Starting phenix.real_space_refine on Fri Jul 3 05:06:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ytp_34091/07_2026/7ytp_34091.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ytp_34091/07_2026/7ytp_34091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ytp_34091/07_2026/7ytp_34091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ytp_34091/07_2026/7ytp_34091.map" model { file = "/net/cci-nas-00/data/ceres_data/7ytp_34091/07_2026/7ytp_34091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ytp_34091/07_2026/7ytp_34091.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ytp_34091/07_2026/7ytp_34091.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ytp_34091/07_2026/7ytp_34091.cif" } 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-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 chiralities: 5 Time building chain proxies: 2.75, per 1000 atoms: 0.23 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: 0.95 Conformation dependent library (CDL) restraints added in 480.5 milliseconds 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: 0.37 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: 1.27 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: 6802 17.80 - 35.61: 505 35.61 - 53.41: 75 53.41 - 71.21: 18 71.21 - 89.02: 10 Dihedral angle restraints: 7410 sinusoidal: 3076 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 7407 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: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.770 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 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 : 12.813 87.343 4544 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 are 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/Z covalent geometry : bond 0.00326 / 0.16 (12424) covalent geometry : angle 0.59824 / 0.31 (16838) SS BOND : bond 0.00134 / 0.07 ( 10) SS BOND : angle 0.74216 / 0.59 ( 20) hydrogen bonds : bond 0.31707 / 21.55 ( 125) hydrogen bonds : angle 7.99614 / 5.52 ( 240) link_BETA1-4 : bond 0.00361 / 0.20 ( 6) link_BETA1-4 : angle 1.07327 / 0.61 ( 18) link_NAG-ASN : bond 0.00899 / 0.35 ( 16) link_NAG-ASN : angle 4.48455 / 2.46 ( 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 : 0.304 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: 0.4472 time to fit residues: 88.6929 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 : 0.362 ------------------------------------------------------------------------------- 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... ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN A 187 ASN A 202 ASN A 534 ASN A 820 HIS B 265 ASN B 337 HIS B 344 GLN B 354 GLN B 515 HIS B 534 ASN B 708 HIS B 709 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.198622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.152163 restraints weight = 12426.366| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.52 r_work: 0.3323 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 12456 Z= 0.262 Angle : 0.854 16.427 16924 Z= 0.414 Chirality : 0.055 0.454 2010 Planarity : 0.006 0.061 2106 Dihedral : 5.710 38.077 1574 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.17 % Favored : 92.41 % Rotamer: Outliers : 1.81 % Allowed : 10.09 % Favored : 88.10 % 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 are not related in a simple way. whole: -1.79 (0.23), residues: 1450 helix: -3.21 (0.31), residues: 158 sheet: -2.30 (0.33), residues: 272 loop : -0.46 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 164 TYR 0.051 0.003 TYR B 356 PHE 0.028 0.003 PHE A 408 TRP 0.011 0.002 TRP B 692 HIS 0.006 0.002 HIS B 708 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.26 (12424) covalent geometry : angle 0.81723 / 0.41 (16838) SS BOND : bond 0.01156 / 0.53 ( 10) SS BOND : angle 1.57573 / 0.94 ( 20) hydrogen bonds : bond 0.06020 / 4.03 ( 125) hydrogen bonds : angle 6.33115 / 4.22 ( 240) link_BETA1-4 : bond 0.00720 / 0.37 ( 6) link_BETA1-4 : angle 1.35583 / 0.69 ( 18) link_NAG-ASN : bond 0.01153 / 0.48 ( 16) link_NAG-ASN : angle 4.58041 / 2.68 ( 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 173 