 helix: -3.21 (0.31), residues: 162 sheet: -2.27 (0.33), residues: 272 loop : -0.39 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 164 TYR 0.048 0.003 TYR B 356 PHE 0.027 0.003 PHE A 408 TRP 0.010 0.002 TRP B 793 HIS 0.005 0.002 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00609 (12424) covalent geometry : angle 0.77062 (16838) SS BOND : bond 0.01093 ( 10) SS BOND : angle 1.43757 ( 20) hydrogen bonds : bond 0.06985 ( 125) hydrogen bonds : angle 6.37101 ( 240) link_BETA1-4 : bond 0.00681 ( 6) link_BETA1-4 : angle 1.77951 ( 18) link_NAG-ASN : bond 0.01110 ( 16) link_NAG-ASN : angle 4.17146 ( 48) *********************** 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 170 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.495 Fit side-chains REVERT: A 151 GLN cc_start: 0.7351 (mt0) cc_final: 0.6764 (tt0) REVERT: A 164 ARG cc_start: 0.6584 (mtm-85) cc_final: 0.6367 (mtm180) REVERT: A 243 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.6942 (p0) REVERT: A 395 ASN cc_start: 0.7829 (m-40) cc_final: 0.6898 (p0) REVERT: A 734 GLN cc_start: 0.6477 (tt0) cc_final: 0.6172 (tm-30) REVERT: A 751 TYR cc_start: 0.7377 (t80) cc_final: 0.7038 (t80) REVERT: A 778 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.5992 (tt) REVERT: B 175 GLU cc_start: 0.7750 (tp30) cc_final: 0.7172 (mm-30) REVERT: B 378 ARG cc_start: 0.8455 (mtp85) cc_final: 0.7543 (mtp85) REVERT: B 537 GLU cc_start: 0.8347 (mp0) cc_final: 0.7945 (mp0) REVERT: B 699 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7830 (mtmm) REVERT: B 777 MET cc_start: 0.6295 (tpt) cc_final: 0.6037 (tpt) outliers start: 24 outliers final: 8 residues processed: 159 average time/residue: 0.5668 time to fit residues: 98.6295 Evaluate side-chains 133 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 679 ASN Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 603 MET 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 141 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 ASN A 241 GLN A 534 ASN A 820 HIS B 246 ASN B 276 ASN B 534 ASN B 782 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.196640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.143826 restraints weight = 12807.570| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.33 r_work: 0.3373 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12456 Z= 0.141 Angle : 0.634 18.520 16924 Z= 0.310 Chirality : 0.047 0.367 2010 Planarity : 0.004 0.052 2106 Dihedral : 6.522 57.599 2080 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.72 % Favored : 94.00 % Rotamer: Outliers : 1.89 % Allowed : 12.48 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.23), residues: 1450 helix: -3.05 (0.33), residues: 162 sheet: -2.25 (0.33), residues: 272 loop : -0.36 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 164 TYR 0.018 0.002 TYR B 356 PHE 0.026 0.002 PHE B 690 TRP 0.010 0.001 TRP B 793 HIS 0.007 0.001 HIS A 820 Details of bonding type rmsd covalent geometry : bond 0.00322 (12424) covalent geometry : angle 0.59781 (16838) SS BOND : bond 0.00643 ( 10) SS BOND : angle 0.86468 ( 20) hydrogen bonds : bond 0.04204 ( 125) hydrogen bonds : angle 6.08705 ( 240) link_BETA1-4 : bond 0.00400 ( 6) link_BETA1-4 : angle 0.97343 ( 18) link_NAG-ASN : bond 0.00594 ( 16) link_NAG-ASN : angle 3.96129 ( 48) *********************** 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 152 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 164 ARG cc_start: 0.6689 (mtm-85) cc_final: 0.6404 (mtm110) REVERT: A 243 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6929 (p0) REVERT: A 395 ASN cc_start: 0.7727 (m-40) cc_final: 0.6774 (p0) REVERT: A 654 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: A 676 ASN cc_start: 0.8075 (m110) cc_final: 0.7782 (t0) REVERT: A 710 GLN cc_start: 0.7003 (mm110) cc_final: 0.6539 (tt0) REVERT: A 734 GLN cc_start: 0.6926 (tt0) cc_final: 0.6393 (tm-30) REVERT: A 777 MET cc_start: 0.6050 (tpt) cc_final: 0.5845 (tpt) REVERT: B 138 GLN cc_start: 0.8296 (mt0) cc_final: 0.7992 (mt0) REVERT: