Starting phenix.real_space_refine on Mon Jul 6 02:18:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y0n_33550/07_2026/7y0n_33550.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y0n_33550/07_2026/7y0n_33550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7y0n_33550/07_2026/7y0n_33550.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y0n_33550/07_2026/7y0n_33550.cif" model { file = "/net/cci-nas-00/data/ceres_data/7y0n_33550/07_2026/7y0n_33550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y0n_33550/07_2026/7y0n_33550.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y0n_33550/07_2026/7y0n_33550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y0n_33550/07_2026/7y0n_33550.map" } resolution = 3.8 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= 0.002 sd= 0.063 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 135 5.16 5 C 20340 2.51 5 N 5256 2.21 5 O 6258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31989 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 7715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7715 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 8 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 7715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7715 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 8 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "C" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 889 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "D" Number of atoms: 7715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7715 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 8 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "E" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 889 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "F" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 889 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "G" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 947 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "H" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 947 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "I" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 947 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "J" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 7.02, per 1000 atoms: 0.22 Number of scatterers: 31989 At special positions: 0 Unit cell: (151.94, 155.15, 230.05, 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 135 16.00 O 6258 8.00 N 5256 7.00 C 20340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 165 " " NAG D1304 " - " ASN D 234 " " NAG D1305 " - " ASN D 282 " " NAG D1306 " - " ASN D 343 " " NAG D1307 " - " ASN D 603 " " NAG D1308 " - " ASN D 616 " " NAG D1309 " - " ASN D 657 " " NAG D1310 " - " ASN D 709 " " NAG D1311 " - " ASN D1074 " " NAG M 1 " - " ASN B 331 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN A 331 " " NAG S 1 " - " ASN A 717 " " NAG T 1 " - " ASN A 801 " " NAG U 1 " - " ASN A1134 " " NAG V 1 " - " ASN A1098 " " NAG W 1 " - " ASN D 331 " " NAG X 1 " - " ASN D 717 " " NAG Y 1 " - " ASN D 801 " " NAG Z 1 " - " ASN D1134 " " NAG a 1 " - " ASN D1098 " Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.4 seconds 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7506 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 65 sheets defined 19.8% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.235A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.636A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 635 through 639 removed outlier: 3.889A pdb=" N GLY A 639 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.590A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.660A pdb=" N THR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.517A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 874 removed outlier: 3.518A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 883 removed outlier: 3.933A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.296A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.543A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.281A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.801A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.593A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.827A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.789A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 997 " --> pdb=" O ILE A 993 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ARG A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A1018 " --> pdb=" O ARG A1014 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG A1019 " --> pdb=" O ALA A1015 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.668A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.228A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.629A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 635 through 