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.480 Fit side-chains REVERT: A 195 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.7977 (mm) REVERT: A 243 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.6988 (p0) REVERT: A 395 ASN cc_start: 0.7851 (m-40) cc_final: 0.6834 (p0) REVERT: A 734 GLN cc_start: 0.6521 (tt0) cc_final: 0.6168 (tm-30) REVERT: A 751 TYR cc_start: 0.7361 (t80) cc_final: 0.7032 (t80) REVERT: B 141 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: B 151 GLN cc_start: 0.7101 (tt0) cc_final: 0.6874 (mm-40) REVERT: B 175 GLU cc_start: 0.7766 (tp30) cc_final: 0.7230 (mm-30) REVERT: B 213 ASP cc_start: 0.8464 (m-30) cc_final: 0.8245 (m-30) REVERT: B 378 ARG cc_start: 0.8378 (mtp85) cc_final: 0.7472 (mtp85) REVERT: B 422 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.6394 (ptt180) REVERT: B 534 ASN cc_start: 0.7470 (OUTLIER) cc_final: 0.7268 (t0) REVERT: B 537 GLU cc_start: 0.8374 (mp0) cc_final: 0.7954 (mp0) REVERT: B 699 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7825 (mtmm) REVERT: B 710 GLN cc_start: 0.6430 (mp10) cc_final: 0.6206 (mm110) REVERT: B 777 MET cc_start: 0.6357 (tpt) cc_final: 0.6076 (tpt) outliers start: 25 outliers final: 8 residues processed: 163 average time/residue: 0.5152 time to fit residues: 91.9115 Evaluate side-chains 135 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 567 LYS 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: 8.9990 chunk 24 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 ASN A 241 GLN ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN A 820 HIS B 76 HIS B 246 ASN B 276 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 = 0.4184 r_free = 0.4184 target = 0.197810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3538 r_free = 0.3538 target = 0.136423 restraints weight = 12785.404| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.40 r_work: 0.3298 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3473 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= 0.125 Angle : 0.619 16.539 16924 Z= 0.302 Chirality : 0.046 0.305 2010 Planarity : 0.004 0.051 2106 Dihedral : 4.899 26.033 1574 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.38 % Favored : 94.34 % Rotamer: Outliers : 2.03 % Allowed : 12.55 % Favored : 85.41 % 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 are not related in a simple way. whole: -1.69 (0.23), residues: 1450 helix: -3.07 (0.33), residues: 162 sheet: -2.23 (0.33), residues: 272 loop : -0.39 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 750 TYR 0.015 0.002 TYR A 233 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/Z covalent geometry : bond 0.00283 / 0.12 (12424) covalent geometry : angle 0.58507 / 0.29 (16838) SS BOND : bond 0.00575 / 0.27 ( 10) SS BOND : angle 0.80359 / 0.53 ( 20) hydrogen bonds : bond 0.04003 / 2.78 ( 125) hydrogen bonds : angle 6.05658 / 3.99 ( 240) link_BETA1-4 : bond 0.00463 / 0.26 ( 6) link_BETA1-4 : angle 0.92883 / 0.52 ( 18) link_NAG-ASN : bond 0.00712 / 0.30 ( 16) link_NAG-ASN : angle 3.77315 / 2.12 ( 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: 28 poor density : 124 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7578 (mt-10) REVERT: A 243 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7024 (p0) REVERT: A 395 ASN cc_start: 0.7962 (m-40) cc_final: 0.6938 (p0) REVERT: A 654 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: A 676 ASN cc_start: 0.8186 (m110) cc_final: 0.7887 (t0) REVERT: A 710 GLN cc_start: 0.7081 (mm110) cc_final: 0.6791 (tt0) REVERT: A 734 GLN cc_start: 0.6920 (tt0) cc_final: 0.6520 (mp-120) REVERT: B 138 GLN cc_start: 0.8287 (mt0) cc_final: 0.8021 (mt0) REVERT: B 151 GLN cc_start: 0.7365 (tt0) cc_final: 0.7142 (mm-40) REVERT: B 378 ARG cc_start: 0.8516 (mtp85) cc_final: 0.7670 (mtp180) REVERT: B 710 GLN cc_start: 0.6586 (mp10) cc_final: 0.6339 (mm110) outliers start: 28 outliers final: 8 residues processed: 139 average time/residue: 0.4620 time to fit residues: 70.7422 Evaluate side-chains 126 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU 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 A residue 812 VAL 