B 378 ARG cc_start: 0.8357 (mtp85) cc_final: 0.7485 (mtp180) REVERT: B 537 GLU cc_start: 0.8197 (mp0) cc_final: 0.7817 (mp0) outliers start: 26 outliers final: 9 residues processed: 138 average time/residue: 0.4659 time to fit residues: 70.7687 Evaluate side-chains 130 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 654 GLU Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 567 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 94 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 202 ASN A 534 ASN ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN B 276 ASN B 534 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 HIS B 820 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.190421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.133357 restraints weight = 12800.584| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.80 r_work: 0.3254 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 12456 Z= 0.267 Angle : 0.789 15.201 16924 Z= 0.386 Chirality : 0.053 0.293 2010 Planarity : 0.005 0.050 2106 Dihedral : 7.231 59.759 2080 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.03 % Favored : 92.55 % Rotamer: Outliers : 2.83 % Allowed : 13.64 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.22), residues: 1450 helix: -3.26 (0.32), residues: 150 sheet: -2.22 (0.33), residues: 268 loop : -0.51 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 376 TYR 0.028 0.003 TYR B 356 PHE 0.023 0.003 PHE A 408 TRP 0.010 0.002 TRP B 793 HIS 0.008 0.002 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00635 (12424) covalent geometry : angle 0.75809 (16838) SS BOND : bond 0.01109 ( 10) SS BOND : angle 1.73760 ( 20) hydrogen bonds : bond 0.04903 ( 125) hydrogen bonds : angle 6.18584 ( 240) link_BETA1-4 : bond 0.00441 ( 6) link_BETA1-4 : angle 1.37921 ( 18) link_NAG-ASN : bond 0.00694 ( 16) link_NAG-ASN : angle 3.97054 ( 48) *********************** 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 168 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 ARG cc_start: 0.6968 (mtm-85) cc_final: 0.6673 (mtm110) REVERT: A 243 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7041 (p0) REVERT: A 360 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8216 (ttp) REVERT: A 551 ASN cc_start: 0.8607 (OUTLIER) cc_final: 0.8391 (m-40) REVERT: A 654 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: A 665 LEU cc_start: 0.7988 (mt) cc_final: 0.7762 (mp) REVERT: A 710 GLN cc_start: 0.7065 (mm110) cc_final: 0.6575 (tt0) REVERT: A 734 GLN cc_start: 0.7038 (tt0) cc_final: 0.6412 (tm-30) REVERT: B 94 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6936 (mt) REVERT: B 138 GLN cc_start: 0.8150 (mt0) cc_final: 0.7869 (mt0) REVERT: B 151 GLN cc_start: 0.6849 (mt0) cc_final: 0.6140 (mt0) REVERT: B 186 ARG cc_start: 0.7634 (mmm160) cc_final: 0.7381 (mmm-85) REVERT: B 196 GLU cc_start: 0.7268 (tt0) cc_final: 0.6793 (tt0) REVERT: B 223 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7943 (mm) REVERT: B 377 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8666 (mt) REVERT: B 378 ARG cc_start: 0.8484 (mtp85) cc_final: 0.7562 (mtp180) REVERT: B 537 GLU cc_start: 0.8230 (mp0) cc_final: 0.7841 (mp0) REVERT: B 782 HIS cc_start: 0.5234 (m90) cc_final: 0.4987 (m-70) outliers start: 39 outliers final: 15 residues processed: 152 average time/residue: 0.4805 time to fit residues: 80.6148 Evaluate side-chains 145 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 352 GLU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 820 HIS 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 313 ILE Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 31 optimal weight: 0.9990 chunk 77 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 143 optimal weight: 30.0000 chunk 10 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 300 ASN A 534 ASN A 800 HIS ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS B 151 GLN B 167 GLN B 276 ASN B 300 ASN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.190807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.143510 