639 removed outlier: 3.891A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.683A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.673A pdb=" N THR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 874 removed outlier: 3.581A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 883 removed outlier: 3.890A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.321A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.739A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.279A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.748A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.574A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.836A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.798A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 997 " --> pdb=" O ILE B 993 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG B1000 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B1019 " --> pdb=" O ALA B1015 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1120 removed outlier: 3.551A pdb=" N THR B1120 " --> pdb=" O THR B1117 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 337 through 343 removed outlier: 3.642A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 370 removed outlier: 4.243A pdb=" N LEU D 368 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 389 removed outlier: 3.632A pdb=" N ASP D 389 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 502 through 506 Processing helix chain 'D' and resid 635 through 639 removed outlier: 3.889A pdb=" N GLY D 639 " --> pdb=" O TYR D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 743 Processing helix chain 'D' and resid 746 through 755 removed outlier: 3.645A pdb=" N GLN D 755 " --> pdb=" O ASN D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.667A pdb=" N THR D 768 " --> pdb=" O ASN D 764 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY D 769 " --> pdb=" O ARG D 765 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE D 770 " --> pdb=" O ALA D 766 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE D 782 " --> pdb=" O THR D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 825 Processing helix chain 'D' and resid 866 through 874 removed outlier: 3.707A pdb=" N ALA D 871 " --> pdb=" O ASP D 867 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN D 872 " --> pdb=" O GLU D 868 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR D 873 " --> pdb=" O MET D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 876 through 883 removed outlier: 3.884A pdb=" N ILE D 882 " --> pdb=" O LEU D 878 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR D 883 " --> pdb=" O ALA D 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 891 removed outlier: 4.348A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 907 removed outlier: 3.640A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG D 905 " --> pdb=" O GLN D 901 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN D 907 " --> pdb=" O ALA D 903 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 919 removed outlier: 4.267A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU D 918 " --> pdb=" O ASN D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.800A pdb=" N THR D 941 " --> pdb=" O SER D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.564A pdb=" N GLN D 949 " --> pdb=" O LEU D 945 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 removed outlier: 3.834A pdb=" N LEU D 981 " --> pdb=" O LEU D 977 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1032 removed outlier: 3.804A pdb=" N GLU D 990 " --> pdb=" O PRO D 986 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE D 997 " --> pdb=" O ILE D 993 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR D 998 " --> pdb=" O ASP D 994 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ARG D1000 " --> pdb=" O LEU D 996 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER D1003 " --> pdb=" O GLY D 999 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR D1007 " --> pdb=" O SER D1003 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU D1017 " --> pdb=" O ILE D1013 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE D1018 " --> pdb=" O ARG D1014 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG D1019 " --> pdb=" O ALA D1015 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D1024 " --> pdb=" O ALA D1020 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1147 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.127A pdb=" N THR G 91 " --> pdb=" O PRO G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.149A pdb=" N THR H 91 " --> pdb=" O PRO H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 4.145A pdb=" N THR I 91 " --> pdb=" O PRO I 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.686A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 4.199A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.794A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 