Starting phenix.real_space_refine on Sun Jul 5 15:26:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n4m_48898/07_2026/9n4m_48898.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n4m_48898/07_2026/9n4m_48898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n4m_48898/07_2026/9n4m_48898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n4m_48898/07_2026/9n4m_48898.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n4m_48898/07_2026/9n4m_48898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n4m_48898/07_2026/9n4m_48898.map" } resolution = 3.77 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= -0.049 sd= 1.292 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 160 5.16 5 Na 4 4.78 5 C 18076 2.51 5 N 4490 2.21 5 O 5308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s 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: 28054 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 6655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 840, 6655 Classifications: {'peptide': 840} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 806} Chain: "B" Number of atoms: 6655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 840, 6655 Classifications: {'peptide': 840} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 806} Chain: "C" Number of atoms: 6655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 840, 6655 Classifications: {'peptide': 840} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 806} Chain: "D" Number of atoms: 6655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 840, 6655 Classifications: {'peptide': 840} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 806} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 316 Ad-hoc single atom residues: {' NA': 4} Unusual residues: {'NAG': 4, 'POV': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 250 Unusual residues: {'NAG': 3, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 212 Unusual residues: {'NAG': 4, 'POV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 250 Unusual residues: {'NAG': 3, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.54, per 1000 atoms: 0.23 Number of scatterers: 28054 At special positions: 0 Unit cell: (128.74, 149.24, 213.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 160 16.00 P 16 15.00 Na 4 11.00 O 5308 8.00 N 4490 7.00 C 18076 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.04 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.04 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " 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 ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA N 3 " - " MAN N 4 " ALPHA1-6 " BMA H 3 " - " MAN H 5 " " BMA N 3 " - " MAN N 5 " BETA1-4 " 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 H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1004 " - " ASN A 67 " " NAG A1005 " - " ASN A 275 " " NAG A1006 " - " ASN A 546 " " NAG A1007 " - " ASN A 751 " " NAG B1003 " - " ASN B 67 " " NAG B1004 " - " ASN B 73 " " NAG B1005 " - " ASN B 412 " " NAG C1003 " - " ASN C 67 " " NAG C1004 " - " ASN C 275 " " NAG C1005 " - " ASN C 546 " " NAG C1006 " - " ASN C 751 " " NAG D1005 " - " ASN D 67 " " NAG D1006 " - " ASN D 73 " " NAG D1007 " - " ASN D 412 " " NAG E 1 " - " ASN A 378 " " NAG F 1 " - " ASN A 412 " " NAG G 1 " - " ASN B 275 " " NAG H 1 " - " ASN B 378 " " NAG I 1 " - " ASN B 546 " " NAG J 1 " - " ASN B 751 " " NAG K 1 " - " ASN C 378 " " NAG L 1 " - " ASN C 412 " " NAG M 1 " - " ASN D 275 " " NAG N 1 " - " ASN D 378 " " NAG O 1 " - " ASN D 546 " " NAG P 1 " - " ASN D 751 " Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.3 seconds 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6272 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 38 sheets defined 41.1% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 removed outlier: 3.554A pdb=" N PHE A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 100 removed outlier: 3.799A pdb=" N SER A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 removed outlier: 3.584A pdb=" N VAL A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 168 Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.525A pdb=" N ARG A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.792A pdb=" N LEU A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.630A pdb=" N MET A 245 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 298 removed outlier: 3.737A pdb=" N ILE A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 294 " --> pdb=" O SER A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 334 removed outlier: 3.593A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 removed outlier: 4.202A pdb=" N SER A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A 364 " --> pdb=" O MET A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 474 removed outlier: 3.526A pdb=" N GLU A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 505 removed outlier: 3.786A pdb=" N LEU A 505 " --> pdb=" O MET A 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 501 through 505' Processing helix chain 'A' and resid 520 through 527 removed outlier: 4.144A pdb=" N VAL A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 576 removed outlier: 3.680A pdb=" N GLY A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 585 removed outlier: 3.663A pdb=" N ARG A 583 " --> pdb=" O PHE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 618 removed outlier: 3.559A pdb=" N PHE A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TRP A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 618 " --> pdb=" O PHE A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 648 removed outlier: 4.077A pdb=" N TRP A 641 " --> pdb=" O GLY A 637 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 646 " --> pdb=" O PHE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 660 removed outlier: 4.632A pdb=" N ALA A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 665 removed outlier: 3.651A pdb=" N MET A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 removed outlier: 3.571A pdb=" N ALA A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 671 through 676' Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.506A pdb=" N PHE A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS A 696 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 712 removed outlier: 3.921A pdb=" N PHE A 708 " --> pdb=" O LYS A 704 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET A 709 " --> pdb=" O MET A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 731 removed outlier: 4.117A pdb=" N VAL A 728 " --> pdb=" O GLY A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 748 Processing helix chain 'A' and resid 773 through 788 removed outlier: 3.811A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A 778 " --> pdb=" O TYR A 774 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 780 " --> pdb=" O ASP A 776 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 783 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN A 784 " --> pdb=" O ILE A 780 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 794 through 799 removed outlier: 3.529A pdb=" N TRP A 798 " --> pdb=" O MET A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 821 removed outlier: 3.979A pdb=" N ILE A 820 " --> pdb=" O GLY A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 853 removed outlier: 3.508A pdb=" N LEU A 831 " --> pdb=" O LEU A 827 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 840 " --> pdb=" O PHE A 836 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 846 " --> pdb=" O PHE A 842 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN A 851 " --> pdb=" O LYS A 847 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 853 " --> pdb=" O ASN A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 868 removed outlier: 3.771A pdb=" N MET A 861 " --> pdb=" O PHE A 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 removed outlier: 3.545A pdb=" N ALA B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 100 removed outlier: 3.594A pdb=" N CYS B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 123 removed outlier: 3.713A pdb=" N VAL B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 164 removed outlier: 3.942A pdb=" N LEU B 161 " --> pdb=" O SER B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 removed outlier: 3.624A pdb=" N LEU B 182 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.567A pdb=" N LYS B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.663A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 245 removed outlier: 3.978A pdb=" N ALA B 236 " --> pdb=" O HIS B 232 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.647A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.819A pdb=" N LEU B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 removed outlier: 4.183A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 364 " --> pdb=" O MET B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 removed outlier: 3.568A pdb=" N GLU B 469 " --> pdb=" O ASP B 465 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 507 removed outlier: 3.996A pdb=" N ASP B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.622A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 560 removed outlier: 3.830A pdb=" N LEU B 559 " --> pdb=" O LEU B 556 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER B 560 " --> pdb=" O ASN B 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 556 through 560' Processing helix chain 'B' and resid 561 through 572 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 607 through 620 Processing