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 370 LYS Chi-restraints excluded: chain B residue 395 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 94 optimal weight: 0.0970 chunk 66 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 51 optimal weight: 0.3980 chunk 64 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 5 optimal weight: 0.4980 chunk 130 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 GLN A 202 ASN ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN B 167 GLN B 276 ASN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 GLN B 782 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.199006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3539 r_free = 0.3539 target = 0.137092 restraints weight = 12752.709| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.54 r_work: 0.3347 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12456 Z= 0.094 Angle : 0.574 16.097 16924 Z= 0.278 Chirality : 0.046 0.503 2010 Planarity : 0.003 0.048 2106 Dihedral : 4.483 26.777 1574 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.66 % Favored : 94.07 % Rotamer: Outliers : 1.52 % Allowed : 14.59 % Favored : 83.89 % 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 are not related in a simple way. whole: -1.52 (0.23), residues: 1450 helix: -2.75 (0.36), residues: 150 sheet: -2.14 (0.34), residues: 272 loop : -0.34 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 750 TYR 0.011 0.001 TYR B 233 PHE 0.025 0.001 PHE B 690 TRP 0.009 0.001 TRP A 793 HIS 0.003 0.001 HIS A 820 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (12424) covalent geometry : angle 0.53814 / 0.27 (16838) SS BOND : bond 0.00386 / 0.18 ( 10) SS BOND : angle 0.60222 / 0.41 ( 20) hydrogen bonds : bond 0.02863 / 1.98 ( 125) hydrogen bonds : angle 5.67886 / 3.70 ( 240) link_BETA1-4 : bond 0.00489 / 0.26 ( 6) link_BETA1-4 : angle 0.83923 / 0.49 ( 18) link_NAG-ASN : bond 0.00694 / 0.28 ( 16) link_NAG-ASN : angle 3.76446 / 2.14 ( 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 146 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7448 (mt0) cc_final: 0.6636 (tt0) REVERT: A 243 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7016 (p0) REVERT: A 395 ASN cc_start: 0.7885 (m-40) cc_final: 0.6890 (p0) REVERT: A 551 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8330 (m-40) REVERT: A 650 LEU cc_start: 0.8516 (mm) cc_final: 0.8126 (mt) REVERT: A 676 ASN cc_start: 0.7691 (m110) cc_final: 0.7440 (t0) REVERT: A 710 GLN cc_start: 0.6918 (mm110) cc_final: 0.6445 (tt0) REVERT: A 734 GLN cc_start: 0.6897 (tt0) cc_final: 0.6362 (tm-30) REVERT: B 138 GLN cc_start: 0.8291 (mt0) cc_final: 0.7874 (mt0) REVERT: B 175 GLU cc_start: 0.7956 (mm-30) cc_final: 0.6939 (tp30) REVERT: B 207 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7605 (mppt) REVERT: B 249 ASN cc_start: 0.7496 (p0) cc_final: 0.7250 (m-40) REVERT: B 710 GLN cc_start: 0.6798 (mp10) cc_final: 0.6483 (mm110) outliers start: 21 outliers final: 3 residues processed: 136 average time/residue: 0.3842 time to fit residues: 58.6500 Evaluate side-chains 122 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 395 ASN 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: 0.0060 chunk 77 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 143 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 overall best weight: 5.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 ASN A 202 ASN ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 276 ASN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 HIS B 820 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.190149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.126675 restraints weight = 12878.562| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.64 r_work: 0.3221 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 12456 Z= 0.305 Angle : 0.812 14.887 16924 Z= 0.396 Chirality : 0.054 0.290 2010 Planarity : 0.005 0.048 2106 Dihedral : 5.486 31.809 1574 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.03 % Favored : 92.55 % Rotamer: Outliers : 3.48 % Allowed : 14.15 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.22), residues: 