122 removed outlier: 4.128A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.304A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 327 through 328 removed outlier: 3.857A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.901A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.183A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.627A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 725 through 727 removed outlier: 3.624A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.709A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AB9, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.190A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.817A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 116 through 122 removed outlier: 4.125A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.301A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 327 through 328 removed outlier: 3.830A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.755A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.248A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 693 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 722 removed outlier: 6.623A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 725 through 727 removed outlier: 3.670A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD4, first strand: chain 'C' and resid 16 through 17 removed outlier: 4.205A pdb=" N ALA C 16 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER C 85 " --> pdb=" O ALA C 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 58 through 60 removed outlier: 5.173A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 69 through 73 Processing sheet with id=AD7, first strand: chain 'D' and resid 28 through 30 removed outlier: 3.700A pdb=" N THR D 63 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL D 267 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE D 65 " --> pdb=" O TYR D 265 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TYR D 265 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS D 195 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS D 202 " --> pdb=" O LYS D 195 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 50 through 55 removed outlier: 4.180A pdb=" N ASP D 53 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG D 273 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 83 through 85 removed outlier: 3.791A pdb=" N ILE D 105 " --> pdb=" O GLN D 239 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 116 through 122 removed outlier: 4.135A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.317A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 327 through 328 removed outlier: 3.849A pdb=" N ARG D 328 " --> pdb=" O ASN D 542 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR D 553 " --> pdb=" O ASP D 586 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 354 through 358 removed outlier: 3.731A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN D 394 " --> pdb=" O GLU D 516 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU D 516 " --> pdb=" O ASN D 394 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG D 509 " --> pdb=" O TRP D 436 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP D 436 " --> pdb=" O ARG D 509 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'D' and resid 654 through 660 removed outlier: 6.166A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N VAL D 656 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 693 " --> pdb=" O SER D 673 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 712 through 722 removed outlier: 6.634A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN D 717 " --> pdb=" O ALA D1070 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER D 721 " --> pdb=" O THR D1066 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY D1059 " --> pdb=" O ALA D1056 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 725 through 727 removed outlier: 3.640A pdb=" N GLU D 725 " --> pdb=" O PHE D1062 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'D' and resid 1081 through 1082 Processing sheet with id=AF3, first strand: chain 'E' and resid 16 through 17 removed outlier: 4.127A pdb=" N ALA E 16 " --> pdb=" O SER E 85 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER E 85 " --> pdb=" O ALA E 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'E' and resid 58 through 60 removed outlier: 5.224A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 69 through 73 Processing sheet with id=AF6, first strand: chain 'F' and resid 16 through 17 removed outlier: 4.216A pdb=" N ALA F 16 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER F 85 " --> pdb=" O ALA F 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.125A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 69 through 73 Processing sheet with