helix chain 'B' and resid 630 through 632 No H-bonds generated for 'chain 'B' and resid 630 through 632' Processing helix chain 'B' and resid 633 through 660 removed outlier: 3.671A pdb=" N GLY B 637 " --> pdb=" O THR B 633 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TRP B 641 " --> pdb=" O GLY B 637 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B 647 " --> pdb=" O PHE B 643 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 696 removed outlier: 3.915A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 710 removed outlier: 3.886A pdb=" N LYS B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 707 " --> pdb=" O ASP B 703 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 708 " --> pdb=" O LYS B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.814A pdb=" N GLY B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 746 Processing helix chain 'B' and resid 774 through 788 removed outlier: 3.523A pdb=" N THR B 779 " --> pdb=" O ARG B 775 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE B 780 " --> pdb=" O ASP B 776 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 781 " --> pdb=" O LYS B 777 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU B 787 " --> pdb=" O LEU B 783 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 788 " --> pdb=" O GLN B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 removed outlier: 3.534A pdb=" N LYS B 795 " --> pdb=" O LEU B 791 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TRP B 799 " --> pdb=" O LYS B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 853 removed outlier: 3.776A pdb=" N VAL B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU B 833 " --> pdb=" O ALA B 829 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 837 " --> pdb=" O LEU B 833 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR B 844 " --> pdb=" O GLY B 840 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN B 851 " --> pdb=" O LYS B 847 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU B 853 " --> pdb=" O ASN B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 867 Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.554A pdb=" N PHE C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 100 removed outlier: 3.799A pdb=" N SER C 92 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 126 removed outlier: 3.583A pdb=" N VAL C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.525A pdb=" N ARG C 184 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 211 through 222 removed outlier: 3.793A pdb=" N LEU C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 241 through 246 removed outlier: 3.630A pdb=" N MET C 245 " --> pdb=" O GLN C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 298 removed outlier: 3.737A pdb=" N ILE C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU C 294 " --> pdb=" O SER C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 334 removed outlier: 3.593A pdb=" N VAL C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 364 removed outlier: 4.202A pdb=" N SER C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 362 " --> pdb=" O ARG C 358 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C 364 " --> pdb=" O MET C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 474 removed outlier: 3.527A pdb=" N GLU C 469 " --> pdb=" O ASP C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 505 removed outlier: 3.786A pdb=" N LEU C 505 " --> pdb=" O MET C 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 501 through 505' Processing helix chain 'C' and resid 520 through 527 removed outlier: 4.145A pdb=" N VAL C 526 " --> pdb=" O VAL C 522 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 527 " --> pdb=" O ARG C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 576 removed outlier: 3.680A pdb=" N GLY C 573 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 585 removed outlier: 3.663A pdb=" N ARG C 583 " --> pdb=" O PHE C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 618 removed outlier: 3.560A pdb=" N PHE C 612 " --> pdb=" O LEU C 608 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TRP C 613 " --> pdb=" O LEU C 609 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 618 " --> pdb=" O PHE C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 635 through 648 removed outlier: 4.077A pdb=" N TRP C 641 " --> pdb=" O GLY C 637 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 646 " --> pdb=" O PHE C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 660 removed outlier: 4.632A pdb=" N ALA C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 665 removed outlier: 3.651A pdb=" N MET C 664 " --> pdb=" O THR C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 676 removed outlier: 3.572A pdb=" N ALA C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 676 " --> pdb=" O ASP C 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 671 through 676' Processing helix chain 'C' and resid 688 through 696 removed outlier: 3.506A pdb=" N PHE C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS C 696 " --> pdb=" O THR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 712 removed outlier: 3.919A pdb=" N PHE C 708 " --> pdb=" O LYS C 704 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET C 709 " --> pdb=" O MET C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 731 removed outlier: 4.118A pdb=" N VAL C 728 " --> pdb=" O GLY C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 748 Processing helix chain 'C' and resid 773 through 788 removed outlier: 3.811A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE C 778 " --> pdb=" O TYR C 774 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 780 " --> pdb=" O ASP C 776 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 783 " --> pdb=" O THR C 779 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 784 " --> pdb=" O ILE C 780 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU C 785 " --> pdb=" O ALA C 781 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 Processing helix chain 'C' and resid 794 through 799 removed outlier: 3.529A pdb=" N TRP C 798 " --> pdb=" O MET C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 821 removed outlier: 3.979A pdb=" N ILE C 820 " --> pdb=" O GLY C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 853 removed outlier: 3.507A pdb=" N LEU C 831 " --> pdb=" O LEU C 827 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 833 " --> pdb=" O ALA C 829 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER C 834 " --> pdb=" O GLY C 830 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL C 837 " --> pdb=" O LEU C 833 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY C 840 " --> pdb=" O PHE C 836 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C 846 " --> pdb=" O PHE C 842 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN C 851 " --> pdb=" O LYS C 847 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU C 853 " --> pdb=" O ASN C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 868 removed outlier: 3.770A pdb=" N MET C 861 " --> pdb=" O PHE C 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 removed outlier: 3.545A pdb=" N ALA D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 100 removed outlier: 3.595A pdb=" N CYS D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 123 removed outlier: 3.713A pdb=" N VAL D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 164 removed outlier: 3.942A pdb=" N LEU D 161 " --> pdb=" O SER D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 removed outlier: 3.624A pdb=" N LEU D 182 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 190 removed outlier: 3.567A pdb=" N LYS D 190 " --> pdb=" O GLN D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 194 Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.663A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 245 removed outlier: 3.978A pdb=" N ALA D 236 " --> pdb=" O HIS D 232 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 299 removed outlier: 3.647A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.819A pdb=" N LEU D 322 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL D 332 " --> pdb=" O HIS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 removed outlier: 4.183A pdb=" N SER D 361 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS D 364 " --> pdb=" O MET D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 removed outlier: 3.568A pdb=" N GLU D 469 " --> pdb=" O ASP D 465 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR D 472 " --> pdb=" O ARG D 468 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 507 removed outlier: 3.997A pdb=" N ASP D 507 " --> pdb=" O ARG D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.622A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL D 526 " --> pdb=" O VAL D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 560 removed outlier: 3.829A pdb=" N LEU D 559 " --> pdb=" O LEU D 556 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER D 560 " --> pdb=" O ASN D 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 556 through 560' Processing helix chain 'D' and resid 561 through 572 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 607 through 620 Processing helix chain 'D' and resid 630 through 632 No H-bonds generated for 'chain 'D' and resid 630 through 632' Processing helix chain 'D' and resid 633 through 660 removed outlier: 3.672A pdb=" N GLY D 637 " --> pdb=" O THR D 633 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TRP D 641 " --> pdb=" O GLY D 637 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE D 642 " --> pdb=" O GLY D 638 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE D 646 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE D 647 " --> pdb=" O PHE D 643 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR D 660 " --> pdb=" O ALA D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 696 removed outlier: 3.916A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 710 removed outlier: 3.886A pdb=" N LYS D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA D 707 " --> pdb=" O ASP D 703 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE D 708 " --> pdb=" O LYS D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 removed outlier: 3.814A pdb=" N GLY D 724 " --> pdb=" O SER D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 746 Processing helix chain 'D' and resid 774 through 788 removed outlier: 3.523A pdb=" N THR D 779 " --> pdb=" O ARG D 775 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE D 780 " --> pdb=" O ASP D 776 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA D 781 " --> pdb=" O LYS D 777 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN D 784 " --> pdb=" O ILE D 780 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 788 " --> pdb=" O GLN D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 799 removed outlier: 3.533A pdb=" N LYS D 795 " --> pdb=" O LEU D 791 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP D 799 " --> pdb=" O LYS D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 853 removed outlier: 3.776A pdb=" N VAL D 832 " --> pdb=" O ALA D 828 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU D 833 " --> pdb=" O ALA D 829 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 837 " --> pdb=" O LEU D 833 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR D 844 " --> pdb=" O GLY D 840 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN D 851 " --> pdb=" O LYS D 847 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU D 853 " --> pdb=" O ASN D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 867 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 39 removed outlier: 7.502A pdb=" N PHE A 38 " --> pdb=" O ASP A 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.233A pdb=" N PHE A 42 " --> pdb=" O ILE A 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 203 removed outlier: 3.578A pdb=" N TYR A 176 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR A 254 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N PHE A 279 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE A 256 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 400 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 434 through 435 Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA7, first strand: chain 'A' and resid 513 through 515 removed outlier: 4.637A pdb=" N ALA A 515 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLY A 765 " --> pdb=" O ALA A 515 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 734 through 735 removed outlier: 3.573A pdb=" N TYR A 542 " --> pdb=" O THR A 753 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 753 " --> pdb=" O TYR A 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 684 through 685 removed outlier: 5.702A pdb=" N ALA A 684 " --> pdb=" O VAL A 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 36 through 42 Processing sheet with id=AB2, first strand: chain 'B' and resid 129 through 131 Processing sheet with id=AB3, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.244A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 175 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 278 through 280 removed outlier: 3.598A pdb=" N ARG B 280 " --> pdb=" O ASP B 390 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B 391 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB6, first strand: chain 'B' and resid 432 through 433 Processing sheet with id=AB7, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AB8, first strand: chain 'B' and resid 489 through 491 removed outlier: 3.577A pdb=" N ALA B 490 " --> pdb=" O ASN B 499 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN B 499 " --> pdb=" O ALA B 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AC1, first strand: chain 'B' and resid 737 through 738 removed outlier: 3.994A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 37 through 39 removed outlier: 7.502A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.233A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC5, first strand: chain 'C' and resid 202 through 203 removed outlier: 3.578A pdb=" N TYR C 176 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR C 254 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N PHE C 279 " --> pdb=" O TYR C 254 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE C 256 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N MET C 276 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C 400 " --> pdb=" O SER C 393 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 434 through 435 Processing sheet with id=AC7, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AC8, first strand: chain 'C' and resid 513 through 515 removed outlier: 4.637A pdb=" N ALA C 515 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY C 765 " --> pdb=" O ALA C 515 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 734 through 735 removed outlier: 3.572A pdb=" N TYR C 542 " --> pdb=" O THR C 753 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 753 " --> pdb=" O TYR C 542 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 684 through 685 removed outlier: 5.702A pdb=" N ALA C 684 " --> pdb=" O VAL C 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'D' and resid 36 through 42 Processing sheet with id=AD3, first strand: chain 'D' and resid 129 through 131 Processing sheet with id=AD4, first strand: chain 'D' and resid 202 through 203 removed outlier: 6.244A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 175 " --> pdb=" O ILE D 227 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 278 through 280 removed outlier: 3.598A pdb=" N ARG D 280 " --> pdb=" O ASP D 390 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL D 391 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AD7, first strand: chain 'D' and resid 432 through 433 Processing sheet with id=AD8, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AD9, first strand: chain 'D' and resid 489 through 491 removed outlier: 3.577A pdb=" N ALA D 490 " --> pdb=" O ASN D 499 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN D 499 " --> pdb=" O ALA D 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AE2, first strand: chain 'D' and resid 737 through 738 removed outlier: 3.993A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) 746 hydrogen bonds defined for protein. 2130 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: 5.23 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4440 1.31 - 1.44: 7639 1.44 - 1.56: 16232 1.56 - 1.68: 51 1.68 - 1.81: 272 Bond restraints: 28634 Sorted by residual: bond pdb=" C ASN B 557 " pdb=" N PRO B 558 " ideal model delta sigma weight residual 1.334 1.379 -0.045 8.40e-03 1.42e+04 2.91e+01 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.513 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C ASN D 557 " pdb=" N PRO D 558 " ideal model delta sigma weight residual 1.334 1.379 -0.045 8.40e-03 1.42e+04 2.86e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.511 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C ASN A 557 " pdb=" N PRO A 558 " ideal model delta sigma weight residual 1.337 1.392 -0.056 1.11e-02 8.12e+03 2.51e+01 ... (remaining 28629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 36109 2.51 - 5.01: 2020 5.01 - 7.52: 324 7.52 - 10.03: 87 10.03 - 12.53: 64 Bond angle restraints: 38604 Sorted by residual: angle pdb=" N ILE C 742 " pdb=" CA ILE C 742 " pdb=" C ILE C 742 " ideal model delta sigma weight residual 113.47 105.80 7.67 1.01e+00 9.80e-01 5.76e+01 angle pdb=" N ILE A 742 " pdb=" CA ILE A 742 " pdb=" C ILE A 742 " ideal model delta sigma weight residual 113.47 105.84 7.63 1.01e+00 9.80e-01 5.71e+01 angle pdb=" C LEU C 85 " pdb=" N TYR C 86 " pdb=" CA TYR C 86 " ideal model delta sigma weight residual 121.54 133.20 -11.66 1.91e+00 2.74e-01 3.73e+01 angle pdb=" C LEU A 85 " pdb=" N TYR A 86 " pdb=" CA TYR A 86 " ideal model delta sigma weight residual 121.54 133.15 -11.61 1.91e+00 2.74e-01 3.69e+01 angle pdb=" N ALA D 263 " pdb=" CA ALA D 263 " pdb=" C ALA D 263 " ideal model delta sigma weight residual 114.75 107.37 7.38 1.26e+00 6.30e-01 3.43e+01 ... (remaining 38599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.64: 16966 29.64 - 59.28: 695 59.28 - 88.92: 130 88.92 - 118.56: 92 118.56 - 148.20: 17 Dihedral angle restraints: 17900 sinusoidal: 8152 harmonic: 9748 Sorted by residual: dihedral pdb=" CA GLU C 808 " pdb=" C GLU C 808 " pdb=" N SER C 809 " pdb=" CA SER C 809 " ideal model delta harmonic sigma weight residual -180.00 -119.07 -60.93 0 5.00e+00 4.00e-02 1.49e+02 dihedral pdb=" CA GLU A 808 " pdb=" C GLU A 808 " pdb=" N SER A 809 " pdb=" CA SER A 809 " ideal model delta harmonic sigma weight residual -180.00 -119.10 -60.90 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA GLU B 811 " pdb=" C GLU B 811 " pdb=" N ALA B 812 " pdb=" CA ALA B 812 " ideal model delta harmonic sigma weight residual -180.00 -123.29 -56.71 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 17897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3702 0.084 - 0.168: 574 0.168 - 0.252: 46 0.252 - 0.336: 14 0.336 - 0.420: 4 Chirality restraints: 4340 Sorted by residual: chirality pdb=" C1 NAG C1005 " pdb=" ND2 ASN C 546 " pdb=" C2 NAG C1005 " pdb=" O5 NAG C1005 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" C1 NAG A1006 " pdb=" ND2 ASN A 546 " pdb=" C2 NAG A1006 " pdb=" O5 NAG A1006 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" C1 NAG D1007 " pdb=" ND2 ASN D 412 " pdb=" C2 NAG D1007 " pdb=" O5 NAG D1007 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.43e+00 ... (remaining 4337 not shown) Planarity restraints: 4796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 267 " 0.074 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO A 268 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO A 268 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 268 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 267 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO C 268 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO C 268 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 268 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 227 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ILE B 227 " 0.059 2.00e-02 2.50e+03 pdb=" O ILE B 227 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE B 228 " -0.020 2.00e-02 2.50e+03 ... (remaining 4793 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 7129 2.80 - 3.32: 24255 3.32 - 3.85: 43678 3.85 - 4.37: 51161 4.37 - 4.90: 84863 Nonbonded interactions: 211086 Sorted by model distance: nonbonded pdb=" O PHE A 555 " pdb=" OH TYR A 651 " model vdw 2.270 3.040 nonbonded pdb=" O PHE C 555 " pdb=" OH TYR C 651 " model vdw 2.271 3.040 nonbonded pdb=" OH TYR A 590 " pdb=" OD1 ASN A 605 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR C 590 " pdb=" OD1 ASN C 605 " model vdw 2.275 3.040 nonbonded pdb=" OG SER C 670 " pdb=" OD1 ASP C 672 " model vdw 2.299 3.040 ... (remaining 211081 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 1002 or resid 1005)) selection = (chain 'B' and (resid 33 through 1002 or resid 1005)) selection = (chain 'C' and (resid 33 through 1002 or resid 1005)) selection = (chain 'D' and (resid 33 through 1002 or resid 1005)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'H' selection = chain 'N' } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.700 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: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.130 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.840 ------------------------------------------------------------------------------- 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 : 0.008 0.107 28686 Z= 0.413 Angle : 1.452 25.332 38752 Z= 0.780 Chirality : 0.061 0.420 4340 Planarity : 0.008 0.113 4770 Dihedral : 18.796 148.205 11604 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.36 % Allowed : 14.95 % Favored : 84.70 % Rotamer: Outliers : 0.21 % Allowed : 5.98 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.56 % 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: -6.51 (0.09), residues: 3352 helix: -4.68 (0.05), residues: 1328 sheet: -4.26 (0.24), residues: 322 loop : -4.06 (0.11), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 384 TYR 0.038 0.002 TYR D 443 PHE 0.023 0.002 PHE B 735 TRP 0.022 0.003 TRP D 134 HIS 0.017 0.002 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00816 / 0.41 (28634) covalent geometry : angle 1.41027 / 0.77 (38604) SS BOND : bond 0.00316 / 0.19 ( 8) SS BOND : angle 0.67793 / 0.43 ( 16) hydrogen bonds : bond 0.31458 / 20.87 ( 746) hydrogen bonds : angle 10.81202 / 7.38 ( 2130) link_ALPHA1-3 : bond 0.01222 / 0.61 ( 2) link_ALPHA1-3 : angle 6.25609 / 3.58 ( 6) link_ALPHA1-6 : bond 0.00656 / 0.33 ( 2) link_ALPHA1-6 : angle 2.08963 / 1.16 ( 6) link_BETA1-4 : bond 0.01617 / 1.06 ( 14) link_BETA1-4 : angle 4.74170 / 3.54 ( 42) link_NAG-ASN : bond 0.01610 / 1.24 ( 26) link_NAG-ASN : angle 6.86843 / 4.58 ( 78) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 824 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.7074 (p90) cc_final: 0.6488 (p90) REVERT: A 120 SER cc_start: 0.8575 (t) cc_final: 0.8085 (t) REVERT: A 133 ARG cc_start: 0.8126 (mtp85) cc_final: 0.7904 (tmt170) REVERT: A 134 TRP cc_start: 0.8297 (t60) cc_final: 0.7571 (t60) REVERT: A 137 GLN cc_start: 0.7880 (mt0) cc_final: 0.7417 (mt0) REVERT: A 247 MET cc_start: 0.6623 (mtt) cc_final: 0.6393 (mtm) REVERT: A 312 LEU cc_start: 0.7776 (mp) cc_final: 0.7573 (pp) REVERT: A 328 HIS cc_start: 0.7270 (m-70) cc_final: 0.7023 (m-70) REVERT: A 374 ARG cc_start: 0.8109 (ttp-170) cc_final: 0.7487 (ptt90) REVERT: A 399 LEU cc_start: 0.8067 (mm) cc_final: 0.7710 (mt) REVERT: A 479 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6829 (tm-30) REVERT: A 521 TYR cc_start: 0.8501 (t80) cc_final: 0.8163 (t80) REVERT: A 562 ASP cc_start: 0.8419 (t0) cc_final: 0.8186 (t0) REVERT: A 584 PHE cc_start: 0.7218 (t80) cc_final: 0.6842 (t80) REVERT: A 587 TYR cc_start: 0.7921 (m-80) cc_final: 0.7672 (m-80) REVERT: A 748 ARG cc_start: 0.6856 (mpt-90) cc_final: 0.6398 (ttp-170) REVERT: A 793 MET cc_start: 0.7442 (mmm) cc_final: 0.7067 (mmt) REVERT: B 86 TYR cc_start: 0.7054 (m-80) cc_final: 0.6303 (m-80) REVERT: B 87 ASP cc_start: 0.7955 (m-30) cc_final: 0.6756 (m-30) REVERT: B 132 THR cc_start: 0.8825 (p) cc_final: 0.8489 (p) REVERT: B 133 ARG cc_start: 0.8145 (tmt-80) cc_final: 0.7679 (tpp80) REVERT: B 140 ASP cc_start: 0.7968 (m-30) cc_final: 0.7728 (t0) REVERT: B 308 ASP cc_start: 0.7472 (p0) cc_final: 0.7146 (t0) REVERT: B 400 GLU cc_start: 0.7673 (tt0) cc_final: 0.7317 (mm-30) REVERT: B 531 LYS cc_start: 0.7045 (mttm) cc_final: 0.6787 (mmtm) REVERT: B 536 LEU cc_start: 0.9204 (pp) cc_final: 0.8986 (pp) REVERT: B 589 TRP cc_start: 0.7778 (m100) cc_final: 0.7472 (m100) REVERT: B 708 PHE cc_start: 0.6671 (t80) cc_final: 0.5795 (m-80) REVERT: B 753 THR cc_start: 0.9090 (t) cc_final: 0.8788 (p) REVERT: C 42 PHE cc_start: 0.7044 (m-80) cc_final: 0.6820 (m-80) REVERT: C 80 THR cc_start: 0.8008 (p) cc_final: 0.7795 (t) REVERT: C 85 LEU cc_start: 0.7690 (mp) cc_final: 0.7220 (mt) REVERT: C 114 SER cc_start: 0.8836 (m) cc_final: 0.8480 (m) REVERT: C 152 ASP cc_start: 0.7541 (t0) cc_final: 0.7151 (t0) REVERT: C 157 SER cc_start: 0.8761 (m) cc_final: 0.8474 (p) REVERT: C 374 ARG cc_start: 0.7667 (ttp-170) cc_final: 0.7223 (ttp-110) REVERT: C 708 PHE cc_start: 0.7095 (t80) cc_final: 0.6264 (t80) REVERT: C 770 MET cc_start: 0.6162 (tpt) cc_final: 0.5863 (ttt) REVERT: C 815 LEU cc_start: 0.7684 (mt) cc_final: 0.7399 (mt) REVERT: C 818 GLN cc_start: 0.7321 (pt0) cc_final: 0.6932 (mm-40) REVERT: D 86 TYR cc_start: 0.7009 (m-80) cc_final: 0.6539 (m-80) REVERT: D 87 ASP cc_start: 0.7881 (m-30) cc_final: 0.6987 (m-30) REVERT: D 132 THR cc_start: 0.8635 (p) cc_final: 0.8352 (p) REVERT: D 166 PHE cc_start: 0.8395 (t80) cc_final: 0.8054 (t80) REVERT: D 308 ASP cc_start: 0.7413 (p0) cc_final: 0.7114 (p0) REVERT: D 345 LEU cc_start: 0.7220 (mm) cc_final: 0.6983 (tp) REVERT: D 350 HIS cc_start: 0.6723 (p90) cc_final: 0.6424 (p90) REVERT: D 360 MET cc_start: 0.8372 (tpt) cc_final: 0.7922 (tpp) REVERT: D 639 ILE cc_start: 0.7730 (mm) cc_final: 0.7326 (mt) REVERT: D 794 MET cc_start: 0.7917 (mtm) cc_final: 0.7205 (mtm) REVERT: D 842 PHE cc_start: 0.7666 (t80) cc_final: 0.7399 (t80) outliers start: 6 outliers final: 1 residues processed: 828 average time/residue: 0.1925 time to fit residues: 248.8221 Evaluate side-chains 443 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 442 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.0370 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.3980 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN A 136 HIS A 141 ASN ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 ASN B 81 GLN B 137 GLN B 141 ASN B 196 ASN B 367 HIS B 549 ASN B 747 GLN C 65 ASN C 98 GLN C 137 GLN C 141 ASN C 196 ASN ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 HIS D 81 GLN D 137 GLN D 141 ASN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 GLN D 549 ASN D 621 GLN D 792 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.205168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.172819 restraints weight = 36771.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.172466 restraints weight = 48717.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.173906 restraints weight = 51148.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.175053 restraints weight = 33012.