1450 helix: -3.23 (0.32), residues: 150 sheet: -2.14 (0.33), residues: 268 loop : -0.49 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 376 TYR 0.026 0.003 TYR B 356 PHE 0.022 0.003 PHE A 506 TRP 0.009 0.002 TRP B 793 HIS 0.009 0.002 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00719 / 0.30 (12424) covalent geometry : angle 0.78277 / 0.39 (16838) SS BOND : bond 0.01193 / 0.57 ( 10) SS BOND : angle 1.73519 / 1.15 ( 20) hydrogen bonds : bond 0.04924 / 3.40 ( 125) hydrogen bonds : angle 6.04358 / 4.01 ( 240) link_BETA1-4 : bond 0.00526 / 0.28 ( 6) link_BETA1-4 : angle 1.38680 / 0.74 ( 18) link_NAG-ASN : bond 0.00796 / 0.36 ( 16) link_NAG-ASN : angle 3.97240 / 2.32 ( 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 175 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 127 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7791 (mt-10) REVERT: A 175 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7925 (mm-30) REVERT: A 243 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7090 (p0) REVERT: A 360 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8316 (ttp) REVERT: A 654 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8323 (tt0) REVERT: A 665 LEU cc_start: 0.8002 (mt) cc_final: 0.7793 (mp) REVERT: A 710 GLN cc_start: 0.7158 (mm110) cc_final: 0.6640 (tt0) REVERT: A 734 GLN cc_start: 0.7027 (tt0) cc_final: 0.6368 (tm-30) REVERT: A 761 MET cc_start: 0.4737 (OUTLIER) cc_final: 0.4526 (pmm) REVERT: A 778 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.5955 (tt) REVERT: B 138 GLN cc_start: 0.8110 (mt0) cc_final: 0.7751 (mt0) REVERT: B 151 GLN cc_start: 0.7028 (mm-40) cc_final: 0.6318 (mt0) REVERT: B 196 GLU cc_start: 0.7308 (tt0) cc_final: 0.6840 (tt0) REVERT: B 207 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7997 (mtmm) REVERT: B 223 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7889 (mm) REVERT: B 537 GLU cc_start: 0.8137 (mp0) cc_final: 0.7764 (mp0) REVERT: B 603 MET cc_start: 0.9191 (mtp) cc_final: 0.8896 (mtp) REVERT: B 710 GLN cc_start: 0.6800 (mp10) cc_final: 0.6406 (mm110) outliers start: 48 outliers final: 17 residues processed: 156 average time/residue: 0.4554 time to fit residues: 78.6885 Evaluate side-chains 148 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 761 MET 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 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 406 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 51 optimal weight: 9.9990 chunk 70 optimal weight: 30.0000 chunk 95 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 134 optimal weight: 0.3980 chunk 131 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 ASN ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN B 167 GLN B 265 ASN B 276 ASN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN B 534 ASN ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.192798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131388 restraints weight = 12725.246| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.63 r_work: 0.3267 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12456 Z= 0.151 Angle : 0.640 14.887 16924 Z= 0.313 Chirality : 0.048 0.402 2010 Planarity : 0.004 0.048 2106 Dihedral : 4.938 25.934 1574 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.86 % Favored : 93.79 % Rotamer: Outliers : 2.83 % Allowed : 15.67 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.22), residues: 1450 helix: -3.12 (0.36), residues: 138 sheet: -2.12 (0.33), residues: 272 loop : -0.45 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 262 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 0.004 0.001 HIS B 708 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (12424) covalent geometry : angle 0.60463 / 0.30 (16838) SS BOND : bond 0.00626 / 0.31 ( 10) SS BOND : angle 0.96766 / 0.64 ( 20) hydrogen bonds : bond 0.03425 / 2.35 ( 125) hydrogen bonds : angle 5.86763 / 3.88 ( 240) link_BETA1-4 : bond 0.00486 / 0.27 ( 6) link_BETA1-4 : angle 1.03658 / 0.58 ( 18) link_NAG-ASN : bond 0.00863 / 0.34 ( 16) link_NAG-ASN : angle 3.92855 / 2.26 ( 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: 39 