id=AF9, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.570A pdb=" N MET G 34 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.146A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AG5, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.653A pdb=" N MET I 34 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AG7, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.971A pdb=" N LEU J 11 " --> pdb=" O LYS J 103 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR J 49 " --> pdb=" O SER J 53 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AG9, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.995A pdb=" N LEU K 11 " --> pdb=" O LYS K 103 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR K 49 " --> pdb=" O SER K 53 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AH2, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.977A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR L 49 " --> pdb=" O SER L 53 " (cutoff:3.500A) 970 hydrogen bonds defined for protein. 2565 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: 9.27 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6944 1.33 - 1.46: 8922 1.46 - 1.58: 16664 1.58 - 1.71: 2 1.71 - 1.83: 174 Bond restraints: 32706 Sorted by residual: bond pdb=" N THR D 333 " pdb=" CA THR D 333 " ideal model delta sigma weight residual 1.460 1.489 -0.029 1.02e-02 9.61e+03 8.20e+00 bond pdb=" N THR B 333 " pdb=" CA THR B 333 " ideal model delta sigma weight residual 1.460 1.489 -0.029 1.02e-02 9.61e+03 8.00e+00 bond pdb=" N ILE D 332 " pdb=" CA ILE D 332 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.95e+00 bond pdb=" N ILE B 332 " pdb=" CA ILE B 332 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.52e+00 bond pdb=" C LEU I 86 " pdb=" N LYS I 87 " ideal model delta sigma weight residual 1.331 1.407 -0.076 2.83e-02 1.25e+03 7.18e+00 ... (remaining 32701 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 43714 2.37 - 4.75: 697 4.75 - 7.12: 76 7.12 - 9.49: 21 9.49 - 11.87: 3 Bond angle restraints: 44511 Sorted by residual: angle pdb=" CA ARG H 85 " pdb=" CB ARG H 85 " pdb=" CG ARG H 85 " ideal model delta sigma weight residual 114.10 125.97 -11.87 2.00e+00 2.50e-01 3.52e+01 angle pdb=" CA ARG G 85 " pdb=" CB ARG G 85 " pdb=" CG ARG G 85 " ideal model delta sigma weight residual 114.10 125.95 -11.85 2.00e+00 2.50e-01 3.51e+01 angle pdb=" CA ARG I 85 " pdb=" CB ARG I 85 " pdb=" CG ARG I 85 " ideal model delta sigma weight residual 114.10 125.93 -11.83 2.00e+00 2.50e-01 3.50e+01 angle pdb=" CA PRO G 41 " pdb=" N PRO G 41 " pdb=" CD PRO G 41 " ideal model delta sigma weight residual 112.00 104.48 7.52 1.40e+00 5.10e-01 2.88e+01 angle pdb=" CA PRO I 41 " pdb=" N PRO I 41 " pdb=" CD PRO I 41 " ideal model delta sigma weight residual 112.00 104.50 7.50 1.40e+00 5.10e-01 2.87e+01 ... (remaining 44506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 17029 17.76 - 35.51: 1488 35.51 - 53.27: 209 53.27 - 71.03: 48 71.03 - 88.79: 51 Dihedral angle restraints: 18825 sinusoidal: 7110 harmonic: 11715 Sorted by residual: dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " pdb=" CB CYS K 88 " ideal model delta sinusoidal sigma weight residual 93.00 -178.90 -88.10 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 88 " pdb=" CB CYS J 88 " ideal model delta sinusoidal sigma weight residual 93.00 -179.95 -87.05 1 1.00e+01 1.00e-02 9.11e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 -179.99 -87.01 1 1.00e+01 1.00e-02 9.10e+01 ... (remaining 18822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3870 0.049 - 0.098: 961 0.098 - 0.147: 326 0.147 - 0.196: 29 0.196 - 0.245: 19 Chirality restraints: 5205 Sorted by residual: chirality pdb=" CB ILE E 52 " pdb=" CA ILE E 52 " pdb=" CG1 ILE E 52 " pdb=" CG2 ILE E 52 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB VAL B 483 " pdb=" CA VAL B 483 " pdb=" CG1 VAL B 483 " pdb=" CG2 VAL B 483 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA ARG G 85 " pdb=" N ARG G 85 " pdb=" C ARG G 85 " pdb=" CB ARG G 85 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 5202 not shown) Planarity restraints: 5712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA I 40 " -0.094 5.00e-02 4.00e+02 1.38e-01 3.06e+01 pdb=" N PRO I 41 " 0.239 5.00e-02 4.00e+02 pdb=" CA PRO I 41 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO I 41 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 40 " 0.094 5.00e-02 4.00e+02 1.38e-01 3.06e+01 pdb=" N PRO G 41 " -0.239 5.00e-02 4.00e+02 pdb=" CA PRO G 41 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO G 41 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 47 " -0.019 2.00e-02 2.50e+03 1.87e-02 8.78e+00 pdb=" CG TRP F 47 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP F 47 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP F 47 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 47 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 