Starting phenix.real_space_refine on Sun Aug 9 09:18:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ygn_72935/08_2026/9ygn_72935.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ygn_72935/08_2026/9ygn_72935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ygn_72935/08_2026/9ygn_72935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ygn_72935/08_2026/9ygn_72935.map" model { file = "/net/cci-nas-00/data/ceres_data/9ygn_72935/08_2026/9ygn_72935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ygn_72935/08_2026/9ygn_72935.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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: 4 Type Number sf(0) Gaussians S 181 5.16 5 C 20861 2.51 5 N 5410 2.21 5 O 6398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32850 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 9259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1191, 9259 Classifications: {'peptide': 1191} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 3, 'PTRANS': 50, 'TRANS': 1137} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 9102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1182, 9102 Classifications: {'peptide': 1182} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 3, 'PTRANS': 50, 'TRANS': 1128} Chain breaks: 3 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 6, 'ARG:plan': 3, 'PHE:plan': 6, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 106 Chain: "C" Number of atoms: 9050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1184, 9050 Classifications: {'peptide': 1184} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 3, 'PTRANS': 50, 'TRANS': 1130} Chain breaks: 3 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 281 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'PHE:plan': 9, 'ARG:plan': 2, 'TYR:plan': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 4, 'GLU:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 131 Chain: "H" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 906 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 906 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 906 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 809 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "M" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 809 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "N" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 809 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "R" 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.98, per 1000 atoms: 0.21 Number of scatterers: 32850 At special positions: 0 Unit cell: (183.08, 178.48, 223.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 181 16.00 O 6398 8.00 N 5410 7.00 C 20861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=75, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.02 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS B 890 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.03 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.04 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG R 1 " - " NAG R 2 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG A1401 " - " ASN A 335 " " NAG A1402 " - " ASN A 433 " " NAG A1403 " - " ASN A 454 " " NAG A1404 " - " ASN A 725 " " NAG A1405 " - " ASN A 793 " " NAG A1406 " - " ASN A 924 " " NAG A1407 " - " ASN A 664 " " NAG B1401 " - " ASN B 664 " " NAG B1402 " - " ASN B 725 " " NAG B1403 " - " ASN B 793 " " NAG C1401 " - " ASN C 664 " " NAG C1402 " - " ASN C 725 " " NAG C1403 " - " ASN C 793 " " NAG D 1 " - " ASN C 58 " " NAG G 1 " - " ASN A 58 " " NAG R 1 " - " ASN B 58 " " NAG Y 1 " - " ASN B1211 " Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.3 seconds 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7924 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 88 sheets defined 21.8% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.958A pdb=" N ILE A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 340 through 344 removed outlier: 4.032A pdb=" N TRP A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 removed outlier: 3.639A pdb=" N VAL A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.852A pdb=" N ILE A 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.772A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.669A pdb=" N ASN A 483 " --> pdb=" O PRO A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 556 removed outlier: 3.530A pdb=" N CYS A 556 " --> pdb=" O GLU A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 556' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 696 through 704 removed outlier: 4.833A pdb=" N ASN A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 819 Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.505A pdb=" N HIS A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 861 removed outlier: 3.724A pdb=" N ASN A 838 " --> pdb=" O THR A 834 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A 851 " --> pdb=" O ASN A 847 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 861 " --> pdb=" O VAL A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 882 removed outlier: 3.916A pdb=" N ASN A 881 " --> pdb=" O ASP A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 911 removed outlier: 4.233A pdb=" N LEU A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 907 " --> pdb=" O LEU A 903 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 924 removed outlier: 4.017A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 941 removed outlier: 3.695A pdb=" N ASN A 941 " --> pdb=" O VAL A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 965 removed outlier: 3.565A pdb=" N ALA A 965 " --> pdb=" O ALA A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 990 removed outlier: 3.571A pdb=" N VAL A 983 " --> pdb=" O PHE A 979 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN A 984 " --> pdb=" O SER A 980 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR A 985 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 990 " --> pdb=" O ARG A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1000 removed outlier: 4.149A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1018 removed outlier: 3.518A pdb=" N ASN A1009 " --> pdb=" O ALA A1005 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN A1017 " --> pdb=" O LEU A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1045 removed outlier: 3.686A pdb=" N LYS A1028 " --> pdb=" O SER A1024 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A1029 " --> pdb=" O ALA A1025 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 removed outlier: 3.672A pdb=" N ASN A1049 " --> pdb=" O GLN A1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1046 through 1049' Processing helix chain 'A' and resid 1059 through 1065 removed outlier: 3.615A pdb=" N LEU A1065 " --> pdb=" O ILE A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1113 removed outlier: 3.863A pdb=" N GLN A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A1096 " --> pdb=" O GLN A1092 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 88 through 91 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.543A pdb=" N THR B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 334 Processing helix chain 'B' and resid 340 through 344 removed outlier: 4.033A pdb=" N TRP B 344 " --> pdb=" O PRO B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 removed outlier: 3.639A pdb=" N VAL B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.852A pdb=" N ILE B 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 401 Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 443 through 448 removed outlier: 3.772A pdb=" N TYR B 448 " --> pdb=" O TRP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.669A pdb=" N ASN B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 556 removed outlier: 3.530A pdb=" N CYS B 556 " --> pdb=" O GLU B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 696 through 704 removed outlier: 3.626A pdb=" N VAL B 700 " --> pdb=" O LYS B 696 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN B 702 " --> pdb=" O SER B 698 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 819 removed outlier: 3.550A pdb=" N VAL B 818 " --> pdb=" O CYS B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 828 removed outlier: 3.776A pdb=" N HIS B 826 " --> pdb=" O TYR B 822 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP B 827 " --> pdb=" O ALA B 823 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU B 828 " --> pdb=" O ALA B 824 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 822 through 828' Processing helix chain 'B' and resid 829 through 831 No H-bonds generated for 'chain 'B' and resid 829 through 831' Processing helix chain 'B' and resid 832 through 861 removed outlier: 3.608A pdb=" N CYS B 836 " --> pdb=" O TYR B 832 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN B 840 " --> pdb=" O CYS B 836 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER B 841 " --> pdb=" O ASP B 837 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 849 " --> pdb=" O GLU B 845 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 857 " --> pdb=" O THR B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 872 No H-bonds generated for 'chain 'B' and resid 870 through 872' Processing helix chain 'B' and resid 878 through 882 removed outlier: 3.827A pdb=" N ASN B 881 " --> pdb=" O ASP B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 911 removed outlier: 4.061A pdb=" N LEU B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 910 " --> pdb=" O LEU B 906 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 924 removed outlier: 3.520A pdb=" N PHE B 918 " --> pdb=" O SER B 914 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 940 removed outlier: 3.703A pdb=" N VAL B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 965 removed outlier: 3.900A pdb=" N SER B 956 " --> pdb=" O GLU B 952 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY B 957 " --> pdb=" O THR B 953 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 962 " --> pdb=" O TYR B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 989 removed outlier: 4.504A pdb=" N GLN B 984 " --> pdb=" O SER B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1000 Processing helix chain 'B' and resid 1000 through 1019 removed outlier: 3.772A pdb=" N ASN B1009 " --> pdb=" O ALA B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1046 removed outlier: 3.565A pdb=" N ILE B1029 " --> pdb=" O ALA B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1049 No H-bonds generated for 'chain 'B' and resid 1047 through 1049' Processing helix chain 'B' and resid 1057 through 1062 removed outlier: 3.545A pdb=" N LEU B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1114 removed outlier: 3.700A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 1198 through 1200 No H-bonds generated for 'chain 'B' and resid 1198 through 1200' Processing helix chain 'C' and resid 88 through 91 removed outlier: 3.529A pdb=" N LYS C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 88 through 91' Processing helix chain 'C' and resid 285 through 295 removed outlier: 3.600A pdb=" N ILE C 290 " --> pdb=" O PHE C 286 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 340 through 344 removed outlier: 4.032A pdb=" N TRP C 344 " --> pdb=" O PRO C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 removed outlier: 3.639A pdb=" N VAL C 363 " --> pdb=" O LEU C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.851A pdb=" N ILE C 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 401 Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 443 through 448 removed outlier: 3.772A pdb=" N TYR C 448 " --> pdb=" O TRP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.669A pdb=" N ASN C 483 " --> pdb=" O PRO C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 556 removed outlier: 3.530A pdb=" N CYS C 556 " --> pdb=" O GLU C 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 553 through 556' Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 699 through 704 removed outlier: 3.630A pdb=" N ASN C 703 " --> pdb=" O TYR C 699 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE C 704 " --> pdb=" O VAL C 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 699 through 704' Processing helix chain 'C' and resid 814 through 819 Processing helix chain 'C' and resid 822 through 833 removed outlier: 3.852A pdb=" N HIS C 826 " --> pdb=" O TYR C 822 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASP C 827 " --> pdb=" O ALA C 823 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU C 828 " --> pdb=" O ALA C 824 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU C 831 " --> pdb=" O ASP C 827 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR C 832 " --> pdb=" O LEU C 828 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY C 833 " --> pdb=" O LEU C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 860 removed outlier: 4.470A pdb=" N ASP C 837 " --> pdb=" O GLY C 833 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE C 839 " --> pdb=" O PHE C 835 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP C 851 " --> pdb=" O ASN C 847 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 858 " --> pdb=" O GLN C 854 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN C 859 " --> pdb=" O LEU C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 873 removed outlier: 3.872A pdb=" N ASN C 872 " --> pdb=" O SER C 869 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 873 " --> pdb=" O ASN C 870 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 869 through 873' Processing helix chain 'C' and resid 878 through 882 removed outlier: 3.700A pdb=" N ASN C 881 " --> pdb=" O ASP C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 901 through 906 removed outlier: 3.876A pdb=" N LEU C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 923 removed outlier: 3.635A pdb=" N GLU C 920 " --> pdb=" O VAL C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 941 removed outlier: 3.605A pdb=" N VAL C 937 " --> pdb=" O ASP C 933 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE C 940 " --> pdb=" O CYS C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 965 removed outlier: 3.588A pdb=" N TYR C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR C 959 " --> pdb=" O ILE C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 975 Processing helix chain 'C' and resid 978 through 989 removed outlier: 4.002A pdb=" N VAL C 983 " --> pdb=" O PHE C 979 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLN C 984 " --> pdb=" O SER C 980 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR C 985 " --> pdb=" O LEU C 981 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY C 989 " --> pdb=" O TYR C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.844A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1008 Processing helix chain 'C' and resid 1009 through 1018 removed outlier: 4.326A pdb=" N ILE C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLN C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN C1017 " --> pdb=" O LEU C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1021 No H-bonds generated for 'chain 'C' and resid 1019 through 1021' Processing helix chain 'C' and resid 1023 through 1046 removed outlier: 3.686A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN C1046 " --> pdb=" O SER C1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1049 No H-bonds generated for 'chain 'C' and resid 1047 through 1049' Processing helix chain 'C' and resid 1060 through 1064 removed outlier: 4.087A pdb=" N ARG C1064 " --> pdb=" O ILE C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1109 removed outlier: 3.569A pdb=" N ALA C1084 " --> pdb=" O GLY C1080 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C1107 " --> pdb=" O ALA C1103 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 29 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.624A pdb=" N GLU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 29 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.625A pdb=" N GLU M 83 " --> pdb=" O SER M 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 29 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.624A pdb=" N GLU N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 67 removed outlier: 3.555A pdb=" N GLY A 65 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 67 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER A 262 " --> pdb=" O PHE A 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.588A pdb=" N PHE A 200 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N PHE A 209 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N SER A 225 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA A 211 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.834A pdb=" N SER A 96 " --> pdb=" O TYR A 235 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR A 235 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 126 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 137 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN A 140 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 187 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 150 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 112 Processing sheet with id=AA6, first strand: chain 'A' and resid 302 through 305 removed outlier: 3.505A pdb=" N PHE A 681 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 318 through 319 removed outlier: 3.752A pdb=" N ARG A 319 " --> pdb=" O ASP A 623 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 620 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A 631 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 658 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY A 657 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 337 through 338 removed outlier: 6.047A pdb=" N THR A 435 " --> pdb=" O VAL A 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.974A pdb=" N GLU A 345 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A 390 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 385 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS A 586 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 353 through 354 removed outlier: 6.549A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 385 " --> pdb=" O ASN A 595 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AB3, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.604A pdb=" N CYS A 466 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS A 536 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 504 through 505 Processing sheet with id=AB5, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 713 removed outlier: 4.022A pdb=" N PHE A 713 " --> pdb=" O VAL A 720 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 724 through 731 removed outlier: 3.533A pdb=" N PHE A 764 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 726 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N THR A 766 " --> pdb=" O LEU A 726 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N SER A 728 " --> pdb=" O THR A 766 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 773 through 775 removed outlier: 3.670A pdb=" N LEU B 867 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 791 removed outlier: 7.122A pdb=" N LEU A1157 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS A1179 " --> pdb=" O LEU A1157 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 794 through 803 removed outlier: 3.553A pdb=" N LYS A1149 " --> pdb=" O THR A 795 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 797 " --> pdb=" O SER A1147 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A1147 " --> pdb=" O ALA A 797 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 803 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A1131 " --> pdb=" O PHE A1146 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N TYR A1148 " --> pdb=" O HIS A1129 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N HIS A1129 " --> pdb=" O TYR A1148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 811 through 812 Processing sheet with id=AC3, first strand: chain 'A' and resid 1162 through 1163 removed outlier: 3.572A pdb=" N CYS A1163 " --> pdb=" O THR A1213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 1169 through 1172 removed outlier: 3.983A pdb=" N GLY A1169 " --> pdb=" O MET A1205 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A1171 " --> pdb=" O VAL A1203 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AC6, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.531A pdb=" N LEU B 61 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 268 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 80 through 81 removed outlier: 6.111A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 225 through 227 removed outlier: 3.616A pdb=" N TYR B 203 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS B 201 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR B 199 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 104 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 105 " --> pdb=" O TRP B 257 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP B 257 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 109 through 112 removed outlier: 4.350A pdb=" N THR B 109 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU B 120 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 186 through 187 removed outlier: 3.915A pdb=" N THR B 149 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL B 138 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE B 124 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR B 123 " --> pdb=" O MET B 238 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY B 127 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS B 234 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 302 through 305 Processing sheet with id=AD3, first strand: chain 'B' and resid 337 through 338 removed outlier: 6.046A pdb=" N THR B 435 " --> pdb=" O VAL B 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 345 through 349 removed outlier: 3.974A pdb=" N GLU B 345 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 390 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS B 586 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 345 through 349 removed outlier: 3.974A pdb=" N GLU B 345 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 390 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AD7, first strand: chain 'B' and resid 466 through 468 removed outlier: 4.604A pdb=" N CYS B 466 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS B 536 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 504 through 505 Processing sheet with id=AD9, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AE1, first strand: chain 'B' and resid 619 through 624 removed outlier: 3.598A pdb=" N VAL B 620 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY B 631 " --> pdb=" O VAL B 620 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ILE B 656 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU B 648 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 