poor density : 125 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7742 (mm-30) REVERT: A 243 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7057 (p0) REVERT: A 275 ASN cc_start: 0.7508 (m-40) cc_final: 0.7034 (m-40) REVERT: A 360 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8143 (ttp) REVERT: A 377 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8443 (mt) REVERT: A 383 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8767 (tttm) REVERT: A 395 ASN cc_start: 0.8009 (OUTLIER) cc_final: 0.7669 (t0) REVERT: A 676 ASN cc_start: 0.8151 (m-40) cc_final: 0.7882 (t0) REVERT: A 710 GLN cc_start: 0.7001 (mm110) cc_final: 0.6443 (tt0) REVERT: A 734 GLN cc_start: 0.6973 (tt0) cc_final: 0.6306 (tm-30) REVERT: B 130 LYS cc_start: 0.7353 (tppp) cc_final: 0.7108 (tppp) REVERT: B 138 GLN cc_start: 0.8131 (mt0) cc_final: 0.7635 (mt0) REVERT: B 186 ARG cc_start: 0.7726 (mmm160) cc_final: 0.7346 (mmm-85) REVERT: B 196 GLU cc_start: 0.7229 (tt0) cc_final: 0.6808 (tt0) REVERT: B 207 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.8011 (mtmm) REVERT: B 250 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7355 (mt0) REVERT: B 603 MET cc_start: 0.9141 (mtp) cc_final: 0.8841 (mtp) REVERT: B 710 GLN cc_start: 0.6816 (mp10) cc_final: 0.6278 (mm110) REVERT: B 777 MET cc_start: 0.5991 (OUTLIER) cc_final: 0.5368 (tpt) outliers start: 39 outliers final: 12 residues processed: 146 average time/residue: 0.4388 time to fit residues: 71.0224 Evaluate side-chains 141 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 383 LYS Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 422 ARG 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 249 ASN Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 777 MET Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 111 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 50 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 ASN A 300 ASN ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN A 800 HIS ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS B 151 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 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.188140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128897 restraints weight = 12775.171| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.57 r_work: 0.3182 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 12456 Z= 0.372 Angle : 0.902 13.408 16924 Z= 0.436 Chirality : 0.058 0.390 2010 Planarity : 0.006 0.050 2106 Dihedral : 5.792 35.787 1574 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.66 % Favored : 91.86 % Rotamer: Outliers : 3.63 % Allowed : 14.88 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.22), residues: 1450 helix: -3.28 (0.34), residues: 120 sheet: -2.17 (0.32), residues: 268 loop : -0.62 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 376 TYR 0.019 0.003 TYR A 233 PHE 0.026 0.004 PHE A 506 TRP 0.009 0.002 TRP B 793 HIS 0.011 0.002 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00878 / 0.37 (12424) covalent geometry : angle 0.87667 / 0.43 (16838) SS BOND : bond 0.01332 / 0.62 ( 10) SS BOND : angle 1.82457 / 1.22 ( 20) hydrogen bonds : bond 0.05524 / 3.77 ( 125) hydrogen bonds : angle 6.16261 / 4.17 ( 240) link_BETA1-4 : bond 0.00513 / 0.28 ( 6) link_BETA1-4 : angle 1.64055 / 0.93 ( 18) link_NAG-ASN : bond 0.00797 / 0.39 ( 16) link_NAG-ASN : angle 3.87250 / 2.31 ( 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 173 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 123 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: A 196 GLU cc_start: 0.7624 (tt0) cc_final: 0.7265 (tt0) REVERT: A 243 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7112 (p0) REVERT: A 275 ASN cc_start: 0.7729 (m-40) cc_final: 0.7311 (m-40) REVERT: A 360 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8167 (ttp) REVERT: A 377 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8652 (mt) REVERT: A 654 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: A 676 ASN cc_start: 0.8301 (m-40) cc_final: 0.7959 (t0) REVERT: A 710 GLN cc_start: 0.7253 (mm110) cc_final: 0.6792 (tt0) REVERT: A 734 GLN