47 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 47 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 47 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 47 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 47 " -0.001 2.00e-02 2.50e+03 ... (remaining 5709 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7319 2.79 - 3.32: 27556 3.32 - 3.84: 51251 3.84 - 4.37: 56464 4.37 - 4.90: 98758 Nonbonded interactions: 241348 Sorted by model distance: nonbonded pdb=" O LYS C 23 " pdb=" OH TYR C 111 " model vdw 2.259 3.040 nonbonded pdb=" O LYS F 23 " pdb=" OH TYR F 111 " model vdw 2.262 3.040 nonbonded pdb=" NH1 ARG G 59 " pdb=" O TYR G 60 " model vdw 2.269 3.120 nonbonded pdb=" NH1 ARG I 59 " pdb=" O TYR I 60 " model vdw 2.274 3.120 nonbonded pdb=" NH1 ARG H 59 " pdb=" O TYR H 60 " model vdw 2.282 3.120 ... (remaining 241343 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 32.140 Find NCS groups from input model: 0.880 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: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 : 0.004 0.100 32814 Z= 0.194 Angle : 0.735 11.866 44790 Z= 0.388 Chirality : 0.050 0.245 5205 Planarity : 0.006 0.138 5664 Dihedral : 13.698 88.787 11184 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.03 % Allowed : 0.53 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.36 (0.12), residues: 3975 helix: -2.80 (0.13), residues: 696 sheet: -0.47 (0.17), residues: 969 loop : -1.67 (0.12), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 408 TYR 0.019 0.001 TYR F 111 PHE 0.026 0.001 PHE G 80 TRP 0.051 0.002 TRP F 47 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (32706) covalent geometry : angle 0.72608 / 0.39 (44511) SS BOND : bond 0.00240 / 0.15 ( 45) SS BOND : angle 1.43389 / 0.95 ( 90) hydrogen bonds : bond 0.27096 / 17.92 ( 970) hydrogen bonds : angle 9.17475 / 6.20 ( 2565) link_BETA1-4 : bond 0.00693 / 0.40 ( 15) link_BETA1-4 : angle 1.16421 / 0.76 ( 45) link_NAG-ASN : bond 0.00352 / 0.23 ( 48) link_NAG-ASN : angle 1.79999 / 1.17 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 1.276 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: C 2 MET cc_start: 0.1862 (tpt) cc_final: 0.1633 (tpt) REVERT: C 107 TYR cc_start: 0.4783 (p90) cc_final: 0.4368 (p90) REVERT: D 495 TYR cc_start: 0.6917 (m-10) cc_final: 0.6673 (m-10) REVERT: F 3 GLN cc_start: 0.6138 (tm-30) cc_final: 0.5901 (tm-30) REVERT: F 37 VAL cc_start: 0.7422 (t) cc_final: 0.7205 (p) REVERT: G 34 MET cc_start: 0.7354 (mmt) cc_final: 0.7053 (ttp) REVERT: G 80 PHE cc_start: 0.7882 (p90) cc_final: 0.7643 (p90) REVERT: I 33 TYR cc_start: 0.8354 (m-10) cc_final: 0.7772 (m-10) REVERT: J 83 PHE cc_start: 0.4122 (m-80) cc_final: 0.3807 (m-80) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.2206 time to fit residues: 75.2212 Evaluate side-chains 174 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.0970 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN A 965 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN D 751 ASN ** D 901 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 = 0.4212 r_free = 0.4212 target = 0.127742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.090182 restraints weight = 100600.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.085304 restraints weight = 69868.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.085445 restraints weight = 70713.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.085879 restraints weight = 63795.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.085931 restraints weight = 56415.526| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32814 Z= 0.108 Angle : 0.549 9.087 44790 Z= 0.285 Chirality : 0.044 0.272 5205 Planarity : 0.004 0.079 5664 Dihedral : 4.392 18.983 4356 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.42 % Allowed : 5.37 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.69 (0.13), residues: 3975 helix: -1.00 (0.17), residues: 717 sheet: -0.35 (0.17), residues: 951 loop : -1.52 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 85 TYR 0.021 0.001 TYR J 92 PHE 0.023 0.001 PHE I 80 TRP 0.018 0.001 TRP E 47 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (32706) covalent geometry : angle 0.54096 / 0.28 (44511) SS BOND : bond 0.00197 / 0.14 ( 45) SS BOND : angle 0.73770 / 0.50 ( 90) hydrogen bonds : bond 0.04935 / 3.31 ( 970) hydrogen bonds : angle 6.34922 / 4.28 ( 2565) link_BETA1-4 : bond 0.00288 / 0.17 ( 15) link_BETA1-4 : angle 1.11193 / 0.73 ( 45) link_NAG-ASN : bond 0.00329 / 0.20 ( 48) link_NAG-ASN : angle 1.64057 / 1.05 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8086 (p90) cc_final: 0.7603 (p90) REVERT: A 508 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7865 (t80) REVERT: A 754 LEU cc_start: 0.9490 (tp) cc_final: 0.9083 (pp) REVERT: B 400 PHE cc_start: 0.8441 (p90) cc_final: 0.8047 (p90) REVERT: B 508 TYR cc_start: 