714 through 715 removed outlier: 3.729A pdb=" N GLY B 718 " --> pdb=" O SER B 715 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 736 through 737 removed outlier: 4.411A pdb=" N LEU B 736 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 790 through 791 Processing sheet with id=AE5, first strand: chain 'B' and resid 795 through 797 removed outlier: 3.978A pdb=" N THR B 795 " --> pdb=" O LYS B1149 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 800 through 803 removed outlier: 3.780A pdb=" N GLU B 801 " --> pdb=" O PHE B1143 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE B1143 " --> pdb=" O GLU B 801 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B1142 " --> pdb=" O GLN B1135 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.470A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 944 " --> pdb=" O THR B 811 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 1162 through 1163 removed outlier: 3.523A pdb=" N CYS B1163 " --> pdb=" O THR B1213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'B' and resid 1170 through 1172 Processing sheet with id=AF1, first strand: chain 'B' and resid 1175 through 1180 Processing sheet with id=AF2, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AF3, first strand: chain 'C' and resid 65 through 67 Processing sheet with id=AF4, first strand: chain 'C' and resid 208 through 214 removed outlier: 3.965A pdb=" N TYR C 212 " --> pdb=" O HIS C 201 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 104 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE C 202 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE C 102 " --> pdb=" O PHE C 202 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 111 through 112 Processing sheet with id=AF6, first strand: chain 'C' and resid 126 through 127 removed outlier: 3.990A pdb=" N ILE C 137 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE C 148 " --> pdb=" O LYS C 186 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS C 186 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA C 150 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 266 through 268 removed outlier: 3.611A pdb=" N VAL C 280 " --> pdb=" O LEU C 267 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 306 through 310 removed outlier: 4.011A pdb=" N GLY C 308 " --> pdb=" O GLY C 675 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLY C 675 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 337 through 338 removed outlier: 6.047A pdb=" N THR C 435 " --> pdb=" O VAL C 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'C' and resid 345 through 349 removed outlier: 3.974A pdb=" N GLU C 345 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS C 390 " --> pdb=" O GLU C 345 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 385 " --> pdb=" O ASN C 595 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 364 through 371 removed outlier: 5.879A pdb=" N VAL C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N SER C 428 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS C 586 " --> pdb=" O LEU C 429 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 385 " --> pdb=" O ASN C 595 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AG4, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.604A pdb=" N CYS C 466 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS C 536 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 504 through 505 Processing sheet with id=AG6, first strand: chain 'C' and resid 550 through 551 Processing sheet with id=AG7, first strand: chain 'C' and resid 620 through 621 removed outlier: 3.634A pdb=" N VAL C 620 " --> pdb=" O GLY C 631 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY C 631 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR C 667 " --> pdb=" O PHE C 658 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 690 through 691 removed outlier: 3.657A pdb=" N PHE C 713 " --> pdb=" O VAL C 720 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 743 through 745 removed outlier: 3.512A pdb=" N ARG C 763 " --> pdb=" O ASP C 745 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 789 through 791 Processing sheet with id=AH2, first strand: chain 'C' and resid 794 through 795 removed outlier: 3.659A pdb=" N LYS C1149 " --> pdb=" O THR C 795 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 801 through 804 removed outlier: 4.592A pdb=" N GLU C 801 " --> pdb=" O PHE C1143 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE C1143 " --> pdb=" O GLU C 801 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA C1137 " --> pdb=" O GLY C1140 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 809 through 812 removed outlier: 4.408A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 1162 through 1163 removed outlier: 4.032A pdb=" N CYS C1163 " --> pdb=" O THR C1213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'C' and resid 1170 through 1172 Processing sheet with id=AH7, first strand: chain 'C' and resid 1175 through 1179 Processing sheet with id=AH8, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.626A pdb=" N HIS H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AI1, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.704A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.626A pdb=" N HIS I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AI4, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.704A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.627A pdb=" N HIS J 77 " --> pdb=" O ASP J 72 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=AI7, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.704A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'L' and resid 9 through 13 removed outlier: 7.125A pdb=" N ALA L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'L' and resid 9 through 13 removed outlier: 7.125A pdb=" N ALA L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AJ2, first strand: chain 'M' and resid 9 through 13 removed outlier: 7.125A pdb=" N ALA M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'M' and resid 9 through 13 removed outlier: 7.125A pdb=" N ALA M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AJ5, first strand: chain 'N' and resid 9 through 13 removed outlier: 7.125A pdb=" N ALA N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'N' and resid 9 through 13 removed outlier: 7.125A pdb=" N ALA N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'N' and resid 19 through 24 965 hydrogen bonds defined for protein. 2538 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: 8.47 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5332 1.32 - 1.44: 9640 1.44 - 1.57: 18453 1.57 - 1.69: 0 1.69 - 1.82: 207 Bond restraints: 33632 Sorted by residual: bond pdb=" N LEU B 324 " pdb=" CA LEU B 324 " ideal model delta sigma weight residual 1.453 1.491 -0.038 9.20e-03 1.18e+04 1.69e+01 bond pdb=" N LEU C 324 " pdb=" CA LEU C 324 " ideal model delta sigma weight residual 1.453 1.491 -0.037 9.20e-03 1.18e+04 1.66e+01 bond pdb=" N ASP C 326 " pdb=" CA ASP C 326 " ideal model delta sigma weight residual 1.454 1.494 -0.041 1.23e-02 6.61e+03 1.10e+01 bond pdb=" N LEU A 670 " pdb=" CA LEU A 670 " ideal model delta sigma weight residual 1.453 1.490 -0.038 1.18e-02 7.18e+03 1.02e+01 bond pdb=" N VAL A 311 " pdb=" CA VAL A 311 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 9.37e+00 ... (remaining 33627 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 44506 1.31 - 2.63: 1044 2.63 - 3.94: 241 3.94 - 5.26: 34 5.26 - 6.57: 11 Bond angle restraints: 45836 Sorted by residual: angle pdb=" N LEU B 608 " pdb=" CA LEU B 608 " pdb=" C LEU B 608 " ideal model delta sigma weight residual 110.50 104.27 6.23 1.41e+00 5.03e-01 1.95e+01 angle pdb=" C ASN A 924 " pdb=" CA ASN A 924 " pdb=" CB ASN A 924 " ideal model delta sigma weight residual 111.88 105.76 6.12 1.41e+00 5.03e-01 1.88e+01 angle pdb=" N ASP C 606 " pdb=" CA ASP C 606 " pdb=" C ASP C 606 " ideal model delta sigma weight residual 111.56 105.62 5.94 1.38e+00 5.25e-01 1.85e+01 angle pdb=" CA PHE B 979 " pdb=" C PHE B 979 " pdb=" N SER B 980 " ideal model delta sigma weight residual 117.07 121.48 -4.41 1.14e+00 7.69e-01 1.49e+01 angle pdb=" N PRO A 671 " pdb=" CA PRO A 671 " pdb=" C PRO A 671 " ideal model delta sigma weight residual 111.22 116.58 -5.36 1.40e+00 5.10e-01 1.46e+01 ... (remaining 45831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 19458 17.05 - 34.09: 702 34.09 - 51.14: 106 51.14 - 68.18: 25 68.18 - 85.23: 2 Dihedral angle restraints: 20293 sinusoidal: 7937 harmonic: 12356 Sorted by residual: dihedral pdb=" CA SER B 604 " pdb=" C SER B 604 " pdb=" N ASN B 605 " pdb=" CA ASN B 605 " ideal model delta harmonic sigma weight residual 180.00 154.94 25.06 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CB CYS B 925 " pdb=" SG CYS B 925 " pdb=" SG CYS B 936 " pdb=" CB CYS B 936 " ideal model delta sinusoidal sigma weight residual 93.00 131.56 -38.56 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CB CYS A 466 " pdb=" SG CYS A 466 " pdb=" SG CYS A 546 " pdb=" CB CYS A 546 " ideal model delta sinusoidal sigma weight residual -86.00 -115.69 29.69 1 1.00e+01 1.00e-02 1.26e+01 ... (remaining 20290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 5215 0.170 - 0.341: 18 0.341 - 0.511: 2 0.511 - 0.682: 0 0.682 - 0.852: 1 Chirality restraints: 5236 Sorted by residual: chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.06e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.83e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.17e+01 ... (remaining 5233 not shown) Planarity restraints: 5891 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1404 " -0.348 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG A1404 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG A1404 " -0.097 2.00e-02 2.50e+03 pdb=" N2 NAG A1404 " 0.534 2.00e-02 2.50e+03 pdb=" O7 NAG A1404 " -0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1402 " 0.209 2.00e-02 2.50e+03 1.73e-01 3.73e+02 pdb=" C7 NAG B1402 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG B1402 " 0.150 2.00e-02 2.50e+03 pdb=" N2 NAG B1402 " -0.282 2.00e-02 2.50e+03 pdb=" O7 NAG B1402 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 2 " 0.161 2.00e-02 2.50e+03 1.35e-01 2.27e+02 pdb=" C7 NAG Y 2 " -0.044 2.00e-02 2.50e+03 pdb=" C8 NAG Y 2 " 0.118 2.00e-02 2.50e+03 pdb=" N2 NAG Y 2 " -0.221 2.00e-02 2.50e+03 pdb=" O7 NAG Y 2 " -0.013 2.00e-02 2.50e+03 ... (remaining 5888 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 64 2.44 - 3.05: 20644 3.05 - 3.67: 47107 3.67 - 4.28: 70534 4.28 - 4.90: 116896 Nonbonded interactions: 255245 Sorted by model distance: nonbonded pdb=" NE2 GLN A 630 " pdb=" ND2 ASN B 821 " model vdw 1.821 3.200 nonbonded pdb=" CD1 TRP A 644 " pdb=" CE1 PHE B 222 " model vdw 2.056 3.560 nonbonded pdb=" O GLN C 683 " pdb=" OD1 ASN C 684 " model vdw 2.169 3.040 nonbonded pdb=" O THR A 161 " pdb=" OG1 THR A 241 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR A 123 " pdb=" O VAL A 139 " model vdw 2.226 3.040 ... (remaining 255240 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 14 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 48 or (resid 49 and (name N or nam \ e CA or name C or name O or name CB )) or resid 50 through 51 or (resid 52 and ( \ name N or name CA or name C or name O or name CB )) or resid 53 or (resid 54 thr \ ough 57 and (name N or name CA or name C or name O or name CB )) or resid 58 thr \ ough 73 or (resid 74 through 75 and (name N or name CA or name C or name O or na \ me CB )) or resid 76 through 90 or (resid 91 and (name N or name CA or name C or \ name O or name CB )) or resid 92 through 93 or (resid 94 through 95 and (name N \ or name CA or name C or name O or name CB )) or resid 96 through 97 or (resid 9 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 99 through 1 \ 04 or (resid 105 and (name N or name CA or name C or name O or name CB )) or res \ id 106 through 120 or (resid 121 and (name N or name CA or name C or name O or n \ ame CB )) or resid 122 through 123 or (resid 124 and (name N or name CA or name \ C or name O or name CB )) or resid 125 through 128 or (resid 129 and (name N or \ name CA or name C or name O or name CB )) or resid 130 through 138 or (resid 139 \ and (name N or name CA or name C or name O or name CB )) or resid 140 through 1 \ 45 or (resid 146 and (name N or name CA or name C or name O or name CB )) or res \ id 147 or (resid 148 and (name N or name CA or name C or name O or name CB )) or \ resid 149 through 184 or (resid 185 and (name N or name CA or name C or name O \ or name CB )) or resid 186 through 199 or (resid 200 and (name N or name CA or n \ ame C or name O or name CB )) or resid 201 through 211 or (resid 212 and (name N \ or name CA or name C or name O or name CB )) or resid 213 through 219 or (resid \ 220 and (name N or name CA or name C or name O or name CB )) or resid 221 or (r \ esid 222 and (name N or name CA or name C or name O or name CB )) or resid 223 t \ hrough 225 or (resid 226 and (name N or name CA or name C or name O or name CB ) \ ) or resid 227 through 234 or (resid 235 and (name N or name CA or name C or nam \ e O or name CB )) or resid 236 through 244 or resid 254 through 256 or (resid 25 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 258 through \ 269 or (resid 270 and (name N or name CA or name C or name O or name CB )) or re \ sid 271 through 279 or (resid 280 and (name N or name CA or name C or name O or \ name CB )) or resid 281 through 284 or (resid 285 through 286 and (name N or nam \ e CA or name C or name O or name CB )) or resid 287 through 311 or (resid 312 an \ d (name N or name CA or name C or name O or name CB )) or resid 313 through 317 \ or (resid 318 through 319 and (name N or name CA or name C or name O or name CB \ )) or resid 320 through 608 or (resid 609 and (name N or name CA or name C or na \ me O or name CB )) or resid 610 or (resid 611 through 612 and (name N or name CA \ or name C or name O or name CB )) or resid 613 through 626 or (resid 627 and (n \ ame N or name CA or name C or name O or name CB )) or resid 628 through 657 or ( \ resid 658 and (name N or name CA or name C or name O or name CB )) or resid 659 \ or (resid 660 through 661 and (name N or name CA or name C or name O or name CB \ )) or resid 662 through 672 or (resid 673 and (name N or name CA or name C or na \ me O or name CB )) or resid 674 through 682 or (resid 683 and (name N or name CA \ or name C or name O or name CB )) or resid 684 through 697 or (resid 698 and (n \ ame N or name CA or name C or name O or name CB )) or resid 699 through 769 or ( \ resid 770 and (name N or name CA or name C or name O or name CB )) or resid 771 \ through 785 or (resid 786 and (name N or name CA or name C or name O or name CB \ )) or resid 787 through 799 or (resid 800 and (name N or name CA or name C or na \ me O or name CB )) or resid 801 through 819 or (resid 820 and (name N or name CA \ or name C or name O or name CB )) or resid 821 through 924 or (resid 925 throug \ h 926 and (name N or name CA or name C or name O or name CB )) or resid 927 thro \ ugh 957 or (resid 958 and (name N or name CA or name C or name O or name CB )) o \ r resid 959 through 998 or (resid 999 through 1000 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 or (resid 1002 through 1007 and (name \ N or name CA or name C or name O or name CB )) or resid 1008 through 1037 or (re \ sid 1038 through 1039 and (name N or name CA or name C or name O or name CB )) o \ r resid 1040 through 1058 or (resid 1059 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1060 through 1061 or (resid 1062 and (name N or name \ CA or name C or name O or name CB )) or resid 1063 through 1065 or (resid 1066 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1067 through 10 \ 70 or (resid 1071 through 1072 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1073 through 1151 or (resid 1152 and (name N or name CA or name \ C or name O or name CB )) or resid 1153 through 1178 or (resid 1179 through 118 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 1182 through \ 1183 or (resid 1184 through 1185 and (name N or name CA or name C or name O or \ name CB )) or resid 1186 through 1403)) selection = (chain 'B' and ((resid 14 and (name N or name CA or name C or name O or name CB \ )) or resid 15 through 37 or (resid 38 through 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 51 or (resid 52 and (name N or na \ me CA or name C or name O or name CB )) or resid 53 through 73 or (resid 74 thro \ ugh 75 and (name N or name CA or name C or name O or name CB )) or resid 76 thro \ ugh 90 or (resid 91 and (name N or name CA or name C or name O or name CB )) or \ resid 92 through 93 or (resid 94 through 95 and (name N or name CA or name C or \ name O or name CB )) or resid 96 through 104 or (resid 105 and (name N or name C \ A or name C or name O or name CB )) or resid 106 through 120 or (resid 121 and ( \ name N or name CA or name C or name O or name CB )) or resid 122 through 123 or \ (resid 124 and (name N or name CA or name C or name O or name CB )) or resid 125 \ through 128 or (resid 129 and (name N or name CA or name C or name O or name CB \ )) or resid 130 through 138 or (resid 139 and (name N or name CA or name C or n \ ame O or name CB )) or resid 140 through 145 or (resid 146 and (name N or name C \ A or name C or name O or name CB )) or resid 147 or (resid 148 and (name N or na \ me CA or name C or name O or name CB )) or resid 149 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )) or resid 158 through 199 \ or (resid 200 and (name N or name CA or name C or name O or name CB )) or resid \ 201 through 211 or (resid 212 and (name N or name CA or name C or name O or nam \ e CB )) or resid 213 through 219 or (resid 220 and (name N or name CA or name C \ or name O or name CB )) or resid 221 or (resid 222 and (name N or name CA or nam \ e C or name O or name CB )) or resid 223 through 256 or (resid 257 and (name N o \ r name CA or name C or name O or name CB )) or resid 258 through 284 or (resid 2 \ 85 through 286 and (name N or name CA or name C or name O or name CB )) or resid \ 287 through 626 or (resid 627 and (name N or name CA or name C or name O or nam \ e CB )) or resid 628 through 682 or (resid 683 and (name N or name CA or name C \ or name O or name CB )) or resid 684 through 734 or (resid 735 and (name N or na \ me CA or name C or name O or name CB )) or resid 736 through 743 or (resid 744 a \ nd (name N or name CA or name C or name O or name CB )) or resid 745 through 763 \ or (resid 764 and (name N or name CA or name C or name O or name CB )) or resid \ 765 through 769 or (resid 770 and (name N or name CA or name C or name O or nam \ e CB )) or resid 771 through 785 or (resid 786 and (name N or name CA or name C \ or name O or name CB )) or resid 787 through 799 or (resid 800 and (name N or na \ me CA or name C or name O or name CB )) or resid 801 through 819 or (resid 820 a \ nd (name N or name CA or name C or name O or name CB )) or resid 821 through 858 \ or (resid 859 through 860 and (name N or name CA or name C or name O or name CB \ )) or resid 861 through 924 or (resid 925 through 926 and (name N or name CA or \ name C or name O or name CB )) or resid 927 through 957 or (resid 958 and (name \ N or name CA or name C or name O or name CB )) or resid 959 through 998 or (res \ id 999 through 1000 and (name N or name CA or name C or name O or name CB )) or \ resid 1001 or (resid 1002 through 1007 and (name N or name CA or name C or name \ O or name CB )) or resid 1008 through 1058 or (resid 1059 and (name N or name CA \ or name C or name O or name CB )) or resid 1060 through 1065 or (resid 1066 and \ (name N or name CA or name C or name O or name CB )) or resid 1067 through 1070 \ or (resid 1071 through 1072 and (name N or name CA or name C or name O or name \ CB )) or resid 1073 through 1151 or (resid 1152 and (name N or name CA or name C \ or name O or name CB )) or resid 1153 through 1178 or (resid 1179 through 1181 \ and (name N or name CA or name C or name O or name CB )) or resid 1182 through 1 \ 183 or (resid 1184 through 1185 and (name N or name CA or name C or name O or na \ me CB )) or resid 1186 through 1403)) selection = (chain 'C' and ((resid 14 and (name N or name CA or name C or name O or name CB \ )) or resid 15 through 37 or (resid 38 through 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 41 or (resid 42 and (name N or na \ me CA or name C or name O or name CB )) or resid 43 through 48 or (resid 49 and \ (name N or name CA or name C or name O or name CB )) or resid 50 through 53 or ( \ resid 54 through 57 and (name N or name CA or name C or name O or name CB )) or \ resid 58 through 97 or (resid 98 and (name N or name CA or name C or name O or n \ ame CB )) or resid 99 through 156 or (resid 157 and (name N or name CA or name C \ or name O or name CB )) or resid 158 through 184 or (resid 185 and (name N or n \ ame CA or name C or name O or name CB )) or resid 186 through 234 or (resid 235 \ and (name N or name CA or name C or name O or name CB )) or resid 236 through 24 \ 4 or resid 254 through 269 or (resid 270 and (name N or name CA or name C or nam \ e O or name CB )) or resid 271 through 279 or (resid 280 and (name N or name CA \ or name C or name O or name CB )) or resid 281 through 311 or (resid 312 and (na \ me N or name CA or name C or name O or name CB )) or resid 313 through 317 or (r \ esid 318 through 319 and (name N or name CA or name C or name O or name CB )) or \ resid 320 through 608 or (resid 609 and (name N or name CA or name C or name O \ or name CB )) or resid 610 or (resid 611 through 612 and (name N or name CA or n \ ame C or name O or name CB )) or resid 613 through 657 or (resid 658 and (name N \ or name CA or name C or name O or name CB )) or resid 659 or (resid 660 through \ 661 and (name N or name CA or name C or name O or name CB )) or resid 662 throu \ gh 672 or (resid 673 and (name N or name CA or name C or name O or name CB )) or \ resid 674 through 734 or (resid 735 and (name N or name CA or name C or name O \ or name CB )) or resid 736 through 743 or (resid 744 and (name N or name CA or n \ ame C or name O or name CB )) or resid 745 through 763 or (resid 764 and (name N \ or name CA or name C or name O or name CB )) or resid 765 through 858 or (resid \ 859 through 860 and (name N or name CA or name C or name O or name CB )) or res \ id 861 through 1037 or (resid 1038 through 1039 and (name N or name CA or name C \ or name O or name CB )) or resid 1040 through 1061 or (resid 1062 and (name N o \ r name CA or name C or name O or name CB )) or resid 1063 through 1403)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'R' selection = chain 'Y' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.810 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: 0.670 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.900 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4141 