restraints weight = 12852.762| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.40 r_work: 0.3289 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12456 Z= 0.252 Angle : 0.747 16.108 16924 Z= 0.367 Chirality : 0.052 0.333 2010 Planarity : 0.005 0.051 2106 Dihedral : 7.036 58.791 2080 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.83 % Favored : 92.76 % Rotamer: Outliers : 3.48 % Allowed : 14.73 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.22), residues: 1450 helix: -3.35 (0.32), residues: 150 sheet: -2.22 (0.32), residues: 268 loop : -0.59 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 357 TYR 0.017 0.003 TYR A 233 PHE 0.023 0.003 PHE B 690 TRP 0.010 0.002 TRP B 793 HIS 0.007 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00593 (12424) covalent geometry : angle 0.71206 (16838) SS BOND : bond 0.00977 ( 10) SS BOND : angle 1.41188 ( 20) hydrogen bonds : bond 0.04525 ( 125) hydrogen bonds : angle 6.07733 ( 240) link_BETA1-4 : bond 0.00500 ( 6) link_BETA1-4 : angle 1.25399 ( 18) link_NAG-ASN : bond 0.00823 ( 16) link_NAG-ASN : angle 4.16577 ( 48) *********************** 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 177 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 129 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 GLN cc_start: 0.6564 (OUTLIER) cc_final: 0.6338 (mm110) REVERT: A 243 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7049 (p0) REVERT: A 275 ASN cc_start: 0.7584 (m-40) cc_final: 0.7164 (m-40) REVERT: A 360 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8074 (ttp) REVERT: A 377 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8513 (mt) REVERT: A 551 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.8420 (m-40) REVERT: A 616 MET cc_start: 0.8704 (mtp) cc_final: 0.8327 (mtp) REVERT: A 665 LEU cc_start: 0.8031 (mt) cc_final: 0.7805 (mp) REVERT: A 676 ASN cc_start: 0.8149 (m-40) cc_final: 0.7877 (t0) REVERT: A 710 GLN cc_start: 0.7118 (mm110) cc_final: 0.6671 (tt0) REVERT: A 734 GLN cc_start: 0.6977 (tt0) cc_final: 0.6417 (tm-30) REVERT: B 151 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6361 (mt0) REVERT: B 186 ARG cc_start: 0.7564 (mmm160) cc_final: 0.7359 (mmm-85) REVERT: B 196 GLU cc_start: 0.7379 (tt0) cc_final: 0.6899 (tt0) REVERT: B 207 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7966 (mtmm) REVERT: B 243 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6838 (m-30) REVERT: B 377 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8717 (mt) REVERT: B 378 ARG cc_start: 0.8435 (mtp85) cc_final: 0.7551 (mtp180) REVERT: B 537 GLU cc_start: 0.8234 (mp0) cc_final: 0.7846 (mp0) REVERT: B 603 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8888 (mtp) REVERT: B 676 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.7547 (t0) REVERT: B 710 GLN cc_start: 0.6623 (mm110) cc_final: 0.6423 (tt0) REVERT: B 734 GLN cc_start: 0.6318 (mt0) cc_final: 0.5708 (mp-120) REVERT: B 782 HIS cc_start: 0.5079 (m90) cc_final: 0.4745 (m-70) outliers start: 48 outliers final: 17 residues processed: 159 average time/residue: 0.4245 time to fit residues: 74.5480 Evaluate side-chains 150 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 756 SER 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 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 377 ILE Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 51 optimal weight: 10.0000 chunk 70 optimal weight: 0.2980 chunk 95 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 83 optimal weight: 0.3980 chunk 8 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 19 optimal weight: 0.0670 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN B 300 ASN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.194034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.131108 restraints weight = 12752.415| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.44 r_work: 0.3289 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12456 Z= 0.097 Angle : 0.578 12.738 16924 Z= 0.287 