cc_start: 0.7013 (tt0) cc_final: 0.6422 (tm-30) REVERT: B 130 LYS cc_start: 0.7423 (tppp) cc_final: 0.7095 (tppp) REVERT: B 138 GLN cc_start: 0.8309 (mt0) cc_final: 0.7876 (mt0) REVERT: B 186 ARG cc_start: 0.7809 (mmm160) cc_final: 0.7511 (mmm-85) REVERT: B 196 GLU cc_start: 0.7617 (tt0) cc_final: 0.7120 (tt0) REVERT: B 197 LYS cc_start: 0.7276 (tptt) cc_final: 0.6901 (tppt) REVERT: B 223 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7996 (mm) REVERT: B 243 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6967 (m-30) REVERT: B 250 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7435 (mt0) REVERT: B 688 LYS cc_start: 0.6626 (mmtt) cc_final: 0.6053 (tttt) REVERT: B 710 GLN cc_start: 0.6966 (mp10) cc_final: 0.6477 (mm110) REVERT: B 751 TYR cc_start: 0.7556 (t80) cc_final: 0.7197 (t80) outliers start: 50 outliers final: 20 residues processed: 158 average time/residue: 0.4861 time to fit residues: 84.1533 Evaluate side-chains 146 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 778 LEU 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 250 GLN Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 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: 5.9990 chunk 100 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 144 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 6 optimal weight: 20.0000 chunk 128 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.193183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.130566 restraints weight = 12712.290| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.55 r_work: 0.3232 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12456 Z= 0.112 Angle : 0.635 13.535 16924 Z= 0.308 Chirality : 0.048 0.540 2010 Planarity : 0.004 0.048 2106 Dihedral : 4.938 25.504 1574 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.66 % Favored : 94.07 % Rotamer: Outliers : 2.25 % Allowed : 16.69 % Favored : 81.06 % 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 are not related in a simple way. whole: -1.68 (0.22), residues: 1450 helix: -2.97 (0.35), residues: 138 sheet: -2.07 (0.33), residues: 268 loop : -0.54 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 262 TYR 0.014 0.001 TYR A 233 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/Z covalent geometry : bond 0.00243 / 0.11 (12424) covalent geometry : angle 0.59638 / 0.30 (16838) SS BOND : bond 0.00439 / 0.24 ( 10) SS BOND : angle 0.73504 / 0.48 ( 20) hydrogen bonds : bond 0.03129 / 2.11 ( 125) hydrogen bonds : angle 5.89468 / 3.91 ( 240) link_BETA1-4 : bond 0.00439 / 0.24 ( 6) link_BETA1-4 : angle 0.96790 / 0.55 ( 18) link_NAG-ASN : bond 0.00832 / 0.33 ( 16) link_NAG-ASN : angle 4.12643 / 2.37 ( 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: 31 poor density : 137 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.7066 (p0) REVERT: A 275 ASN cc_start: 0.7665 (m-40) cc_final: 0.7328 (m-40) REVERT: A 360 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8159 (ttp) REVERT: A 676 ASN cc_start: 0.8050 (m-40) cc_final: 0.7816 (t0) REVERT: A 690 PHE cc_start: 0.7388 (t80) cc_final: 0.7121 (t80) REVERT: A 710 GLN cc_start: 0.7057 (mm110) cc_final: 0.6478 (tt0) REVERT: A 734 GLN cc_start: 0.6913 (tt0) cc_final: 0.6257 (tm-30) REVERT: A 777 MET cc_start: 0.5752 (tmm) cc_final: 0.5428 (tmm) REVERT: B 130 LYS cc_start: 0.7407 (tppp) cc_final: 0.7058 (tppp) REVERT: B 186 ARG cc_start: 0.7714 (mmm160) cc_final: 0.7365 (mmm-85) REVERT: B 196 GLU cc_start: 0.7408 (tt0) cc_final: 0.6978 (tt0) REVERT: B 197 LYS cc_start: 0.7192 (tptt) cc_final: 0.6789 (tppt) REVERT: B 207 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7960 (mtmm) REVERT: B 243 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6931 (m-30) REVERT: B 250 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7407 (mt0) REVERT: B 311 LYS cc_start: 0.8525 (tttm) cc_final: 0.7980 (ttmp) REVERT: B 688 LYS cc_start: 0.6592 (mmtt) cc_final: 0.6037 (tttt) REVERT: B 710 GLN cc_start: 0.6915 (mp10) cc_final: 0.6189 (mm110) REVERT: B 751 TYR cc_start: 0.7379 (t80) cc_final: 0.7121 (t80) outliers start: 31 outliers final: 10 residues processed: 155 average time/residue: 