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33728 Z= 0.162 Angle : 0.509 6.571 46049 Z= 0.295 Chirality : 0.046 0.852 5236 Planarity : 0.006 0.301 5874 Dihedral : 8.579 85.230 12144 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.56 % Allowed : 6.31 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.12), residues: 4198 helix: -3.01 (0.13), residues: 660 sheet: -0.70 (0.19), residues: 841 loop : -2.02 (0.11), residues: 2697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C1120 TYR 0.008 0.001 TYR B 622 PHE 0.007 0.001 PHE C 202 TRP 0.011 0.001 TRP J 47 HIS 0.003 0.000 HIS J 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.16 (33632) covalent geometry : angle 0.50314 / 0.29 (45836) SS BOND : bond 0.00222 / 0.12 ( 75) SS BOND : angle 0.63470 / 0.41 ( 150) hydrogen bonds : bond 0.28917 / 19.27 ( 934) hydrogen bonds : angle 9.67359 / 6.58 ( 2538) link_BETA1-4 : bond 0.00227 / 0.11 ( 4) link_BETA1-4 : angle 0.94506 / 0.52 ( 12) link_NAG-ASN : bond 0.00468 / 0.29 ( 17) link_NAG-ASN : angle 2.31502 / 1.64 ( 51) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 663 time to evaluate : 1.212 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: symmetry clash REVERT: A 51 VAL cc_start: 0.4464 (OUTLIER) cc_final: 0.3846 (t) REVERT: A 362 LEU cc_start: 0.8355 (mt) cc_final: 0.8134 (mp) REVERT: A 417 ASP cc_start: 0.8066 (t0) cc_final: 0.7569 (t0) REVERT: A 434 VAL cc_start: 0.4075 (OUTLIER) cc_final: 0.3533 (m) REVERT: A 435 THR cc_start: 0.7206 (m) cc_final: 0.6952 (p) REVERT: A 523 ASP cc_start: 0.7259 (t0) cc_final: 0.6803 (p0) REVERT: A 528 TYR cc_start: 0.5616 (p90) cc_final: 0.5379 (p90) REVERT: A 637 SER cc_start: 0.7932 (t) cc_final: 0.7681 (t) REVERT: A 673 TYR cc_start: 0.6934 (t80) cc_final: 0.5605 (m-10) REVERT: A 862 MET cc_start: 0.0667 (ptt) cc_final: 0.0348 (mtm) REVERT: A 1130 ILE cc_start: 0.7993 (mm) cc_final: 0.7748 (mp) REVERT: B 40 VAL cc_start: 0.3216 (OUTLIER) cc_final: 0.2981 (t) REVERT: B 135 TYR cc_start: 0.1610 (m-80) cc_final: 0.0953 (m-80) REVERT: B 467 PHE cc_start: 0.4061 (m-80) cc_final: 0.3258 (m-10) REVERT: B 516 CYS cc_start: 0.0833 (OUTLIER) cc_final: 0.0579 (t) REVERT: B 646 ASN cc_start: 0.3040 (m-40) cc_final: 0.2835 (m110) REVERT: B 650 ASP cc_start: 0.5464 (t70) cc_final: 0.5143 (m-30) REVERT: B 717 LEU cc_start: 0.4368 (mt) cc_final: 0.3491 (tp) REVERT: B 871 LEU cc_start: 0.3211 (tt) cc_final: 0.2894 (mp) REVERT: B 984 GLN cc_start: 0.6310 (mt0) cc_final: 0.5798 (mm-40) REVERT: B 1003 LEU cc_start: 0.6420 (tt) cc_final: 0.5771 (mm) REVERT: B 1026 LEU cc_start: 0.7382 (tp) cc_final: 0.7042 (tp) REVERT: B 1044 LEU cc_start: 0.8138 (tp) cc_final: 0.7910 (tp) REVERT: B 1066 ASP cc_start: 0.7731 (m-30) cc_final: 0.7472 (m-30) REVERT: B 1151 THR cc_start: 0.7799 (OUTLIER) cc_final: 0.7321 (p) REVERT: B 1211 ASN cc_start: 0.1568 (OUTLIER) cc_final: 0.1250 (t0) REVERT: C 111 LEU cc_start: 0.6430 (mt) cc_final: 0.5777 (tp) REVERT: C 330 ASP cc_start: 0.5810 (OUTLIER) cc_final: 0.5510 (p0) REVERT: C 425 LEU cc_start: 0.5547 (tp) cc_final: 0.5274 (tp) REVERT: C 474 CYS cc_start: 0.0848 (OUTLIER) cc_final: -0.0065 (m) REVERT: C 851 ASP cc_start: 0.7827 (m-30) cc_final: 0.7524 (m-30) REVERT: C 936 CYS cc_start: 0.5582 (m) cc_final: 0.5135 (m) REVERT: C 954 GLN cc_start: 0.6659 (mt0) cc_final: 0.6429 (mt0) REVERT: C 956 SER cc_start: 0.7262 (t) cc_final: 0.6941 (m) REVERT: C 977 VAL cc_start: 0.7711 (p) cc_final: 0.7419 (m) REVERT: C 1159 SER cc_start: 0.5412 (t) cc_final: 0.5198 (m) REVERT: C 1205 MET cc_start: 0.0988 (tpt) cc_final: -0.0070 (mmt) REVERT: L 49 TYR cc_start: 0.5671 (p90) cc_final: 0.5362 (p90) REVERT: L 104 LEU cc_start: 0.6207 (tp) cc_final: 0.4856 (tp) REVERT: N 96 TRP cc_start: 0.2009 (t-100) cc_final: 0.1708 (t-100) outliers start: 57 outliers final: 12 residues processed: 715 average time/residue: 0.1907 time to fit residues: 227.6921 Evaluate side-chains 373 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 353 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1211 ASN Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 795 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 197 optimal weight: 0.0050 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.9980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 248 ASN A 265 GLN A 445 ASN A 483 ASN ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 847 ASN A 870 ASN A 954 GLN A1036 ASN A1046 GLN A1071 GLN A1117 GLN A1181 ASN B 188 ASN B 355 ASN B 445 ASN B 535 GLN B 694 ASN B 709 GLN B 826 HIS B 838 ASN B1016 GLN B1036 ASN B1041 ASN B1046 GLN B1049 ASN B1059 GLN B1111 ASN B1180 GLN B1201 ASN C 108 ASN C 201 HIS C 445 ASN C 535 GLN ** C 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 ASN C 870 ASN C 881 ASN C1016 GLN C1046 GLN C1092 GLN H 3 GLN I 3 GLN J 3 GLN L 6 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN N 38 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.233461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.205352 restraints weight = 81426.403| |-----------------------------------------------------------------------------| r_work (start): 0.4695 rms_B_bonded: 3.89 r_work: 0.4535 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5890 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33728 Z= 0.147 Angle : 0.603 10.485 46049 Z= 0.310 Chirality : 0.045 0.325 5236 Planarity : 0.004 0.044 5874 Dihedral : 4.770 58.713 5024 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.59 % Allowed : 11.25 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.12), residues: 4198 helix: -0.87 (0.18), residues: 713 sheet: -0.57 (0.18), residues: 804 loop : -1.76 (0.11), residues: 2681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 94 TYR 0.035 0.002 TYR A 958 PHE 0.021 0.002 PHE B1048 TRP 0.015 0.002 TRP H 47 HIS 0.007 0.001 HIS B 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (33632) covalent geometry : angle 0.59855 / 0.31 (45836) SS BOND : bond 0.00449 / 0.31 ( 75) SS BOND : angle 0.85416 / 0.58 ( 150) hydrogen bonds : bond 0.04866 / 3.23 ( 934) hydrogen bonds : angle 6.36886 / 4.32 ( 2538) link_BETA1-4 : bond 0.00603 / 0.27 ( 4) link_BETA1-4 : angle 1.12812 / 0.63 ( 12) link_NAG-ASN : bond 0.00398 / 0.28 ( 17) link_NAG-ASN : angle 1.87284 / 1.24 ( 51) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 416 time to evaluate : 1.048 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: A 155 MET cc_start: 0.6905 (mmm) cc_final: 0.6331 (mmp) REVERT: A 221 THR cc_start: 0.7663 (p) cc_final: 0.7433 (t) REVERT: A 290 ILE cc_start: 0.6724 (mm) cc_final: 0.6482 (mm) REVERT: A 351 ASN cc_start: 0.6291 (t0) cc_final: 0.5716 (t0) REVERT: A 473 PHE cc_start: 0.6939 (t80) cc_final: 0.6542 (t80) REVERT: A 637 SER cc_start: 0.7894 (t) cc_final: 0.7648 (t) REVERT: A 673 TYR cc_start: 0.6324 (t80) cc_final: 0.5008 (m-10) REVERT: A 732 SER cc_start: 0.6578 (t) cc_final: 0.6271 (p) REVERT: A 862 MET cc_start: 0.1948 (ptt) cc_final: 0.1630 (mmm) REVERT: A 884 PHE cc_start: 0.4824 (m-80) cc_final: 0.4451 (m-80) REVERT: A 909 ASN cc_start: 0.6948 (m-40) cc_final: 0.6718 (m-40) REVERT: A 967 MET cc_start: 0.6475 (mtt) cc_final: 0.6017 (mtt) REVERT: B 40 VAL cc_start: 0.4003 (OUTLIER) cc_final: 0.3718 (t) REVERT: B 444 TRP cc_start: 0.5374 (p-90) cc_final: 0.4192 (p-90) REVERT: B 467 PHE cc_start: 0.4179 (m-80) cc_final: 0.3182 (m-10) REVERT: B 650 ASP cc_start: 0.5939 (t70) cc_final: 0.5262 (m-30) REVERT: B 764 PHE cc_start: 0.4429 (t80) cc_final: 0.3890 (t80) REVERT: B 838 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7529 (p0) REVERT: B 936 CYS cc_start: 0.5087 (m) cc_final: 0.4886 (m) REVERT: B 984 GLN cc_start: 0.6474 (mt0) cc_final: 0.6203 (mt0) REVERT: B 1003 LEU cc_start: 0.7112 (tt) cc_final: 0.6370 (mm) REVERT: C 111 LEU cc_start: 0.6525 (mt) cc_final: 0.6020 (tt) REVERT: C 155 MET cc_start: 0.0739 (mmp) cc_final: -0.0649 (tpp) REVERT: C 238 MET cc_start: 0.0648 (ppp) cc_final: 0.0439 (ppp) REVERT: C 270 PHE cc_start: 0.3944 (m-80) cc_final: 0.2971 (m-80) REVERT: C 474 CYS cc_start: 0.1986 (OUTLIER) cc_final: -0.0265 (p) REVERT: C 902 LEU cc_start: 0.7626 (tt) cc_final: 0.7054 (mt) REVERT: C 916 VAL cc_start: 0.8252 (p) cc_final: 0.7960 (p) REVERT: C 956 SER cc_start: 0.8401 (t) cc_final: 0.8198 (m) REVERT: C 1111 ASN cc_start: 0.7742 (p0) cc_final: 0.7151 (p0) REVERT: C 1205 MET cc_start: 0.1226 (tpt) cc_final: 0.0256 (mmt) outliers start: 95 outliers final: 46 residues processed: 491 average time/residue: 0.1731 time to fit residues: 147.7511 Evaluate side-chains 362 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 313 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 694 ASN Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 838 ASN Chi-restraints excluded: chain B residue 1075 ASP Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 998 ASN Chi-restraints excluded: chain C residue 1122 ASN Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 72 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 4 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 323 optimal weight: 0.0010 chunk 198 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 226 optimal weight: 0.6980 chunk 214 optimal weight: 0.3980 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 204 GLN A 535 GLN A 605 ASN A1049 ASN A1092 GLN B 652 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 GLN ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 ASN C 722 ASN C 799 HIS C1092 GLN H 39 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.222875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.190939 restraints weight = 77222.008| |-----------------------------------------------------------------------------| r_work (start): 0.4541 rms_B_bonded: 3.91 r_work: 0.4326 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 33728 Z= 0.158 Angle : 0.625 24.837 46049 Z= 0.317 Chirality : 0.046 0.585 5236 Planarity : 0.004 0.042 5874 Dihedral : 4.717 59.277 5016 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.22 % Allowed : 12.80 % Favored : 83.97 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.12), residues: 4198 helix: 0.07 (0.20), residues: 703 sheet: -0.34 (0.17), residues: 848 loop : -1.75 (0.12), residues: 2647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 100 TYR 0.027 0.002 TYR I 50 PHE 0.041 0.002 PHE B1212 TRP 0.059 0.002 TRP M 91 HIS 0.012 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (33632) covalent geometry : angle 0.60794 / 0.31 (45836) SS BOND : bond 0.00270 / 0.18 ( 75) SS BOND : angle 0.84984 / 0.65 ( 150) hydrogen bonds : bond 0.04229 / 2.85 ( 934) hydrogen bonds : angle 5.86626 / 3.96 ( 2538) link_BETA1-4 : bond 0.03156 / 1.58 ( 4) link_BETA1-4 : angle 2.41279 / 1.41 ( 12) link_NAG-ASN : bond 0.00789 / 0.27 ( 17) link_NAG-ASN : angle 4.09461 / 2.68 ( 51) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 369 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 VAL cc_start: 0.5800 (OUTLIER) cc_final: 0.5504 (t) REVERT: A 155 MET cc_start: 0.7103 (mmm) cc_final: 0.6597 (mmp) REVERT: A 186 LYS cc_start: 0.7118 (mmmt) cc_final: 0.6418 (tptt) REVERT: A 209 PHE cc_start: 0.5119 (t80) cc_final: 0.4890 (t80) REVERT: A 238 MET cc_start: 0.3397 (mpp) cc_final: 0.2892 (mtm) REVERT: A 351 ASN cc_start: 0.7289 (t0) cc_final: 0.6349 (t0) REVERT: A 362 LEU cc_start: 0.8580 (mp) cc_final: 0.8339 (mm) REVERT: A 673 TYR cc_start: 0.6477 (t80) cc_final: 0.5293 (m-10) REVERT: A 732 SER cc_start: 0.7795 (t) cc_final: 0.7567 (p) REVERT: A 763 ARG cc_start: 0.5428 (ttp-110) cc_final: 0.4698 (mtm-85) REVERT: A 862 MET cc_start: 0.3102 (ptt) cc_final: 0.2344 (mmm) REVERT: A 909 ASN cc_start: 0.7427 (m-40) cc_final: 0.7147 (m-40) REVERT: A 958 TYR cc_start: 0.6641 (m-10) cc_final: 0.6395 (m-10) REVERT: A 1126 ASN cc_start: 0.7451 (t0) cc_final: 0.7012 (p0) REVERT: B 444 TRP cc_start: 0.5453 (p-90) cc_final: 0.4269 (p-90) REVERT: B 467 PHE cc_start: 0.4235 (m-80) cc_final: 0.3210 (m-10) REVERT: B 650 ASP cc_start: 0.6399 (t70) cc_final: 0.5086 (m-30) REVERT: B 984 GLN cc_start: 0.7009 (mt0) cc_final: 0.6708 (mm-40) REVERT: B 994 MET cc_start: 0.7225 (mmm) cc_final: 0.6917 (mmt) REVERT: B 1003 LEU cc_start: 0.7324 (tt) cc_final: 0.6545 (mm) REVERT: B 1055 SER cc_start: 0.7857 (p) cc_final: 0.7418 (m) REVERT: B 1058 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7956 (mp) REVERT: B 1064 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6983 (ptm160) REVERT: C 85 LEU cc_start: 0.2191 (mt) cc_final: 0.1909 (mt) REVERT: C 155 MET cc_start: 0.0767 (mmp) cc_final: -0.0571 (tpp) REVERT: C 238 MET cc_start: 0.0616 (ppp) cc_final: 0.0406 (ppp) REVERT: C 474 CYS cc_start: 0.1956 (OUTLIER) cc_final: -0.0392 (p) REVERT: C 879 VAL cc_start: 0.3206 (p) cc_final: 0.2983 (m) REVERT: C 1205 MET cc_start: 0.1663 (tpt) cc_final: 0.1396 (mmt) REVERT: H 39 GLN cc_start: 0.5955 (tt0) cc_final: 0.5728 (tt0) REVERT: H 94 ARG cc_start: 0.7517 (ttp-110) cc_final: 0.7307 (ttp-110) REVERT: L 45 LYS cc_start: 0.8161 (ptmm) cc_final: 0.7880 (ptmm) outliers start: 118 outliers final: 60 residues processed: 466 average time/residue: 0.1807 time to fit residues: 145.5584 Evaluate side-chains 353 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 289 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 634 LYS Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain B residue 799 HIS Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1075 ASP Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 998 ASN Chi-restraints excluded: chain C residue 1218 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 72 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 354 optimal weight: 0.0670 chunk 113 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 332 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 208 optimal weight: 0.0060 overall best weight: 0.9338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 ASN A1092 GLN B 278 ASN B 552 ASN B 694 ASN B 826 HIS B 847 ASN B 856 GLN B1009 ASN ** B1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 GLN ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 722 ASN C 863 GLN C1092 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.212796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.175531 restraints weight = 73275.698| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 4.12 r_work: 0.4130 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 33728 Z= 0.166 Angle : 0.647 16.521 46049 Z= 0.325 Chirality : 0.046 0.311 5236 Planarity : 0.004 0.066 5874 Dihedral : 4.985 59.656 5013 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.49 % Allowed : 13.49 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.12), residues: 4198 helix: 0.23 (0.20), residues: 721 sheet: -0.44 (0.17), residues: 893 loop : -1.75 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 94 TYR 0.026 0.002 TYR C 746 PHE 0.026 0.002 PHE B1212 TRP 0.040 0.002 TRP A1184 HIS 0.017 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (33632) covalent geometry : angle 0.63306 / 0.32 (45836) SS BOND : bond 0.00366 / 0.24 ( 75) SS BOND : angle 1.00383 / 0.72 ( 150) hydrogen bonds : bond 0.03549 / 2.37 ( 934) hydrogen bonds : angle 5.56820 / 3.77 ( 2538) link_BETA1-4 : bond 0.02025 / 1.01 ( 4) link_BETA1-4 : angle 2.96458 / 1.66 ( 12) link_NAG-ASN : bond 0.01756 / 1.14 ( 17) link_NAG-ASN : angle 3.53768 / 2.63 ( 51) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 361 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.5427 (OUTLIER) cc_final: 0.5187 (tp) REVERT: A 186 LYS cc_start: 0.7003 (mmmt) cc_final: 0.6419 (tptt) REVERT: A 199 TYR cc_start: 0.6330 (m-80) cc_final: 0.6089 (m-80) REVERT: A 290 ILE cc_start: 0.7765 (mm) cc_final: 0.7429 (mt) REVERT: A 336 VAL cc_start: 0.8458 (t) cc_final: 0.8240 (m) REVERT: A 351 ASN cc_start: 0.8023 (t0) cc_final: 0.7046 (t0) REVERT: A 577 PHE cc_start: 0.9018 (p90) cc_final: 0.8744 (p90) REVERT: A 673 TYR cc_start: 0.6688 (t80) cc_final: 0.5537 (m-10) REVERT: A 732 SER cc_start: 0.8294 (t) cc_final: 0.8040 (p) REVERT: A 862 MET cc_start: 0.3101 (ptt) cc_final: 0.2548 (mmm) REVERT: A 909 ASN cc_start: 0.7699 (m-40) cc_final: 0.7467 (m-40) REVERT: A 1126 ASN cc_start: 0.7790 (t0) cc_final: 0.7298 (p0) REVERT: B 650 ASP cc_start: 0.6464 (t70) cc_final: 0.5623 (m-30) REVERT: B 738 MET cc_start: 0.8937 (mmp) cc_final: 0.8628 (mmp) REVERT: B 789 GLN cc_start: 0.4760 (pp30) cc_final: 0.3935 (mt0) REVERT: B 984 GLN cc_start: 0.7235 (mt0) cc_final: 0.6714 (mm-40) REVERT: B 1003 LEU cc_start: 0.7625 (tt) cc_final: 0.6716 (mm) REVERT: B 1064 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7508 (ptm160) REVERT: B 1172 PRO cc_start: 0.6218 (Cg_endo) cc_final: 0.5815 (Cg_exo) REVERT: C 85 LEU cc_start: 0.2246 (mt) cc_final: 0.2024 (mt) REVERT: C 155 MET cc_start: 0.0949 (mmp) cc_final: -0.0652 (tpp) REVERT: C 854 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: H 29 ILE cc_start: 0.7131 (mm) cc_final: 0.6611 (mt) REVERT: L 45 LYS cc_start: 0.8327 (ptmm) cc_final: 0.8118 (ptmm) outliers start: 128 outliers final: 77 residues processed: 461 average time/residue: 0.1763 time to fit residues: 142.1864 Evaluate side-chains 375 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 295 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 476 CYS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 886 SER Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 634 LYS Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 694 ASN Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain B residue 786 PHE Chi-restraints excluded: chain B residue 799 HIS Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1075 ASP Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1187 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 854 GLN Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 998 ASN Chi-restraints excluded: chain C residue 1013 LEU Chi-restraints excluded: chain C residue 1093 LEU Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 52 TYR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 267 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 409 optimal weight: 10.0000 chunk 342 optimal weight: 0.7980 chunk 272 optimal weight: 4.9990 chunk 22 optimal weight: 30.0000 chunk 137 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 chunk 367 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 445 ASN A 605 ASN A 611 ASN A 982 ASN ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 GLN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN B 646 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 ASN ** B 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 ASN B1016 GLN B1059 GLN B1135 GLN B1180 GLN ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 GLN ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 ASN C 799 HIS C 847 ASN C 863 GLN C1017 ASN C1145 HIS ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.192250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.142586 restraints weight = 66996.700| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 4.13 r_work: 0.3705 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.8162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 33728 Z= 0.288 Angle : 0.875 33.431 46049 Z= 0.444 Chirality : 0.054 0.483 5236 Planarity : 0.006 0.079 5874 Dihedral : 5.988 55.077 5009 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.34 % Favored : 92.57 % Rotamer: Outliers : 4.64 % Allowed : 13.95 % Favored : 81.41 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.12), residues: 4198 helix: -0.39 (0.18), residues: 725 sheet: -0.62 (0.17), residues: 888 loop : -1.94 (0.11), residues: 2585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 986 TYR 0.033 0.003 TYR B 212 PHE 0.038 0.003 PHE A1143 TRP 0.040 0.002 TRP B 257 HIS 0.078 0.003 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.29 (33632) covalent geometry : angle 0.86661 / 0.44 (45836) SS BOND : bond 0.00814 / 0.54 ( 75) SS BOND : angle 1.26905 / 0.95 ( 150) hydrogen bonds : bond 0.04434 / 2.92 ( 934) hydrogen bonds : angle 6.09282 / 4.17 ( 2538) link_BETA1-4 : bond 0.01012 / 0.52 ( 4) link_BETA1-4 : angle 1.27835 / 0.77 ( 12) link_NAG-ASN : bond 0.01146 / 0.73 ( 17) link_NAG-ASN : angle 3.32840 / 2.27 ( 51) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 342 time to evaluate : 1.141 Fit side-chains revert: symmetry clash REVERT: A 185 PHE cc_start: 0.6491 (t80) cc_final: 0.6027 (t80) REVERT: A 186 LYS cc_start: 0.7385 (mmmt) cc_final: 0.6928 (tmtt) REVERT: A 336 VAL cc_start: 0.8763 (t) cc_final: 0.8523 (p) REVERT: A 393 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8383 (mt) REVERT: A 482 VAL cc_start: 0.7692 (OUTLIER) cc_final: 0.7377 (p) REVERT: A 828 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8474 (tt) REVERT: A 862 MET cc_start: 0.4304 (ptt) cc_final: 0.4072 (mmm) REVERT: A 984 GLN cc_start: 0.8314 (mt0) cc_final: 0.7980 (tt0) REVERT: A 1002 LYS cc_start: 0.8140 (ttpp) cc_final: 0.7678 (mptt) REVERT: A 1041 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8411 (t0) REVERT: B 120 GLU cc_start: 0.5875 (mm-30) cc_final: 0.5471 (tt0) REVERT: B 122 SER cc_start: 0.4543 (m) cc_final: 0.4120 (m) REVERT: B 224 PHE cc_start: 0.5835 (OUTLIER) cc_final: 0.4458 (p90) REVERT: B 255 GLU cc_start: 0.4923 (OUTLIER) cc_final: 0.3719 (pm20) REVERT: B 396 ARG cc_start: 0.5882 (OUTLIER) cc_final: 0.4973 (ttt180) REVERT: B 426 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.6225 (t80) REVERT: B 649 TYR cc_start: 0.8213 (t80) cc_final: 0.7867 (t80) REVERT: B 652 ASN cc_start: 0.7728 (m-40) cc_final: 0.7340 (p0) REVERT: B 746 TYR cc_start: 0.6893 (OUTLIER) cc_final: 0.5633 (m-80) REVERT: B 828 LEU cc_start: 0.9296 (tp) cc_final: 0.9028 (tp) REVERT: B 831 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: B 1075 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8219 (t70) REVERT: C 209 PHE cc_start: 0.6935 (t80) cc_final: 0.6725 (t80) REVERT: C 294 THR cc_start: 0.7753 (OUTLIER) cc_final: 0.7544 (m) REVERT: C 433 ASN cc_start: 0.0317 (OUTLIER) cc_final: -0.0379 (m110) REVERT: C 762 TYR cc_start: 0.4686 (OUTLIER) cc_final: 0.3574 (t80) REVERT: C 918 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8507 (m-10) REVERT: C 987 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8669 (tt) REVERT: H 29 ILE cc_start: 0.8034 (mm) cc_final: 0.7707 (mt) REVERT: H 39 GLN cc_start: 0.7218 (tt0) cc_final: 0.6861 (tt0) outliers start: 170 outliers final: 91 residues processed: 491 average time/residue: 0.1728 time to fit residues: 144.5828 Evaluate side-chains 353 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 246 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1090 SER Chi-restraints excluded: chain A residue 1152 SER Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 634 LYS Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 799 HIS Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 831 GLU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 992 VAL Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1075 ASP Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 762 TYR Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 918 PHE Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 987 ILE Chi-restraints excluded: chain C residue 1013 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 197 optimal weight: 2.9990 chunk 384 optimal weight: 7.9990 chunk 191 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 373 optimal weight: 0.0570 chunk 161 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 274 optimal weight: 9.9990 chunk 20 optimal weight: 0.0010 chunk 240 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 overall best weight: 0.