Chirality : 0.045 0.320 2010 Planarity : 0.003 0.049 2106 Dihedral : 6.154 56.953 2080 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.52 % Favored : 94.21 % Rotamer: Outliers : 1.89 % Allowed : 16.76 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.22), residues: 1450 helix: -2.88 (0.38), residues: 126 sheet: -2.11 (0.33), residues: 268 loop : -0.50 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 750 TYR 0.013 0.001 TYR A 380 PHE 0.021 0.001 PHE B 690 TRP 0.009 0.001 TRP B 793 HIS 0.003 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00207 (12424) covalent geometry : angle 0.55060 (16838) SS BOND : bond 0.00385 ( 10) SS BOND : angle 0.71933 ( 20) hydrogen bonds : bond 0.02703 ( 125) hydrogen bonds : angle 5.83024 ( 240) link_BETA1-4 : bond 0.00426 ( 6) link_BETA1-4 : angle 0.96544 ( 18) link_NAG-ASN : bond 0.00735 ( 16) link_NAG-ASN : angle 3.31510 ( 48) *********************** 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 164 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7063 (p0) REVERT: A 275 ASN cc_start: 0.7653 (m-40) cc_final: 0.7230 (m-40) REVERT: A 665 LEU cc_start: 0.7971 (mt) cc_final: 0.7758 (mp) REVERT: A 676 ASN cc_start: 0.7890 (m-40) cc_final: 0.7675 (t0) REVERT: A 710 GLN cc_start: 0.7083 (mm110) cc_final: 0.6519 (tt0) REVERT: A 734 GLN cc_start: 0.7000 (tt0) cc_final: 0.6388 (tm-30) REVERT: B 186 ARG cc_start: 0.7737 (mmm160) cc_final: 0.7421 (mmm-85) REVERT: B 196 GLU cc_start: 0.7320 (tt0) cc_final: 0.6908 (tt0) REVERT: B 207 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7984 (mtmm) REVERT: B 243 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6949 (m-30) REVERT: B 537 GLU cc_start: 0.8255 (mp0) cc_final: 0.7866 (mp0) REVERT: B 777 MET cc_start: 0.6076 (OUTLIER) cc_final: 0.5428 (tpt) outliers start: 26 outliers final: 8 residues processed: 154 average time/residue: 0.4879 time to fit residues: 82.6733 Evaluate side-chains 142 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 406 THR Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain B residue 207 LYS 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 406 THR Chi-restraints excluded: chain B residue 777 MET Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 111 optimal weight: 8.9990 chunk 142 optimal weight: 30.0000 chunk 143 optimal weight: 6.9990 chunk 73 optimal weight: 30.0000 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS B 151 GLN B 300 ASN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.191307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.129510 restraints weight = 12707.305| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.54 r_work: 0.3258 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12456 Z= 0.181 Angle : 0.665 13.744 16924 Z= 0.327 Chirality : 0.049 0.305 2010 Planarity : 0.004 0.049 2106 Dihedral : 6.492 59.574 2080 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.76 % Favored : 92.83 % Rotamer: Outliers : 2.98 % Allowed : 16.62 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.22), residues: 1450 helix: -2.93 (0.37), residues: 126 sheet: -2.10 (0.33), residues: 268 loop : -0.50 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 376 TYR 0.014 0.002 TYR A 233 PHE 0.021 0.002 PHE B 690 TRP 0.009 0.001 TRP B 793 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00426 (12424) covalent geometry : angle 0.63156 (16838) SS BOND : bond 0.00825 ( 10) SS BOND : angle 1.26009 ( 20) hydrogen bonds : bond 0.03775 ( 125) hydrogen bonds : angle 5.82573 ( 240) link_BETA1-4 : bond 0.00426 ( 6) link_BETA1-4 : angle 1.14254 ( 18) link_NAG-ASN : bond 0.00703 ( 16) link_NAG-ASN : angle 3.87942 ( 48) *********************** 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 168 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 127 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7101 (p0) REVERT: A 275 ASN cc_start: 0.7657 (m-40) cc_final: 0.7309 (m-40) REVERT: A 383 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8753 (tttm) REVERT: A 395 ASN cc_start: 0.8121 (OUTLIER) cc_final: 0.7804 (t0) REVERT: A 676 ASN cc_start: 0.8121 (m-40) cc_final: 0.7860 (t0) REVERT: A 710 GLN cc_start: 0.7188 (mm110) cc_final: 0.6656 (tt0) REVERT: A 711 LEU cc_start: 0.7102 (mt) cc_final: 0.6872 (mt) REVERT: A 734 GLN cc_start: 0.6865 (tt0) cc_final: 0.6273 (tm-30) REVERT: B 151 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6316 (mt0) REVERT: B 186 ARG cc_start: 0.7681 (mmm160) cc_final: 0.7326 (mmm-85) REVERT: B 196 GLU cc_start: 0.7307 (tt0) cc_final: 0.6880 (tt0) REVERT: B 207 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7992 (mtmm) REVERT: B 243 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6877 (m-30) REVERT: B 377 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8648 (mt) REVERT: B 537 GLU cc_start: 0.8343 (mp0) cc_final: 0.7939 (mp0) REVERT: B 687 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7565 (mp) outliers start: 41 outliers final: 16 residues processed: 153 average time/residue: 0.5296 time to fit residues: 89.5587 Evaluate side-chains 149 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 383 LYS Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 533 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 151 GLN Chi-restraints excluded: chain B residue 207 LYS 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 314 ASN Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 144 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 128 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 534 ASN ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.189949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3435 r_free = 0.3435 target = 0.129068 restraints weight = 12770.437| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.64 r_work: 0.3222 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12456 Z= 0.242 Angle : 0.732 12.364 16924 Z= 0.358 Chirality : 0.051 0.307 2010 Planarity : 0.005 0.049 2106 Dihedral : 6.764 59.254 2080 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.48 % Favored : 93.10 % Rotamer: Outliers : 3.12 % Allowed : 17.20 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.22), residues: 1450 helix: -2.72 (0.40), residues: 108 sheet: -2.10 (0.32), residues: 268 loop : -0.53 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 376 TYR 0.016 0.002 TYR A 233 PHE 0.022 0.003 PHE B 506 TRP 0.009 0.001 TRP B 793 HIS 0.007 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00570 (12424) covalent geometry : angle 0.70578 (16838) SS BOND : bond 0.00972 ( 10) SS BOND : angle 1.39092 ( 20) hydrogen bonds : bond 0.04248 ( 125) hydrogen bonds : angle 5.92683 ( 240) link_BETA1-4 : bond 0.00449 ( 6) link_BETA1-4 : angle 1.26185 ( 18) link_NAG-ASN : bond 0.00720 ( 16) link_NAG-ASN : angle 3.57068 ( 48) *********************** 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 168 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 GLN cc_start: 0.6716 (OUTLIER) cc_final: 0.6471 (mm110) REVERT: A 243 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7109 (p0) REVERT: A 275 ASN cc_start: 0.7675 (m-40) cc_final: 0.7342 (m-40) REVERT: A 377 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8482 (mt) REVERT: A 383 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8798 (tttm) REVERT: A 551 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8479 (m-40) REVERT: A 654 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: A 676 ASN cc_start: 0.8224 (m-40) cc_final: 0.7946 (t0) REVERT: A 710 GLN cc_start: 0.7192 (mm110) cc_final: 0.6687 (tt0) REVERT: A 711 LEU cc_start: 0.7184 (mt) cc_final: 0.6938 (mt) REVERT: A 734 GLN cc_start: 0.6986 (tt0) cc_final: 0.6323 (tm-30) REVERT: A 777 MET cc_start: 0.5925 (OUTLIER) cc_final: 0.5683 (tmm) REVERT: B 151 GLN cc_start: 0.7111 (mm-40) cc_final: 0.6588 (mm-40) REVERT: B 186 ARG cc_start: 0.7800 (mmm160) cc_final: 0.7457 (mmm-85) REVERT: B 196 GLU cc_start: 0.7528 (tt0) cc_final: 0.7036 (tt0) REVERT: B 197 LYS cc_start: 0.7245 (tptt) cc_final: 0.6871 (tppt) REVERT: B 207 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.8007 (mtmm) REVERT: B 243 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6945 (m-30) REVERT: B 377 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8609 (mt) REVERT: B 419 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7738 (mt0) REVERT: B 537 GLU cc_start: 0.8285 (mp0) cc_final: 0.7873 (mp0) REVERT: B 687 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7554 (mp) outliers start: 43 outliers final: 21 residues processed: 154 average time/residue: 0.5479 time to fit residues: 92.6874 Evaluate side-chains 155 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 383 LYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 820 HIS 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 313 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 419 GLN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 128 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 91 optimal weight: 0.0270 chunk 72 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 127 optimal weight: 8.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- 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 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.193260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.133707 restraints weight = 12712.823| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.56 r_work: 0.3285 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12456 Z= 0.108 Angle : 0.607 13.694 16924 Z= 0.298 Chirality : 0.046 0.413 2010 Planarity : 0.003 0.049 2106 Dihedral : 6.086 57.189 2080 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.14 % Favored : 93.59 % Rotamer: Outliers : 2.25 % Allowed : 18.21 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.22), residues: 1450 helix: -2.77 (0.38), residues: 134 sheet: -2.05 (0.33), residues: 268 loop : -0.48 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 262 TYR 0.015 0.001 TYR A 185 PHE 0.021 0.001 PHE B 690 TRP 0.009 0.001 TRP B 793 HIS 0.003 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00242 (12424) covalent geometry : angle 0.57161 (16838) SS BOND : bond 0.00435 ( 10) SS BOND : angle 0.74718 ( 20) hydrogen bonds : bond 0.02959 ( 125) hydrogen bonds : angle 5.76368 ( 240) link_BETA1-4 : bond 0.00427 ( 6) link_BETA1-4 : angle 0.99045 ( 18) link_NAG-ASN : bond 0.00665 ( 16) link_NAG-ASN : angle 3.85153 ( 48) *********************** 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 157 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 HIS cc_start: 0.5943 (m90) cc_final: 0.4528 (t-170) REVERT: A 243 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7054 (p0) REVERT: A 275 ASN cc_start: 0.7591 (m-40) cc_final: 0.7271 (m-40) REVERT: A 676 ASN cc_start: 0.7980 (m-40) cc_final: 0.7769 (t0) REVERT: A 710 GLN cc_start: 0.7039 (mm110) cc_final: 0.6434 (tt0) REVERT: A 734 GLN cc_start: 0.6804 (tt0) cc_final: 0.6193 (tm-30) REVERT: B 151 GLN cc_start: 0.6924 (OUTLIER) cc_final: 0.6712 (mt0) REVERT: B 196 GLU cc_start: 0.7375 (tt0) cc_final: 0.7007 (tt0) REVERT: B 197 LYS cc_start: 0.7258 (tptt) cc_final: 0.6929 (tppt) REVERT: B 207 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7910 (mtmm) REVERT: B 275 ASN cc_start: 0.7740 (m-40) cc_final: 0.7411 (m-40) REVERT: B 537 GLU cc_start: 0.8271 (mp0) cc_final: 0.7871 (mp0) REVERT: B 687 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7510 (mp) REVERT: B 734 GLN cc_start: 0.6443 (mt0) cc_final: 0.5765 (mp-120) outliers start: 31 outliers final: 12 residues processed: 146 average time/residue: 0.5076 time to fit residues: 82.1450 Evaluate side-chains 139 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 406 THR Chi-restraints excluded: chain A residue 533 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 273 CYS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 105 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 72 optimal weight: 30.0000 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 129 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.190455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.133329 