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.176072 restraints weight = 28787.287| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3806 r_free = 0.3806 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 28686 Z= 0.158 Angle : 0.868 28.240 38752 Z= 0.417 Chirality : 0.049 0.405 4340 Planarity : 0.006 0.092 4770 Dihedral : 20.614 142.922 5226 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.78 % Favored : 86.22 % Rotamer: Outliers : 2.98 % Allowed : 13.95 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.31 % 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: -5.31 (0.11), residues: 3352 helix: -3.17 (0.09), residues: 1376 sheet: -4.05 (0.24), residues: 336 loop : -3.74 (0.13), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 270 TYR 0.014 0.002 TYR D 78 PHE 0.026 0.002 PHE D 59 TRP 0.049 0.002 TRP B 798 HIS 0.014 0.001 HIS D 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (28634) covalent geometry : angle 0.81323 / 0.41 (38604) SS BOND : bond 0.00697 / 0.43 ( 8) SS BOND : angle 1.53890 / 0.97 ( 16) hydrogen bonds : bond 0.04953 / 3.28 ( 746) hydrogen bonds : angle 5.71906 / 3.84 ( 2130) link_ALPHA1-3 : bond 0.01589 / 0.80 ( 2) link_ALPHA1-3 : angle 3.28209 / 1.72 ( 6) link_ALPHA1-6 : bond 0.01712 / 0.85 ( 2) link_ALPHA1-6 : angle 3.10916 / 1.65 ( 6) link_BETA1-4 : bond 0.00492 / 0.33 ( 14) link_BETA1-4 : angle 3.15267 / 2.31 ( 42) link_NAG-ASN : bond 0.01083 / 0.82 ( 26) link_NAG-ASN : angle 6.30975 / 4.14 ( 78) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 518 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.6860 (p90) cc_final: 0.6604 (p90) REVERT: A 134 TRP cc_start: 0.8019 (t60) cc_final: 0.7675 (t60) REVERT: A 196 ASN cc_start: 0.7120 (t0) cc_final: 0.6898 (t0) REVERT: A 200 LYS cc_start: 0.7278 (ttmt) cc_final: 0.6894 (tttt) REVERT: A 374 ARG cc_start: 0.7858 (ttp-170) cc_final: 0.7600 (ptt90) REVERT: A 380 THR cc_start: 0.7282 (OUTLIER) cc_final: 0.7052 (t) REVERT: A 433 LEU cc_start: 0.6769 (mm) cc_final: 0.6412 (mt) REVERT: A 506 ILE cc_start: 0.5591 (mt) cc_final: 0.5277 (mt) REVERT: A 521 TYR cc_start: 0.8275 (t80) cc_final: 0.7662 (t80) REVERT: A 534 MET cc_start: 0.8037 (ttm) cc_final: 0.7812 (ttm) REVERT: A 748 ARG cc_start: 0.7207 (mpt-90) cc_final: 0.6802 (ttm170) REVERT: A 872 GLN cc_start: 0.6244 (tm-30) cc_final: 0.5874 (tm-30) REVERT: B 123 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8090 (t0) REVERT: B 133 ARG cc_start: 0.8234 (tmt-80) cc_final: 0.7963 (tpp80) REVERT: B 308 ASP cc_start: 0.6792 (p0) cc_final: 0.6543 (p0) REVERT: B 536 LEU cc_start: 0.9071 (pp) cc_final: 0.8842 (pp) REVERT: B 589 TRP cc_start: 0.7868 (m100) cc_final: 0.7338 (m100) REVERT: B 753 THR cc_start: 0.9186 (t) cc_final: 0.8790 (p) REVERT: C 37 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7051 (ttm-80) REVERT: C 114 SER cc_start: 0.8313 (m) cc_final: 0.8059 (m) REVERT: C 323 MET cc_start: 0.8082 (tpt) cc_final: 0.7873 (tpp) REVERT: C 433 LEU cc_start: 0.7297 (mm) cc_final: 0.6956 (mt) REVERT: C 780 ILE cc_start: 0.8057 (mt) cc_final: 0.7815 (mt) REVERT: C 841 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6662 (tt0) REVERT: D 123 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.7637 (t0) REVERT: D 166 PHE cc_start: 0.8276 (t80) cc_final: 0.7932 (t80) REVERT: D 436 THR cc_start: 0.9062 (m) cc_final: 0.8859 (p) REVERT: D 611 SER cc_start: 0.8582 (m) cc_final: 0.8370 (m) outliers start: 87 outliers final: 43 residues processed: 581 average time/residue: 0.1779 time to fit residues: 168.1114 Evaluate side-chains 445 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 398 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 387 PHE Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain D residue 792 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 73 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 chunk 293 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 300 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 ASN ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 328 HIS ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 336 GLN ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN C 604 ASN D 328 HIS ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.197268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.163528 restraints weight = 36990.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.165284 restraints weight = 61320.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.166722 restraints weight = 50817.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.168273 restraints weight = 32839.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.169171 restraints weight = 27421.519| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 28686 Z= 0.204 Angle : 0.845 23.942 38752 Z= 0.406 Chirality : 0.049 0.447 4340 Planarity : 0.005 0.093 4770 Dihedral : 18.686 151.228 5226 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 14.50 % Favored : 85.38 % Rotamer: Outliers : 3.90 % Allowed : 15.70 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.31 % 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: -4.60 (0.12), residues: 3352 helix: -2.18 (0.12), residues: 1394 sheet: -3.86 (0.26), residues: 324 loop : -3.72 (0.13), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 158 TYR 0.021 0.002 TYR D 86 PHE 0.031 0.002 PHE A 459 TRP 0.054 0.002 TRP B 798 HIS 0.023 0.002 HIS D 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (28634) covalent geometry : angle 0.79488 / 0.39 (38604) SS BOND : bond 0.00271 / 0.16 ( 8) SS BOND : angle 1.23530 / 0.97 ( 16) hydrogen bonds : bond 0.04409 / 2.93 ( 746) hydrogen bonds : angle 5.26648 / 3.55 ( 2130) link_ALPHA1-3 : bond 0.01534 / 0.76 ( 2) link_ALPHA1-3 : angle 3.26777 / 1.72 ( 6) link_ALPHA1-6 : bond 0.01526 / 0.76 ( 2) link_ALPHA1-6 : angle 2.44194 / 1.38 ( 6) link_BETA1-4 : bond 0.00556 / 0.37 ( 14) link_BETA1-4 : angle 3.29046 / 2.43 ( 42) link_NAG-ASN : bond 0.00947 / 0.74 ( 26) link_NAG-ASN : angle 5.87445 / 3.85 ( 78) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 427 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.6979 (p90) cc_final: 0.6718 (p90) REVERT: A 196 ASN cc_start: 0.7186 (t0) cc_final: 0.6966 (t0) REVERT: A 521 TYR cc_start: 0.8126 (t80) cc_final: 0.7666 (t80) REVERT: A 748 ARG cc_start: 0.7327 (mpt-90) cc_final: 0.6967 (ttm170) REVERT: A 793 MET cc_start: 0.6928 (mmm) cc_final: 0.6119 (mtt) REVERT: B 98 GLN cc_start: 0.7872 (tt0) cc_final: 0.7636 (tt0) REVERT: B 123 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8102 (t0) REVERT: B 140 ASP cc_start: 0.6919 (t0) cc_final: 0.6675 (t0) REVERT: B 480 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8107 (mt) REVERT: B 536 LEU cc_start: 0.9175 (pp) cc_final: 0.8890 (pp) REVERT: B 589 TRP cc_start: 0.7766 (m100) cc_final: 0.7299 (m100) REVERT: B 753 THR cc_start: 0.9276 (t) cc_final: 0.8874 (p) REVERT: B 758 LEU cc_start: 0.8675 (mm) cc_final: 0.8402 (mt) REVERT: C 85 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.7061 (mp) REVERT: C 86 TYR cc_start: 0.7444 (m-80) cc_final: 0.7199 (m-80) REVERT: C 114 SER cc_start: 0.8456 (m) cc_final: 0.8245 (m) REVERT: D 123 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.7740 (t0) REVERT: D 187 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6743 (mt-10) REVERT: D 436 THR cc_start: 0.9200 (m) cc_final: 0.8954 (p) REVERT: D 459 PHE cc_start: 0.7576 (m-80) cc_final: 0.7197 (m-10) REVERT: D 589 TRP cc_start: 0.7406 (m100) cc_final: 0.7194 (m100) outliers start: 114 outliers final: 70 residues processed: 509 average time/residue: 0.1545 time to fit residues: 130.6468 Evaluate side-chains 452 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 377 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 387 PHE Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 585 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain D residue 716 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 178 optimal weight: 4.9990 chunk 222 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 chunk 199 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 233 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 184 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 GLN C 417 GLN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN D 792 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.199451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.166574 restraints weight = 36368.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.167743 restraints weight = 60976.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.169208 restraints weight = 51778.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.170054 restraints weight = 33705.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.171099 restraints weight = 29489.659| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28686 Z= 0.149 Angle : 0.785 22.917 38752 Z= 0.372 Chirality : 0.047 0.446 4340 Planarity : 0.005 0.087 4770 Dihedral : 17.563 162.611 5226 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.07 % Favored : 86.93 % Rotamer: Outliers : 3.69 % Allowed : 16.93 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.31 % 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: -3.96 (0.13), residues: 3352 helix: -1.52 (0.13), residues: 1402 sheet: -3.94 (0.26), residues: 296 loop : -3.44 (0.13), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 66 TYR 0.018 0.001 TYR C 252 PHE 0.024 0.001 PHE A 579 TRP 0.064 0.002 TRP B 798 HIS 0.013 0.001 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (28634) covalent geometry : angle 0.72622 / 0.36 (38604) SS BOND : bond 0.00766 / 0.39 ( 8) SS BOND : angle 1.20936 / 0.90 ( 16) hydrogen bonds : bond 0.03594 / 2.38 ( 746) hydrogen bonds : angle 4.90891 / 3.33 ( 2130) link_ALPHA1-3 : bond 0.01390 / 0.70 ( 2) link_ALPHA1-3 : angle 3.39222 / 1.78 ( 6) link_ALPHA1-6 : bond 0.01650 / 0.83 ( 2) link_ALPHA1-6 : angle 2.71304 / 1.46 ( 6) link_BETA1-4 : bond 0.00617 / 0.40 ( 14) link_BETA1-4 : angle 3.27673 / 2.45 ( 42) link_NAG-ASN : bond 0.00987 / 0.74 ( 26) link_NAG-ASN : angle 6.14300 / 4.36 ( 78) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 414 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.6990 (p90) cc_final: 0.6716 (p90) REVERT: A 245 MET cc_start: 0.6855 (tpp) cc_final: 0.6637 (tpp) REVERT: A 521 TYR cc_start: 0.8134 (t80) cc_final: 0.7762 (t80) REVERT: A 748 ARG cc_start: 0.7349 (mpt-90) cc_final: 0.6835 (ttm170) REVERT: A 793 MET cc_start: 0.6977 (mmm) cc_final: 0.6449 (mtt) REVERT: B 98 GLN cc_start: 0.7870 (tt0) cc_final: 0.7664 (tt0) REVERT: B 123 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8163 (t0) REVERT: B 140 ASP cc_start: 0.7042 (t0) cc_final: 0.6808 (t0) REVERT: B 443 TYR cc_start: 0.6683 (OUTLIER) cc_final: 0.5315 (p90) REVERT: B 536 LEU cc_start: 0.9172 (pp) cc_final: 0.8870 (pp) REVERT: B 589 TRP cc_start: 0.7722 (m100) cc_final: 0.7320 (m100) REVERT: B 758 LEU cc_start: 0.8737 (mm) cc_final: 0.8493 (mt) REVERT: C 114 SER cc_start: 0.8597 (m) cc_final: 0.8386 (m) REVERT: C 248 MET cc_start: 0.7275 (mmm) cc_final: 0.6620 (mmm) REVERT: C 791 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7240 (mp) REVERT: D 123 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.7902 (t0) REVERT: D 436 THR cc_start: 0.9161 (m) cc_final: 0.8952 (p) REVERT: D 589 TRP cc_start: 0.7479 (m100) cc_final: 0.7223 (m100) outliers start: 108 outliers final: 67 residues processed: 494 average time/residue: 0.1580 time to fit residues: 130.5048 Evaluate side-chains 448 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 377 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 603 GLU Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 585 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain D residue 837 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 84 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 192 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 255 optimal weight: 6.9990 chunk 28 optimal weight: 0.0980 chunk 291 optimal weight: 30.0000 chunk 94 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 591 ASN A 604 ASN B 136 HIS ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.196777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.163365 restraints weight = 36454.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.166257 restraints weight = 60212.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.167144 restraints weight = 47496.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.168546 restraints weight = 29666.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.169448 restraints weight = 25166.266| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28686 Z= 0.164 Angle : 0.780 22.313 38752 Z= 0.367 Chirality : 0.048 0.454 4340 Planarity : 0.005 0.087 4770 Dihedral : 16.840 173.218 5226 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 14.35 % Favored : 85.62 % Rotamer: Outliers : 4.14 % Allowed : 17.89 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.19 % 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: -3.64 (0.13), residues: 3352 helix: -1.19 (0.13), residues: 1408 sheet: -3.80 (0.27), residues: 296 loop : -3.33 (0.13), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 66 TYR 0.019 0.002 TYR C 86 PHE 0.028 0.002 PHE C 359 TRP 0.070 0.002 TRP B 798 HIS 0.010 0.001 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (28634) covalent geometry : angle 0.72258 / 0.35 (38604) SS BOND : bond 0.00266 / 0.15 ( 8) SS BOND : angle 1.06292 / 0.75 ( 16) hydrogen bonds : bond 0.03524 / 2.34 ( 746) hydrogen bonds : angle 4.80657 / 3.27 ( 2130) link_ALPHA1-3 : bond 0.01322 / 0.67 ( 2) link_ALPHA1-3 : angle 3.40802 / 1.80 ( 6) link_ALPHA1-6 : bond 0.02047 / 1.02 ( 2) link_ALPHA1-6 : angle 2.40487 / 1.28 ( 6) link_BETA1-4 : bond 0.00556 / 0.36 ( 14) link_BETA1-4 : angle 3.36635 / 2.51 ( 42) link_NAG-ASN : bond 0.01018 / 0.74 ( 26) link_NAG-ASN : angle 6.04175 / 4.26 ( 78) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 397 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.6989 (p90) cc_final: 0.6744 (p90) REVERT: A 245 MET cc_start: 0.6872 (tpp) cc_final: 0.6653 (tpp) REVERT: A 257 THR cc_start: 0.8313 (m) cc_final: 0.8012 (p) REVERT: A 748 ARG cc_start: 0.7342 (mpt-90) cc_final: 0.6896 (ttm170) REVERT: A 793 MET cc_start: 0.6993 (mmm) cc_final: 0.6561 (mtt) REVERT: B 98 GLN cc_start: 0.7869 (tt0) cc_final: 0.7666 (tt0) REVERT: B 123 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8154 (t0) REVERT: B 215 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7647 (mp) REVERT: B 223 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7418 (mt-10) REVERT: B 443 TYR cc_start: 0.6679 (OUTLIER) cc_final: 0.5175 (p90) REVERT: B 465 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.6863 (t0) REVERT: B 569 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.6803 (tt) REVERT: B 589 TRP cc_start: 0.7748 (m100) cc_final: 0.7369 (m100) REVERT: B 753 THR cc_start: 0.9275 (t) cc_final: 0.8926 (p) REVERT: B 758 LEU cc_start: 0.8810 (mm) cc_final: 0.8578 (mt) REVERT: C 114 SER cc_start: 0.8619 (m) cc_final: 0.8387 (m) REVERT: D 123 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.7942 (t0) REVERT: D 436 THR cc_start: 0.9177 (m) cc_final: 0.8961 (p) REVERT: D 443 TYR cc_start: 0.6719 (OUTLIER) cc_final: 0.5061 (p90) REVERT: D 589 TRP cc_start: 0.7528 (m100) cc_final: 0.7253 (m100) outliers start: 121 outliers final: 76 residues processed: 480 average time/residue: 0.1619 time to fit residues: 130.2082 Evaluate side-chains 454 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 371 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 603 GLU Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 195 TYR Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 585 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 837 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 275 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 255 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 209 optimal weight: 0.7980 chunk 171 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN C 196 ASN D 136 HIS ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.196259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.163289 restraints weight = 36340.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.166380 restraints weight = 59713.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.167605 restraints weight = 44592.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.168168 restraints weight = 30267.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.170043 restraints weight = 25723.392| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28686 Z= 0.165 Angle : 0.770 22.142 38752 Z= 0.365 Chirality : 0.047 0.457 4340 Planarity : 0.005 0.085 4770 Dihedral : 16.224 174.201 5226 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 14.08 % Favored : 85.89 % Rotamer: Outliers : 4.14 % Allowed : 18.50 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.12 % 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: -3.41 (0.14), residues: 3352 helix: -0.98 (0.13), residues: 1424 sheet: -3.60 (0.27), residues: 314 loop : -3.24 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 374 TYR 0.019 0.001 TYR C 86 PHE 0.025 0.002 PHE A 579 TRP 0.068 0.002 TRP D 798 HIS 0.009 0.001 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (28634) covalent geometry : angle 0.71325 / 0.35 (38604) SS BOND : bond 0.00219 / 0.12 ( 8) SS BOND : angle 0.83601 / 0.65 ( 16) hydrogen bonds : bond 0.03396 / 2.27 ( 746) hydrogen bonds : angle 4.70348 / 3.20 ( 2130) link_ALPHA1-3 : bond 0.01258 / 0.63 ( 2) link_ALPHA1-3 : angle 3.33328 / 1.76 ( 6) link_ALPHA1-6 : bond 0.02143 / 1.08 ( 2) link_ALPHA1-6 : angle 1.70033 / 0.93 ( 6) link_BETA1-4 : bond 0.00550 / 0.36 ( 14) link_BETA1-4 : angle 3.38136 / 2.55 ( 42) link_NAG-ASN : bond 0.00979 / 0.72 ( 26) link_NAG-ASN : angle 5.92937 / 4.18 ( 78) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 401 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.6992 (p90) cc_final: 0.6738 (p90) REVERT: A 241 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7840 (mt0) REVERT: A 257 THR cc_start: 0.8288 (m) cc_final: 0.8004 (p) REVERT: A 497 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6432 (tm-30) REVERT: A 748 ARG cc_start: 0.7302 (mpt-90) cc_final: 0.6900 (ttm170) REVERT: A 793 MET cc_start: 0.6975 (mmm) cc_final: 0.6546 (mtt) REVERT: B 123 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8125 (t0) REVERT: B 166 PHE cc_start: 0.7606 (t80) cc_final: 0.7204 (t80) REVERT: B 215 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7672 (mp) REVERT: B 443 TYR cc_start: 0.6752 (OUTLIER) cc_final: 0.5199 (p90) REVERT: B 753 THR cc_start: 0.9266 (t) cc_final: 0.8957 (p) REVERT: B 758 LEU cc_start: 0.8916 (mm) cc_final: 0.8665 (mt) REVERT: C 114 SER cc_start: 0.8668 (m) cc_final: 0.8203 (t) REVERT: C 705 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7919 (tpp) REVERT: D 123 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8104 (t0) REVERT: D 436 THR cc_start: 0.9180 (m) cc_final: 0.8922 (p) REVERT: D 443 TYR cc_start: 0.6703 (OUTLIER) cc_final: 0.5463 (p90) REVERT: D 569 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.6475 (tt) REVERT: D 589 TRP cc_start: 0.7472 (m100) cc_final: 0.7271 (m100) REVERT: D 627 MET cc_start: 0.7656 (mmt) cc_final: 0.7402 (mmt) outliers start: 121 outliers final: 84 residues processed: 483 average time/residue: 0.1603 time to fit residues: 130.1401 Evaluate side-chains 465 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 372 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 861 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 603 GLU Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 585 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 195 TYR Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 585 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 837 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 175 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 255 optimal weight: 0.0870 chunk 123 optimal weight: 40.0000 chunk 28 optimal weight: 3.9990 chunk 299 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 198 optimal weight: 0.0770 chunk 231 optimal weight: 0.5980 overall best weight: 1.3520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.195075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.161734 restraints weight = 36377.