0.4198 time to fit residues: 71.6454 Evaluate side-chains 145 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 360 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 586 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 250 GLN Chi-restraints excluded: chain B residue 273 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 128 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 72 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.190666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.140384 restraints weight = 12714.925| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.32 r_work: 0.3299 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12456 Z= 0.208 Angle : 0.700 11.633 16924 Z= 0.340 Chirality : 0.051 0.316 2010 Planarity : 0.004 0.048 2106 Dihedral : 5.153 26.165 1574 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.83 % Favored : 92.76 % Rotamer: Outliers : 2.03 % Allowed : 17.20 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.22), residues: 1450 helix: -2.58 (0.42), 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 0.004 0.001 ARG B 376 TYR 0.015 0.002 TYR A 233 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/Z covalent geometry : bond 0.00491 / 0.21 (12424) covalent geometry : angle 0.67218 / 0.33 (16838) SS BOND : bond 0.00864 / 0.41 ( 10) SS BOND : angle 1.30617 / 0.88 ( 20) hydrogen bonds : bond 0.03925 / 2.69 ( 125) hydrogen bonds : angle 5.88381 / 3.92 ( 240) link_BETA1-4 : bond 0.00453 / 0.25 ( 6) link_BETA1-4 : angle 1.21193 / 0.70 ( 18) link_NAG-ASN : bond 0.00658 / 0.28 ( 16) link_NAG-ASN : angle 3.61788 / 2.09 ( 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 154 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7044 (p0) REVERT: A 275 ASN cc_start: 0.7636 (m-40) cc_final: 0.7307 (m-40) REVERT: A 360 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7972 (ttp) REVERT: A 377 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8472 (mt) REVERT: A 676 ASN cc_start: 0.8174 (m-40) cc_final: 0.7924 (t0) REVERT: A 690 PHE cc_start: 0.7353 (t80) cc_final: 0.7035 (t80) REVERT: A 710 GLN cc_start: 0.7185 (mm110) cc_final: 0.6744 (tt0) REVERT: A 711 LEU cc_start: 0.7202 (mt) cc_final: 0.6911 (mt) REVERT: A 734 GLN cc_start: 0.7001 (tt0) cc_final: 0.6458 (tm-30) REVERT: A 777 MET cc_start: 0.5775 (OUTLIER) cc_final: 0.5530 (tmm) REVERT: B 151 GLN cc_start: 0.7095 (mt0) cc_final: 0.6590 (mt0) REVERT: B 186 ARG cc_start: 0.7632 (mmm160) cc_final: 0.7378 (mmm-85) REVERT: B 196 GLU cc_start: 0.7505 (tt0) cc_final: 0.7005 (tt0) REVERT: B 197 LYS cc_start: 0.7272 (tptt) cc_final: 0.6937 (tppt) REVERT: B 207 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7978 (mtmm) REVERT: B 243 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6856 (m-30) REVERT: B 250 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7417 (mt0) REVERT: B 688 LYS cc_start: 0.6550 (mmtt) cc_final: 0.6120 (tppt) REVERT: B 710 GLN cc_start: 0.6840 (mp10) cc_final: 0.6350 (mm110) outliers start: 28 outliers final: 15 residues processed: 143 average time/residue: 0.4338 time to fit residues: 68.6477 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 : 0.415 ------------------------------------------------------------------------------- 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 360 MET Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 THR 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 243 ASP Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 105 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.189391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139746 restraints weight = 12739.542| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.34 r_work: 0.3287 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12456 Z= 0.262 Angle : 0.778 14.846 16924 Z= 0.377 Chirality : 0.054 0.541 2010 Planarity : 0.005 0.048 2106 Dihedral : 5.410 25.832 1574 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.86 % Favored : 91.79 % Rotamer: Outliers : 2.47 % Allowed : 17.05 % Favored : 80.48 % 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 are not related in a simple way. whole: -1.66 (0.22), residues: 1450 helix: -2.77 (0.40), residues: 108 sheet: -2.14 (0.32), residues: 268 loop : -0.61 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 376 TYR 0.020 0.003 TYR A 380 PHE 0.023 0.003 PHE B 506 TRP 0.008 0.002 TRP B 793 HIS 0.007 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.26 (12424) covalent geometry : angle 0.74284 / 0.37 (16838) SS BOND : bond 0.01034 / 0.49 ( 10) SS BOND : angle 1.44958 / 0.97 ( 20) hydrogen bonds : bond 0.04526 / 3.09 ( 125) hydrogen bonds : angle 6.08385 / 4.07 ( 240) link_BETA1-4 : bond 0.00507 / 0.28 ( 6) link_BETA1-4 : angle 1.37293 / 0.80 ( 18) link_NAG-ASN : bond 0.00867 / 0.35 ( 16) link_NAG-ASN : angle 4.28342 / 2.54 ( 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 157 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 HIS cc_start: 0.6013 (m90) cc_final: 0.4492 (t-170) REVERT: A 243 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7034 (p0) REVERT: A 275 ASN cc_start: 0.7673 (m-40) cc_final: 0.7328 (m-40) REVERT: A 360 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7990 (ttp) REVERT: A 377 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8497 (mt) REVERT: A 419 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7688 (mt0) REVERT: A 676 ASN cc_start: 0.8161 (m-40) cc_final: 0.7913 (t0) REVERT: A 710 GLN cc_start: 0.7075 (mm110) cc_final: 0.6746 (tt0) REVERT: A 734 GLN cc_start: 0.7160 (tt0) cc_final: 0.6555 (tm-30) REVERT: B 130 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7285 (tppp) REVERT: B 151 GLN cc_start: 0.7150 (mt0) cc_final: 0.6668 (mt0) REVERT: B 186 ARG cc_start: 0.7723 (mmm160) cc_final: 0.7507 (mmm-85) REVERT: B 196 GLU cc_start: 0.7567 (tt0) cc_final: 0.7054 (tt0) REVERT: B 197 LYS cc_start: 0.7304 (tptt) cc_final: 0.6965 (tppt) REVERT: B 207 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7985 (mtmm) REVERT: B 243 ASP cc_start: 0.7087 (OUTLIER) cc_final: 0.6803 (m-30) REVERT: B 250 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7452 (mt0) REVERT: B 275 ASN cc_start: 0.7893 (m-40) cc_final: 0.7533 (m-40) REVERT: B 688 LYS cc_start: 0.6776 (mmtt) cc_final: 0.6217 (tttt) REVERT: B 710 GLN cc_start: 0.6875 (mp10) cc_final: 0.6476 (mm110) outliers start: 34 outliers final: 19 residues processed: 145 average time/residue: 0.4483 time to fit residues: 71.9032 Evaluate side-chains 150 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain B residue 130 LYS 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 250 GLN Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 103 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 130 optimal weight: 0.0980 chunk 72 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.192146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3539 r_free = 0.3539 target = 0.136053 restraints weight = 12646.086| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.69 r_work: 0.3298 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12456 Z= 0.126 Angle : 0.621 11.007 16924 Z= 0.305 Chirality : 0.048 0.345 2010 Planarity : 0.004 0.048 2106 Dihedral : 4.931 24.786 1574 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.48 % Favored : 93.24 % Rotamer: Outliers : 2.10 % Allowed : 17.49 % 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 are not related in a simple way. whole: -1.67 (0.22), residues: 1450 helix: -2.86 (0.37), residues: 134 sheet: -2.07 (0.32), residues: 268 loop : -0.56 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 376 TYR 0.018 0.002 TYR A 185 PHE 0.020 0.002 PHE B 690 TRP 0.008 0.001 TRP A 793 HIS 0.003 0.001 HIS B 708 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (12424) covalent geometry : angle 0.59650 / 0.30 (16838) SS BOND : bond 0.00521 / 0.26 ( 10) SS BOND : angle 0.85873 / 0.58 ( 20) hydrogen bonds : bond 0.03157 / 2.18 ( 125) hydrogen bonds : angle 5.91427 / 3.96 ( 240) link_BETA1-4 : bond 0.00462 / 0.25 ( 6) link_BETA1-4 : angle 1.02750 / 0.59 ( 18) link_NAG-ASN : bond 0.00618 / 0.27 ( 16) link_NAG-ASN : angle 3.23315 / 1.86 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4174.71 seconds wall clock time: 71 minutes 52.73 seconds (4312.73 seconds total)