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN A1126 ASN ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 982 ASN B 998 ASN B1041 ASN C 142 HIS C 265 GLN ** C 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 881 ASN C 998 ASN C1017 ASN C1030 GLN H 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.194768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.153427 restraints weight = 66515.168| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 3.61 r_work: 0.3778 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.8399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33728 Z= 0.125 Angle : 0.628 33.211 46049 Z= 0.312 Chirality : 0.044 0.242 5236 Planarity : 0.004 0.060 5874 Dihedral : 5.005 57.457 5005 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.86 % Favored : 94.12 % Rotamer: Outliers : 2.84 % Allowed : 16.19 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.12), residues: 4198 helix: 0.28 (0.19), residues: 728 sheet: -0.47 (0.17), residues: 905 loop : -1.79 (0.12), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 206 TYR 0.022 0.002 TYR A 746 PHE 0.027 0.002 PHE A 222 TRP 0.018 0.001 TRP A 174 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (33632) covalent geometry : angle 0.62278 / 0.31 (45836) SS BOND : bond 0.00280 / 0.19 ( 75) SS BOND : angle 1.02719 / 0.74 ( 150) hydrogen bonds : bond 0.03374 / 2.25 ( 934) hydrogen bonds : angle 5.55325 / 3.78 ( 2538) link_BETA1-4 : bond 0.00916 / 0.45 ( 4) link_BETA1-4 : angle 1.28913 / 0.71 ( 12) link_NAG-ASN : bond 0.00310 / 0.18 ( 17) link_NAG-ASN : angle 2.13285 / 1.47 ( 51) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 290 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 124 ILE cc_start: 0.6547 (OUTLIER) cc_final: 0.6298 (tp) REVERT: A 155 MET cc_start: 0.6079 (mmm) cc_final: 0.5481 (tpp) REVERT: A 186 LYS cc_start: 0.7273 (mmmt) cc_final: 0.6913 (tmtt) REVERT: A 199 TYR cc_start: 0.6562 (m-80) cc_final: 0.6213 (m-80) REVERT: A 290 ILE cc_start: 0.8406 (mm) cc_final: 0.8171 (mm) REVERT: A 336 VAL cc_start: 0.8719 (t) cc_final: 0.8505 (p) REVERT: A 583 ASN cc_start: 0.8026 (m110) cc_final: 0.7282 (t0) REVERT: A 686 SER cc_start: 0.7429 (p) cc_final: 0.7192 (m) REVERT: A 885 LYS cc_start: 0.7714 (mttm) cc_final: 0.7342 (ptmt) REVERT: A 916 VAL cc_start: 0.7939 (m) cc_final: 0.7698 (p) REVERT: A 1002 LYS cc_start: 0.8133 (ttpp) cc_final: 0.7745 (mptt) REVERT: A 1094 SER cc_start: 0.9315 (t) cc_final: 0.9026 (m) REVERT: A 1096 ILE cc_start: 0.9202 (tp) cc_final: 0.8984 (tp) REVERT: A 1099 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8937 (mp) REVERT: A 1104 SER cc_start: 0.9229 (t) cc_final: 0.8799 (m) REVERT: A 1185 MET cc_start: 0.7217 (ttp) cc_final: 0.6963 (mtm) REVERT: B 149 THR cc_start: 0.8115 (p) cc_final: 0.7735 (p) REVERT: B 213 TYR cc_start: 0.7589 (t80) cc_final: 0.7286 (t80) REVERT: B 652 ASN cc_start: 0.7940 (m-40) cc_final: 0.7566 (p0) REVERT: B 738 MET cc_start: 0.9304 (mmp) cc_final: 0.8994 (mmt) REVERT: B 746 TYR cc_start: 0.6604 (OUTLIER) cc_final: 0.5271 (m-80) REVERT: C 218 MET cc_start: 0.3170 (tmm) cc_final: 0.1095 (mmp) REVERT: C 901 SER cc_start: 0.8913 (m) cc_final: 0.8658 (p) REVERT: C 918 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8437 (m-10) REVERT: C 1159 SER cc_start: 0.9099 (t) cc_final: 0.8686 (m) REVERT: H 39 GLN cc_start: 0.7353 (tt0) cc_final: 0.7152 (tt0) outliers start: 104 outliers final: 68 residues processed: 374 average time/residue: 0.1740 time to fit residues: 113.3315 Evaluate side-chains 320 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 248 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 634 LYS Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain B residue 799 HIS Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 992 VAL Chi-restraints excluded: chain B residue 1041 ASN Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 918 PHE Chi-restraints excluded: chain C residue 998 ASN Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 315 optimal weight: 0.0070 chunk 172 optimal weight: 7.9990 chunk 380 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 251 optimal weight: 10.0000 chunk 406 optimal weight: 8.9990 chunk 200 optimal weight: 0.5980 chunk 386 optimal weight: 20.0000 chunk 31 optimal weight: 0.6980 chunk 239 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 605 ASN A 982 ASN ** A 988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 HIS B 535 GLN B 826 HIS B 988 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN C1016 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.187103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.143292 restraints weight = 65208.321| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 4.39 r_work: 0.3622 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.9161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 33728 Z= 0.204 Angle : 0.692 29.962 46049 Z= 0.347 Chirality : 0.047 0.395 5236 Planarity : 0.005 0.063 5874 Dihedral : 5.120 59.202 5004 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.30 % Allowed : 16.24 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.12), residues: 4198 helix: 0.17 (0.19), residues: 724 sheet: -0.51 (0.17), residues: 902 loop : -1.82 (0.11), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 763 TYR 0.025 0.002 TYR B 212 PHE 0.033 0.002 PHE B 224 TRP 0.038 0.002 TRP B 174 HIS 0.018 0.002 HIS B 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (33632) covalent geometry : angle 0.68604 / 0.34 (45836) SS BOND : bond 0.00393 / 0.27 ( 75) SS BOND : angle 1.14402 / 0.85 ( 150) hydrogen bonds : bond 0.03599 / 2.43 ( 934) hydrogen bonds : angle 5.60579 / 3.83 ( 2538) link_BETA1-4 : bond 0.00633 / 0.30 ( 4) link_BETA1-4 : angle 0.95913 / 0.55 ( 12) link_NAG-ASN : bond 0.00465 / 0.37 ( 17) link_NAG-ASN : angle 2.33478 / 1.52 ( 51) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 284 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 THR cc_start: 0.8068 (OUTLIER) cc_final: 0.7716 (p) REVERT: A 155 MET cc_start: 0.6176 (mmm) cc_final: 0.5534 (tpp) REVERT: A 160 HIS cc_start: 0.4974 (p-80) cc_final: 0.4473 (p90) REVERT: A 185 PHE cc_start: 0.6524 (t80) cc_final: 0.6310 (t80) REVERT: A 186 LYS cc_start: 0.7414 (mmmt) cc_final: 0.7019 (tmtt) REVERT: A 583 ASN cc_start: 0.8129 (m110) cc_final: 0.7362 (t0) REVERT: A 608 LEU cc_start: 0.8609 (pt) cc_final: 0.8314 (pp) REVERT: A 885 LYS cc_start: 0.8011 (mttm) cc_final: 0.7726 (ptmt) REVERT: A 984 GLN cc_start: 0.8411 (mt0) cc_final: 0.8070 (tt0) REVERT: A 1002 LYS cc_start: 0.8323 (ttpp) cc_final: 0.7943 (mptt) REVERT: A 1034 ASN cc_start: 0.8493 (m-40) cc_final: 0.8266 (m-40) REVERT: A 1094 SER cc_start: 0.9353 (t) cc_final: 0.9076 (m) REVERT: A 1099 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8978 (mp) REVERT: A 1205 MET cc_start: 0.5132 (mmp) cc_final: 0.4876 (mmt) REVERT: B 204 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8275 (pp30) REVERT: B 224 PHE cc_start: 0.5617 (OUTLIER) cc_final: 0.4523 (p90) REVERT: B 255 GLU cc_start: 0.4600 (OUTLIER) cc_final: 0.3922 (pm20) REVERT: B 396 ARG cc_start: 0.5998 (OUTLIER) cc_final: 0.5263 (ttt180) REVERT: B 652 ASN cc_start: 0.8193 (m-40) cc_final: 0.7687 (p0) REVERT: B 738 MET cc_start: 0.9304 (mmp) cc_final: 0.8836 (mmt) REVERT: B 746 TYR cc_start: 0.7158 (OUTLIER) cc_final: 0.5709 (m-80) REVERT: B 1075 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8233 (t70) REVERT: C 218 MET cc_start: 0.3682 (tmm) cc_final: 0.2146 (mmp) outliers start: 121 outliers final: 75 residues processed: 382 average time/residue: 0.1760 time to fit residues: 116.8349 Evaluate side-chains 323 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 240 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1049 ASN Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 634 LYS Chi-restraints excluded: chain B residue 649 TYR Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain B residue 799 HIS Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 992 VAL Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1075 ASP Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1013 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 388 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 382 optimal weight: 0.5980 chunk 147 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 192 optimal weight: 0.6980 chunk 327 optimal weight: 1.9990 chunk 162 optimal weight: 10.0000 chunk 45 optimal weight: 0.0770 chunk 389 optimal weight: 3.9990 chunk 239 optimal weight: 0.0060 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 982 ASN ** A 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 ASN A1126 ASN ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 998 ASN C1091 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.189402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.145041 restraints weight = 65630.950| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 4.18 r_work: 0.3682 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.9284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33728 Z= 0.112 Angle : 0.611 30.230 46049 Z= 0.300 Chirality : 0.043 0.202 5236 Planarity : 0.004 0.052 5874 Dihedral : 4.782 57.059 5004 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.46 % Allowed : 17.83 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.13), residues: 4198 helix: 0.61 (0.20), residues: 719 sheet: -0.38 (0.17), residues: 901 loop : -1.69 (0.11), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 79 TYR 0.024 0.001 TYR B 213 PHE 0.026 0.001 PHE B 786 TRP 0.026 0.001 TRP B 174 HIS 0.009 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (33632) covalent geometry : angle 0.60607 / 0.30 (45836) SS BOND : bond 0.00231 / 0.16 ( 75) SS BOND : angle 0.93774 / 0.66 ( 150) hydrogen bonds : bond 0.03158 / 2.10 ( 934) hydrogen bonds : angle 5.36153 / 3.65 ( 2538) link_BETA1-4 : bond 0.00714 / 0.35 ( 4) link_BETA1-4 : angle 1.20053 / 0.64 ( 12) link_NAG-ASN : bond 0.00304 / 0.18 ( 17) link_NAG-ASN : angle 1.92435 / 1.28 ( 51) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 261 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 THR cc_start: 0.8007 (OUTLIER) cc_final: 0.7622 (p) REVERT: A 155 MET cc_start: 0.6245 (mmm) cc_final: 0.5535 (tpp) REVERT: A 185 PHE cc_start: 0.6634 (t80) cc_final: 0.6344 (t80) REVERT: A 186 LYS cc_start: 0.7366 (mmmt) cc_final: 0.6958 (tmtt) REVERT: A 234 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.7143 (t-90) REVERT: A 583 ASN cc_start: 0.8100 (m110) cc_final: 0.7368 (t0) REVERT: A 608 LEU cc_start: 0.8535 (pt) cc_final: 0.8315 (pp) REVERT: A 885 LYS cc_start: 0.7868 (mttm) cc_final: 0.7619 (ptmt) REVERT: A 1002 LYS cc_start: 0.8251 (ttpp) cc_final: 0.7896 (mptt) REVERT: A 1094 SER cc_start: 0.9261 (t) cc_final: 0.8983 (m) REVERT: A 1099 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8923 (mp) REVERT: A 1185 MET cc_start: 0.7349 (ttp) cc_final: 0.6962 (mtm) REVERT: A 1205 MET cc_start: 0.5192 (mmp) cc_final: 