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.164201 restraints weight = 59368.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.165626 restraints weight = 46236.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.166585 restraints weight = 31015.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.168234 restraints weight = 26512.433| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28686 Z= 0.161 Angle : 0.763 21.939 38752 Z= 0.361 Chirality : 0.048 0.464 4340 Planarity : 0.005 0.084 4770 Dihedral : 15.727 160.379 5226 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.20 % Favored : 85.80 % Rotamer: Outliers : 4.27 % Allowed : 18.74 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.12 % 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: -3.19 (0.14), residues: 3352 helix: -0.77 (0.14), residues: 1410 sheet: -3.52 (0.28), residues: 292 loop : -3.14 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 374 TYR 0.020 0.001 TYR C 86 PHE 0.026 0.002 PHE A 579 TRP 0.070 0.002 TRP B 798 HIS 0.008 0.001 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (28634) covalent geometry : angle 0.70733 / 0.35 (38604) SS BOND : bond 0.00320 / 0.14 ( 8) SS BOND : angle 0.78050 / 0.54 ( 16) hydrogen bonds : bond 0.03307 / 2.22 ( 746) hydrogen bonds : angle 4.68017 / 3.18 ( 2130) link_ALPHA1-3 : bond 0.01040 / 0.52 ( 2) link_ALPHA1-3 : angle 3.49375 / 1.87 ( 6) link_ALPHA1-6 : bond 0.01425 / 0.72 ( 2) link_ALPHA1-6 : angle 1.29804 / 0.74 ( 6) link_BETA1-4 : bond 0.00564 / 0.37 ( 14) link_BETA1-4 : angle 3.36966 / 2.52 ( 42) link_NAG-ASN : bond 0.00987 / 0.72 ( 26) link_NAG-ASN : angle 5.85120 / 4.11 ( 78) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 390 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.6990 (p90) cc_final: 0.6757 (p90) REVERT: A 218 MET cc_start: 0.7009 (mmt) cc_final: 0.5788 (mmm) REVERT: A 241 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7815 (mt0) REVERT: A 257 THR cc_start: 0.8304 (m) cc_final: 0.8007 (p) REVERT: A 526 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7682 (t) REVERT: A 793 MET cc_start: 0.7030 (mmm) cc_final: 0.6602 (mtt) REVERT: B 123 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8124 (t0) REVERT: B 166 PHE cc_start: 0.7680 (t80) cc_final: 0.7254 (t80) REVERT: B 215 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7678 (mp) REVERT: B 443 TYR cc_start: 0.6740 (OUTLIER) cc_final: 0.5423 (p90) REVERT: B 465 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.6962 (t70) REVERT: B 590 TYR cc_start: 0.6614 (OUTLIER) cc_final: 0.5867 (p90) REVERT: B 620 MET cc_start: 0.8430 (tpp) cc_final: 0.8197 (mtt) REVERT: B 753 THR cc_start: 0.9275 (t) cc_final: 0.8944 (p) REVERT: B 758 LEU cc_start: 0.9022 (mm) cc_final: 0.8766 (mt) REVERT: C 87 ASP cc_start: 0.7475 (t0) cc_final: 0.6653 (t70) REVERT: C 114 SER cc_start: 0.8699 (m) cc_final: 0.8253 (t) REVERT: C 374 ARG cc_start: 0.7899 (ttp-110) cc_final: 0.7575 (ttp-110) REVERT: D 123 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8073 (t0) REVERT: D 436 THR cc_start: 0.9167 (m) cc_final: 0.8902 (p) REVERT: D 443 TYR cc_start: 0.6692 (OUTLIER) cc_final: 0.5538 (p90) REVERT: D 569 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.6411 (tt) REVERT: D 583 ARG cc_start: 0.6433 (OUTLIER) cc_final: 0.6232 (mtp180) REVERT: D 589 TRP cc_start: 0.7504 (m100) cc_final: 0.7296 (m100) REVERT: D 758 LEU cc_start: 0.9035 (mm) cc_final: 0.8737 (mt) outliers start: 125 outliers final: 87 residues processed: 476 average time/residue: 0.1595 time to fit residues: 127.1946 Evaluate side-chains 464 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 366 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 585 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 195 TYR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 583 ARG Chi-restraints excluded: chain D residue 585 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 735 PHE Chi-restraints excluded: chain D residue 837 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 42 optimal weight: 0.1980 chunk 287 optimal weight: 1.9990 chunk 206 optimal weight: 7.9990 chunk 256 optimal weight: 10.0000 chunk 285 optimal weight: 3.9990 chunk 308 optimal weight: 0.4980 chunk 271 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 213 optimal weight: 0.0970 chunk 72 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN C 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.198386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.165294 restraints weight = 36501.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.167652 restraints weight = 59540.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.168753 restraints weight = 49167.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.169816 restraints weight = 31196.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.171523 restraints weight = 26303.095| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 28686 Z= 0.127 Angle : 0.741 21.718 38752 Z= 0.349 Chirality : 0.046 0.463 4340 Planarity : 0.004 0.083 4770 Dihedral : 15.284 143.656 5226 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.07 % Favored : 86.93 % Rotamer: Outliers : 3.56 % Allowed : 19.94 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.12 % 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: -2.97 (0.14), residues: 3352 helix: -0.56 (0.14), residues: 1402 sheet: -3.39 (0.29), residues: 288 loop : -3.06 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 374 TYR 0.021 0.001 TYR C 86 PHE 0.026 0.001 PHE A 555 TRP 0.081 0.002 TRP D 798 HIS 0.008 0.001 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (28634) covalent geometry : angle 0.68578 / 0.34 (38604) SS BOND : bond 0.00226 / 0.12 ( 8) SS BOND : angle 0.81169 / 0.56 ( 16) hydrogen bonds : bond 0.03057 / 2.04 ( 746) hydrogen bonds : angle 4.54113 / 3.09 ( 2130) link_ALPHA1-3 : bond 0.00992 / 0.50 ( 2) link_ALPHA1-3 : angle 3.60052 / 1.94 ( 6) link_ALPHA1-6 : bond 0.01215 / 0.61 ( 2) link_ALPHA1-6 : angle 1.32520 / 0.74 ( 6) link_BETA1-4 : bond 0.00613 / 0.40 ( 14) link_BETA1-4 : angle 3.31984 / 2.51 ( 42) link_NAG-ASN : bond 0.01004 / 0.73 ( 26) link_NAG-ASN : angle 5.76178 / 4.03 ( 78) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 389 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.6897 (p90) cc_final: 0.6650 (p90) REVERT: A 218 MET cc_start: 0.6939 (mmt) cc_final: 0.5811 (mmm) REVERT: A 241 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7806 (mt0) REVERT: A 257 THR cc_start: 0.8279 (m) cc_final: 0.7994 (p) REVERT: A 793 MET cc_start: 0.6938 (mmm) cc_final: 0.6581 (mtt) REVERT: B 123 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8149 (t0) REVERT: B 166 PHE cc_start: 0.7567 (t80) cc_final: 0.7139 (t80) REVERT: B 400 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7004 (mt-10) REVERT: B 443 TYR cc_start: 0.6696 (OUTLIER) cc_final: 0.5629 (p90) REVERT: B 590 TYR cc_start: 0.6637 (OUTLIER) cc_final: 0.5857 (p90) REVERT: B 620 MET cc_start: 0.8361 (tpp) cc_final: 0.7866 (mtt) REVERT: B 753 THR cc_start: 0.9252 (t) cc_final: 0.8945 (p) REVERT: B 758 LEU cc_start: 0.8974 (mm) cc_final: 0.8731 (mt) REVERT: C 87 ASP cc_start: 0.7473 (t0) cc_final: 0.6658 (t70) REVERT: C 114 SER cc_start: 0.8702 (m) cc_final: 0.8237 (t) REVERT: C 374 ARG cc_start: 0.7883 (ttp-110) cc_final: 0.7571 (ttp-110) REVERT: C 705 MET cc_start: 0.8277 (mmm) cc_final: 0.7952 (tpp) REVERT: D 123 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8104 (t0) REVERT: D 316 MET cc_start: 0.8266 (mmt) cc_final: 0.8012 (mmt) REVERT: D 436 THR cc_start: 0.9163 (m) cc_final: 0.8905 (p) REVERT: D 569 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.6357 (tt) REVERT: D 758 LEU cc_start: 0.9005 (mm) cc_final: 0.8738 (mt) outliers start: 104 outliers final: 79 residues processed: 459 average time/residue: 0.1502 time to fit residues: 115.7564 Evaluate side-chains 453 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 368 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 585 SER Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 195 TYR Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 585 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 837 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 154 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 149 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 225 optimal weight: 0.0970 chunk 286 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 306 optimal weight: 4.9990 chunk 252 optimal weight: 0.6980 chunk 139 optimal weight: 8.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.197183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.165849 restraints weight = 36167.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.168887 restraints weight = 61650.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.169665 restraints weight = 42306.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.170188 restraints weight = 31287.