restraints weight = 12742.778| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.79 r_work: 0.3255 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12456 Z= 0.216 Angle : 0.698 11.379 16924 Z= 0.343 Chirality : 0.050 0.305 2010 Planarity : 0.004 0.048 2106 Dihedral : 6.530 59.615 2080 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.90 % Favored : 92.69 % Rotamer: Outliers : 1.74 % Allowed : 18.87 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.22), residues: 1450 helix: -2.54 (0.43), residues: 108 sheet: -2.06 (0.33), residues: 268 loop : -0.47 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 376 TYR 0.021 0.003 TYR A 185 PHE 0.021 0.002 PHE B 506 TRP 0.008 0.001 TRP B 793 HIS 0.006 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00510 (12424) covalent geometry : angle 0.67360 (16838) SS BOND : bond 0.00886 ( 10) SS BOND : angle 1.29584 ( 20) hydrogen bonds : bond 0.03978 ( 125) hydrogen bonds : angle 5.83749 ( 240) link_BETA1-4 : bond 0.00393 ( 6) link_BETA1-4 : angle 1.21638 ( 18) link_NAG-ASN : bond 0.00615 ( 16) link_NAG-ASN : angle 3.35712 ( 48) ********************** 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 146 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 HIS cc_start: 0.5940 (m90) cc_final: 0.4469 (t-170) REVERT: A 243 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7035 (p0) REVERT: A 275 ASN cc_start: 0.7649 (m-40) cc_final: 0.7320 (m-40) REVERT: A 383 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8760 (tttm) REVERT: A 676 ASN cc_start: 0.8164 (m-40) cc_final: 0.7909 (t0) REVERT: A 710 GLN cc_start: 0.7220 (mm110) cc_final: 0.6762 (tt0) REVERT: A 711 LEU cc_start: 0.7131 (mt) cc_final: 0.6830 (mt) REVERT: A 734 GLN cc_start: 0.6996 (tt0) cc_final: 0.6424 (tm-30) REVERT: B 186 ARG cc_start: 0.7755 (mmm160) cc_final: 0.7426 (mmm-85) REVERT: B 196 GLU cc_start: 0.7507 (tt0) cc_final: 0.7041 (tt0) REVERT: B 197 LYS cc_start: 0.7275 (tptt) cc_final: 0.6940 (tppt) REVERT: B 207 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8053 (mtmm) REVERT: B 275 ASN cc_start: 0.7848 (m-40) cc_final: 0.7457 (m-40) REVERT: B 734 GLN cc_start: 0.6636 (mt0) cc_final: 0.5919 (mp-120) outliers start: 24 outliers final: 17 residues processed: 139 average time/residue: 0.5016 time to fit residues: 76.5691 Evaluate side-chains 139 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 383 LYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain B residue 207 LYS 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 314 ASN Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 103 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 29 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.193127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.137419 restraints weight = 12649.663| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.81 r_work: 0.3304 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12456 Z= 0.107 Angle : 0.594 9.751 16924 Z= 0.295 Chirality : 0.046 0.316 2010 Planarity : 0.003 0.048 2106 Dihedral : 5.994 57.088 2080 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.86 % Favored : 93.86 % Rotamer: Outliers : 1.45 % Allowed : 19.23 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.23), residues: 1450 helix: -2.33 (0.43), residues: 116 sheet: -2.00 (0.32), residues: 278 loop : -0.39 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 262 TYR 0.024 0.001 TYR A 185 PHE 0.021 0.001 PHE B 690 TRP 0.008 0.001 TRP B 793 HIS 0.003 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00237 (12424) covalent geometry : angle 0.56925 (16838) SS BOND : bond 0.00470 ( 10) SS BOND : angle 0.75675 ( 20) hydrogen bonds : bond 0.02847 ( 125) hydrogen bonds : angle 5.69994 ( 240) link_BETA1-4 : bond 0.00435 ( 6) link_BETA1-4 : angle 0.97334 ( 18) link_NAG-ASN : bond 0.00605 ( 16) link_NAG-ASN : angle 3.19058 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4648.60 seconds wall clock time: 79 minutes 51.09 seconds (4791.09 seconds total)