0.4883 (mmt) REVERT: B 396 ARG cc_start: 0.6020 (OUTLIER) cc_final: 0.5370 (ttt180) REVERT: B 426 TYR cc_start: 0.7156 (OUTLIER) cc_final: 0.6473 (t80) REVERT: B 652 ASN cc_start: 0.8225 (m-40) cc_final: 0.7750 (p0) REVERT: B 738 MET cc_start: 0.9184 (mmp) cc_final: 0.8920 (mmt) REVERT: B 746 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.5722 (m-80) REVERT: B 994 MET cc_start: 0.8204 (mmt) cc_final: 0.7847 (mmt) REVERT: C 155 MET cc_start: 0.2475 (OUTLIER) cc_final: 0.1975 (mmp) REVERT: C 218 MET cc_start: 0.3590 (tmm) cc_final: 0.2258 (mmp) REVERT: C 609 TYR cc_start: 0.6666 (OUTLIER) cc_final: 0.6075 (t80) REVERT: J 80 LEU cc_start: -0.3615 (OUTLIER) cc_final: -0.3889 (tp) REVERT: L 92 ASP cc_start: 0.8879 (t0) cc_final: 0.8626 (t0) outliers start: 90 outliers final: 52 residues processed: 331 average time/residue: 0.1795 time to fit residues: 103.4761 Evaluate side-chains 299 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 238 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 649 TYR Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain B residue 799 HIS Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 992 VAL Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 165 optimal weight: 5.9990 chunk 275 optimal weight: 6.9990 chunk 386 optimal weight: 5.9990 chunk 190 optimal weight: 0.9990 chunk 314 optimal weight: 0.8980 chunk 183 optimal weight: 0.6980 chunk 260 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 319 optimal weight: 0.8980 chunk 158 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 611 ASN A 982 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1092 GLN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.183384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.139525 restraints weight = 64343.899| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 3.99 r_work: 0.3543 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.9925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33728 Z= 0.189 Angle : 0.688 30.534 46049 Z= 0.342 Chirality : 0.046 0.259 5236 Planarity : 0.005 0.100 5874 Dihedral : 5.054 59.053 5004 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.54 % Allowed : 17.75 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.12), residues: 4198 helix: 0.28 (0.19), residues: 740 sheet: -0.42 (0.18), residues: 855 loop : -1.75 (0.11), residues: 2603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 79 TYR 0.028 0.002 TYR B 213 PHE 0.032 0.002 PHE B 224 TRP 0.060 0.002 TRP A 444 HIS 0.011 0.001 HIS B1145 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (33632) covalent geometry : angle 0.68157 / 0.34 (45836) SS BOND : bond 0.00370 / 0.26 ( 75) SS BOND : angle 1.26506 / 0.92 ( 150) hydrogen bonds : bond 0.03422 / 2.30 ( 934) hydrogen bonds : angle 5.42489 / 3.71 ( 2538) link_BETA1-4 : bond 0.00485 / 0.23 ( 4) link_BETA1-4 : angle 0.82563 / 0.48 ( 12) link_NAG-ASN : bond 0.00533 / 0.46 ( 17) link_NAG-ASN : angle 2.25289 / 1.46 ( 51) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 257 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7856 (p) REVERT: A 155 MET cc_start: 0.6390 (mmm) cc_final: 0.5577 (tpp) REVERT: A 185 PHE cc_start: 0.6624 (t80) cc_final: 0.6386 (t80) REVERT: A 186 LYS cc_start: 0.7451 (mmmt) cc_final: 0.7011 (tmtt) REVERT: A 234 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.7140 (t-90) REVERT: A 408 PHE cc_start: 0.8360 (m-10) cc_final: 0.8123 (m-80) REVERT: A 583 ASN cc_start: 0.8215 (m110) cc_final: 0.7470 (t0) REVERT: A 608 LEU cc_start: 0.8605 (pt) cc_final: 0.8392 (pp) REVERT: A 885 LYS cc_start: 0.7919 (mttm) cc_final: 0.7695 (ptmt) REVERT: A 952 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8452 (mm-30) REVERT: A 1002 LYS cc_start: 0.8475 (ttpp) cc_final: 0.8066 (mptt) REVERT: A 1094 SER cc_start: 0.9338 (t) cc_final: 0.9057 (m) REVERT: A 1099 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.8990 (mp) REVERT: A 1126 ASN cc_start: 0.7312 (p0) cc_final: 0.7041 (p0) REVERT: B 106 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8687 (t) REVERT: B 180 GLU cc_start: 0.6767 (tp30) cc_final: 0.6454 (tp30) REVERT: B 204 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8423 (pp30) REVERT: B 255 GLU cc_start: 0.4591 (OUTLIER) cc_final: 0.4374 (pm20) REVERT: B 396 ARG cc_start: 0.6008 (OUTLIER) cc_final: 0.5256 (ttt180) REVERT: B 426 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.5584 (t80) REVERT: B 652 ASN cc_start: 0.8376 (m-40) cc_final: 0.7923 (p0) REVERT: B 738 MET cc_start: 0.9252 (mmp) cc_final: 0.8782 (mmt) REVERT: B 746 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6004 (m-80) REVERT: B 831 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: B 994 MET cc_start: 0.8299 (mmt) cc_final: 0.7946 (mmt) REVERT: B 1157 LEU cc_start: 0.7619 (tp) cc_final: 0.7160 (mp) REVERT: C 218 MET cc_start: 0.4539 (tmm) cc_final: 0.3344 (mmp) REVERT: C 433 ASN cc_start: 0.0241 (OUTLIER) cc_final: -0.0533 (m110) REVERT: C 904 GLU cc_start: 0.6483 (mt-10) cc_final: 0.6263 (mt-10) REVERT: J 80 LEU cc_start: -0.3609 (OUTLIER) cc_final: -0.3888 (tp) outliers start: 93 outliers final: 66 residues processed: 332 average time/residue: 0.1832 time to fit residues: 106.2753 Evaluate side-chains 309 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 231 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 649 TYR Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain B residue 799 HIS Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 831 GLU Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 992 VAL Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1212 PHE Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 264 optimal weight: 3.9990 chunk 258 optimal weight: 2.9990 chunk 389 optimal weight: 8.9990 chunk 383 optimal weight: 40.0000 chunk 323 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 239 optimal weight: 0.8980 chunk 327 optimal weight: 0.6980 chunk 257 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1092 GLN H 77 HIS ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.183363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.138747 restraints weight = 64609.277| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 4.76 r_work: 0.3545 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 1.0143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33728 Z= 0.154 Angle : 0.640 26.300 46049 Z= 0.317 Chirality : 0.045 0.213 5236 Planarity : 0.004 0.053 5874 Dihedral : 4.913 57.119 5004 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.05 % Allowed : 18.65 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.12), residues: 4198 helix: 0.41 (0.19), residues: 741 sheet: -0.40 (0.18), residues: 874 loop : -1.70 (0.11), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 79 TYR 0.023 0.001 TYR C 673 PHE 0.020 0.002 PHE B 224 TRP 0.026 0.001 TRP A 444 HIS 0.011 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (33632) covalent geometry : angle 0.63440 / 0.32 (45836) SS BOND : bond 0.00283 / 0.20 ( 75) SS BOND : angle 1.14162 / 0.80 ( 150) hydrogen bonds : bond 0.03206 / 2.13 ( 934) hydrogen bonds : angle 5.35875 / 3.66 ( 2538) link_BETA1-4 : bond 0.00625 / 0.30 ( 4) link_BETA1-4 : angle 1.01706 / 0.56 ( 12) link_NAG-ASN : bond 0.00328 / 0.26 ( 17) link_NAG-ASN : angle 2.02614 / 1.29 ( 51) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8396 Ramachandran restraints generated. 4198 Oldfield, 0 Emsley, 4198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 252 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7662 (mt) cc_final: 0.7163 (mt) REVERT: A 64 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7931 (p) REVERT: A 155 MET cc_start: 0.6080 (mmm) cc_final: 0.5556 (tpp) REVERT: A 185 PHE cc_start: 0.6809 (t80) cc_final: 0.6560 (t80) REVERT: A 186 LYS cc_start: 0.7456 (mmmt) cc_final: 0.6985 (tmtt) REVERT: A 234 HIS cc_start: 0.7849 (OUTLIER) cc_final: 0.7141 (t-90) REVERT: A 408 PHE cc_start: 0.8329 (m-10) cc_final: 0.8076 (m-80) REVERT: A 583 ASN cc_start: 0.8201 (m110) cc_final: 0.7525 (t0) REVERT: A 885 LYS cc_start: 0.7896 (mttm) cc_final: 0.7691 (ptmt) REVERT: A 1002 LYS cc_start: 0.8455 (ttpp) cc_final: 0.8094 (mptt) REVERT: A 1094 SER cc_start: 0.9323 (t) cc_final: 0.9034 (m) REVERT: A 1099 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.8997 (mp) REVERT: A 1126 ASN cc_start: 0.7524 (p0) cc_final: 0.7288 (p0) REVERT: B 180 GLU cc_start: 0.6799 (tp30) cc_final: 0.6537 (tp30) REVERT: B 204 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8731 (pt0) REVERT: B 224 PHE cc_start: 0.5775 (OUTLIER) cc_final: 0.5013 (p90) REVERT: B 396 ARG cc_start: 0.6016 (OUTLIER) cc_final: 0.5389 (ttt180) REVERT: B 426 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.5619 (t80) REVERT: B 652 ASN cc_start: 0.8367 (m-40) cc_final: 0.7844 (p0) REVERT: B 746 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6027 (m-80) REVERT: B 994 MET cc_start: 0.8233 (mmt) cc_final: 0.7866 (mmt) REVERT: C 218 MET cc_start: 0.4475 (tmm) cc_final: 0.3647 (mmp) REVERT: C 305 ASP cc_start: 0.8628 (p0) cc_final: 0.8417 (p0) REVERT: C 609 TYR cc_start: 0.6647 (OUTLIER) cc_final: 0.6038 (t80) REVERT: C 904 GLU cc_start: 0.6562 (mt-10) cc_final: 0.6262 (mt-10) REVERT: C 934 LEU cc_start: 0.8724 (tp) cc_final: 0.8441 (pt) REVERT: J 80 LEU cc_start: -0.3577 (OUTLIER) cc_final: -0.3863 (tp) outliers start: 75 outliers final: 56 residues processed: 312 average time/residue: 0.1777 time to fit residues: 96.9230 Evaluate side-chains 302 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 236 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 649 TYR Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain B residue 799 HIS Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 992 VAL Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 58 optimal weight: 8.9990 chunk 87 optimal weight: 0.5980 chunk 153 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 246 optimal weight: 3.9990 chunk 307 optimal weight: 0.6980 chunk 97 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 283 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 988 ASN A1017 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.180990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.125936 restraints weight = 64199.356| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 4.23 r_work: 0.3525 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 1.0284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33728 Z= 0.126 Angle : 0.622 24.331 46049 Z= 0.305 Chirality : 0.044 0.216 5236 Planarity : 0.004 0.055 5874 Dihedral : 4.734 58.035 5003 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.05 % Allowed : 18.65 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.13), residues: 4198 helix: 0.58 (0.20), residues: 736 sheet: -0.37 (0.17), residues: 898 loop : -1.63 (0.12), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L 79 TYR 0.020 0.001 TYR C 673 PHE 0.023 0.001 PHE B 786 TRP 0.028 0.001 TRP B 174 HIS 0.008 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (33632) covalent geometry : angle 0.61743 / 0.30 (45836) SS BOND : bond 0.00254 / 0.18 ( 75) SS BOND : angle 1.04800 / 0.72 ( 150) hydrogen bonds : bond 0.03066 / 2.04 ( 934) hydrogen bonds : angle 5.23333 / 3.56 ( 2538) link_BETA1-4 : bond 0.00653 / 0.31 ( 4) link_BETA1-4 : angle 1.04494 / 0.56 ( 12) link_NAG-ASN : bond 0.00321 / 0.22 ( 17) link_NAG-ASN : angle 1.90804 / 1.22 ( 51) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9693.27 seconds wall clock time: 166 minutes 25.90 seconds (9985.90 seconds total)