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.172247 restraints weight = 25644.420| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28686 Z= 0.140 Angle : 0.751 21.702 38752 Z= 0.354 Chirality : 0.047 0.470 4340 Planarity : 0.004 0.081 4770 Dihedral : 14.969 128.798 5226 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.78 % Favored : 86.22 % Rotamer: Outliers : 3.28 % Allowed : 20.62 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.12 % 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: -2.85 (0.14), residues: 3352 helix: -0.46 (0.14), residues: 1404 sheet: -3.35 (0.30), residues: 268 loop : -3.00 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 58 TYR 0.022 0.001 TYR C 86 PHE 0.026 0.002 PHE A 579 TRP 0.057 0.002 TRP D 798 HIS 0.008 0.001 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (28634) covalent geometry : angle 0.69667 / 0.34 (38604) SS BOND : bond 0.00184 / 0.10 ( 8) SS BOND : angle 0.82529 / 0.55 ( 16) hydrogen bonds : bond 0.03080 / 2.06 ( 746) hydrogen bonds : angle 4.51197 / 3.08 ( 2130) link_ALPHA1-3 : bond 0.00878 / 0.44 ( 2) link_ALPHA1-3 : angle 3.52667 / 1.91 ( 6) link_ALPHA1-6 : bond 0.01094 / 0.55 ( 2) link_ALPHA1-6 : angle 1.30297 / 0.72 ( 6) link_BETA1-4 : bond 0.00561 / 0.37 ( 14) link_BETA1-4 : angle 3.30073 / 2.48 ( 42) link_NAG-ASN : bond 0.00994 / 0.72 ( 26) link_NAG-ASN : angle 5.74295 / 4.00 ( 78) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 380 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.7408 (ttp80) cc_final: 0.7080 (ttt90) REVERT: A 241 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7877 (mt0) REVERT: A 257 THR cc_start: 0.8309 (m) cc_final: 0.8013 (p) REVERT: A 565 MET cc_start: 0.7703 (tpp) cc_final: 0.7368 (tpt) REVERT: A 682 TYR cc_start: 0.5782 (m-10) cc_final: 0.5462 (m-10) REVERT: A 778 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7591 (tt) REVERT: A 793 MET cc_start: 0.7018 (mmm) cc_final: 0.6589 (mtt) REVERT: B 123 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8193 (t0) REVERT: B 152 ASP cc_start: 0.6911 (t0) cc_final: 0.6568 (m-30) REVERT: B 166 PHE cc_start: 0.7628 (t80) cc_final: 0.7195 (t80) REVERT: B 400 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7021 (mt-10) REVERT: B 443 TYR cc_start: 0.6611 (OUTLIER) cc_final: 0.5580 (p90) REVERT: B 590 TYR cc_start: 0.6429 (OUTLIER) cc_final: 0.5698 (p90) REVERT: B 620 MET cc_start: 0.8436 (tpp) cc_final: 0.7939 (mtt) REVERT: B 753 THR cc_start: 0.9266 (t) cc_final: 0.8970 (p) REVERT: B 758 LEU cc_start: 0.9046 (mm) cc_final: 0.8789 (mt) REVERT: C 87 ASP cc_start: 0.7516 (t0) cc_final: 0.7112 (t70) REVERT: C 114 SER cc_start: 0.8665 (m) cc_final: 0.8179 (t) REVERT: C 374 ARG cc_start: 0.7877 (ttp-110) cc_final: 0.7577 (ttp-110) REVERT: C 705 MET cc_start: 0.8246 (mmm) cc_final: 0.7908 (tpp) REVERT: D 123 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8107 (t0) REVERT: D 436 THR cc_start: 0.9159 (m) cc_final: 0.8928 (p) REVERT: D 758 LEU cc_start: 0.9056 (mm) cc_final: 0.8766 (mt) outliers start: 96 outliers final: 76 residues processed: 445 average time/residue: 0.1503 time to fit residues: 112.6985 Evaluate side-chains 446 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 364 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 585 SER Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 195 TYR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 585 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 735 PHE Chi-restraints excluded: chain D residue 837 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 295 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 315 optimal weight: 6.9990 chunk 224 optimal weight: 0.1980 chunk 171 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 239 optimal weight: 0.9980 chunk 257 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 164 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN C 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.199091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.166824 restraints weight = 36386.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.169248 restraints weight = 58158.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.170005 restraints weight = 47411.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.170594 restraints weight = 32681.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.171616 restraints weight = 28565.374| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28686 Z= 0.123 Angle : 0.745 21.674 38752 Z= 0.350 Chirality : 0.047 0.474 4340 Planarity : 0.004 0.082 4770 Dihedral : 14.659 126.966 5226 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.59 % Favored : 87.41 % Rotamer: Outliers : 2.87 % Allowed : 21.20 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.12 % 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: -2.72 (0.14), residues: 3352 helix: -0.35 (0.14), residues: 1404 sheet: -3.25 (0.30), residues: 276 loop : -2.93 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 58 TYR 0.020 0.001 TYR C 86 PHE 0.028 0.001 PHE A 337 TRP 0.055 0.002 TRP D 798 HIS 0.008 0.001 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (28634) covalent geometry : angle 0.69064 / 0.34 (38604) SS BOND : bond 0.00215 / 0.10 ( 8) SS BOND : angle 0.79361 / 0.55 ( 16) hydrogen bonds : bond 0.02936 / 1.97 ( 746) hydrogen bonds : angle 4.44923 / 3.04 ( 2130) link_ALPHA1-3 : bond 0.00828 / 0.42 ( 2) link_ALPHA1-3 : angle 3.53339 / 1.92 ( 6) link_ALPHA1-6 : bond 0.01007 / 0.51 ( 2) link_ALPHA1-6 : angle 1.31503 / 0.73 ( 6) link_BETA1-4 : bond 0.00604 / 0.39 ( 14) link_BETA1-4 : angle 3.26451 / 2.47 ( 42) link_NAG-ASN : bond 0.01015 / 0.74 ( 26) link_NAG-ASN : angle 5.70967 / 3.95 ( 78) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 384 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.7382 (ttp80) cc_final: 0.7082 (ttt90) REVERT: A 241 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7857 (mt0) REVERT: A 257 THR cc_start: 0.8244 (m) cc_final: 0.7955 (p) REVERT: A 565 MET cc_start: 0.7662 (tpp) cc_final: 0.7339 (tpt) REVERT: A 737 MET cc_start: 0.7846 (mmm) cc_final: 0.7476 (mmt) REVERT: A 793 MET cc_start: 0.6972 (mmm) cc_final: 0.6561 (mtt) REVERT: B 123 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8155 (t0) REVERT: B 152 ASP cc_start: 0.7003 (t0) cc_final: 0.6699 (m-30) REVERT: B 166 PHE cc_start: 0.7518 (t80) cc_final: 0.7115 (t80) REVERT: B 443 TYR cc_start: 0.6457 (OUTLIER) cc_final: 0.5607 (p90) REVERT: B 590 TYR cc_start: 0.6377 (OUTLIER) cc_final: 0.5667 (p90) REVERT: B 753 THR cc_start: 0.9280 (t) cc_final: 0.8982 (p) REVERT: B 758 LEU cc_start: 0.9004 (mm) cc_final: 0.8754 (mt) REVERT: C 87 ASP cc_start: 0.7575 (t0) cc_final: 0.7176 (t70) REVERT: C 114 SER cc_start: 0.8716 (m) cc_final: 0.8226 (t) REVERT: C 374 ARG cc_start: 0.7850 (ttp-110) cc_final: 0.7556 (ttp-110) REVERT: C 479 GLU cc_start: 0.6839 (tm-30) cc_final: 0.6617 (tm-30) REVERT: C 480 ILE cc_start: 0.7799 (mp) cc_final: 0.7407 (mm) REVERT: C 793 MET cc_start: 0.6898 (mmm) cc_final: 0.6089 (mtt) REVERT: D 123 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8115 (t0) REVERT: D 436 THR cc_start: 0.9183 (m) cc_final: 0.8953 (p) REVERT: D 758 LEU cc_start: 0.9041 (mm) cc_final: 0.8767 (mt) outliers start: 84 outliers final: 70 residues processed: 445 average time/residue: 0.1570 time to fit residues: 117.3553 Evaluate side-chains 439 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 364 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 585 SER Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 195 TYR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 837 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 290 optimal weight: 0.0010 chunk 297 optimal weight: 0.4980 chunk 247 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 333 optimal weight: 6.9990 chunk 129 optimal weight: 0.5980 chunk 173 optimal weight: 4.9990 chunk 259 optimal weight: 2.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN ** B 621 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 = 0.4284 r_free = 0.4284 target = 0.198556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.164613 restraints weight = 36757.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.166216 restraints weight = 58073.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.167514 restraints weight = 52505.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.168769 restraints weight = 34147.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.170288 restraints weight = 28644.491| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28686 Z= 0.130 Angle : 0.750 21.627 38752 Z= 0.352 Chirality : 0.047 0.495 4340 Planarity : 0.004 0.080 4770 Dihedral : 14.413 125.883 5226 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.22 % Favored : 86.78 % Rotamer: Outliers : 2.80 % Allowed : 21.68 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.12 % 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: -2.60 (0.14), residues: 3352 helix: -0.24 (0.14), residues: 1398 sheet: -3.12 (0.32), residues: 266 loop : -2.89 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 58 TYR 0.029 0.001 TYR C 86 PHE 0.026 0.001 PHE B 337 TRP 0.051 0.002 TRP D 798 HIS 0.008 0.001 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (28634) covalent geometry : angle 0.69584 / 0.34 (38604) SS BOND : bond 0.00204 / 0.09 ( 8) SS BOND : angle 0.81021 / 0.55 ( 16) hydrogen bonds : bond 0.02986 / 2.00 ( 746) hydrogen bonds : angle 4.41076 / 3.01 ( 2130) link_ALPHA1-3 : bond 0.00740 / 0.37 ( 2) link_ALPHA1-3 : angle 3.48986 / 1.89 ( 6) link_ALPHA1-6 : bond 0.00979 / 0.49 ( 2) link_ALPHA1-6 : angle 1.29198 / 0.71 ( 6) link_BETA1-4 : bond 0.00604 / 0.39 ( 14) link_BETA1-4 : angle 3.24924 / 2.45 ( 42) link_NAG-ASN : bond 0.01006 / 0.73 ( 26) link_NAG-ASN : angle 5.72944 / 3.95 ( 78) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4983.75 seconds wall clock time: 87 minutes 5.70 seconds (5225.70 seconds total)