0.8077 (m-80) cc_final: 0.7696 (t80) REVERT: B 513 LEU cc_start: 0.9625 (mm) cc_final: 0.9397 (tp) REVERT: C 37 VAL cc_start: 0.7557 (t) cc_final: 0.7344 (p) REVERT: C 47 TRP cc_start: 0.3783 (t60) cc_final: 0.3290 (t60) REVERT: D 377 PHE cc_start: 0.6462 (t80) cc_final: 0.6157 (t80) REVERT: D 400 PHE cc_start: 0.8010 (p90) cc_final: 0.7704 (p90) REVERT: D 508 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.7642 (t80) REVERT: G 34 MET cc_start: 0.7299 (mmt) cc_final: 0.6996 (ttp) REVERT: G 85 ARG cc_start: 0.6924 (pmt-80) cc_final: 0.6250 (pmt-80) REVERT: H 85 ARG cc_start: 0.7043 (pmt-80) cc_final: 0.6304 (pmt-80) REVERT: I 85 ARG cc_start: 0.7360 (pmt-80) cc_final: 0.6914 (pmt-80) REVERT: J 32 TYR cc_start: 0.7327 (m-80) cc_final: 0.7108 (m-80) REVERT: J 83 PHE cc_start: 0.3901 (m-80) cc_final: 0.3487 (m-80) outliers start: 14 outliers final: 4 residues processed: 199 average time/residue: 0.2210 time to fit residues: 69.5714 Evaluate side-chains 181 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain D residue 508 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 96 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 chunk 198 optimal weight: 7.9990 chunk 203 optimal weight: 40.0000 chunk 164 optimal weight: 5.9990 chunk 272 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 751 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 965 GLN ** D 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.128428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.099539 restraints weight = 119676.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.091480 restraints weight = 162979.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.089817 restraints weight = 127758.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.088835 restraints weight = 115426.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.089052 restraints weight = 112471.559| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 32814 Z= 0.278 Angle : 0.685 8.159 44790 Z= 0.352 Chirality : 0.047 0.180 5205 Planarity : 0.005 0.120 5664 Dihedral : 4.887 21.085 4356 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.04 % Allowed : 8.87 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.65 (0.13), residues: 3975 helix: -0.51 (0.18), residues: 714 sheet: -0.46 (0.17), residues: 933 loop : -1.59 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 102 TYR 0.028 0.002 TYR A1047 PHE 0.025 0.002 PHE I 80 TRP 0.052 0.002 TRP A 104 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.28 (32706) covalent geometry : angle 0.67460 / 0.35 (44511) SS BOND : bond 0.00332 / 0.24 ( 45) SS BOND : angle 1.08681 / 0.68 ( 90) hydrogen bonds : bond 0.05367 / 3.55 ( 970) hydrogen bonds : angle 6.38281 / 4.31 ( 2565) link_BETA1-4 : bond 0.00304 / 0.17 ( 15) link_BETA1-4 : angle 1.30120 / 0.87 ( 45) link_NAG-ASN : bond 0.00459 / 0.30 ( 48) link_NAG-ASN : angle 2.04094 / 1.34 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8367 (p90) cc_final: 0.7789 (p90) REVERT: A 508 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7886 (t80) REVERT: A 754 LEU cc_start: 0.9450 (tp) cc_final: 0.9076 (pp) REVERT: B 400 PHE cc_start: 0.8381 (p90) cc_final: 0.7815 (p90) REVERT: B 508 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.7653 (t80) REVERT: C 37 VAL cc_start: 0.7587 (t) cc_final: 0.7311 (p) REVERT: D 104 TRP cc_start: 0.7149 (p90) cc_final: 0.6940 (p90) REVERT: D 400 PHE cc_start: 0.8477 (p90) cc_final: 0.7899 (p90) REVERT: D 402 ILE cc_start: 0.4337 (OUTLIER) cc_final: 0.3860 (pt) REVERT: E 47 TRP cc_start: 0.3977 (t60) cc_final: 0.2765 (t60) REVERT: G 34 MET cc_start: 0.7234 (mmt) cc_final: 0.6924 (ttp) REVERT: G 39 GLN cc_start: 0.7060 (tp40) cc_final: 0.6652 (mp10) REVERT: H 34 MET cc_start: 0.6755 (tpp) cc_final: 0.5787 (ttt) REVERT: I 80 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7743 (m-80) REVERT: J 92 TYR cc_start: 0.5790 (t80) cc_final: 0.5517 (t80) outliers start: 35 outliers final: 21 residues processed: 193 average time/residue: 0.2198 time to fit residues: 67.9037 Evaluate side-chains 195 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain I residue 80 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 267 optimal weight: 4.9990 chunk 328 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 30.0000 chunk 204 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.128006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.095921 restraints weight = 118504.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.091836 restraints weight = 128970.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.092807 restraints weight = 106900.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.092585 restraints weight = 82335.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.092572 restraints weight = 84679.423| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 32814 Z= 0.238 Angle : 0.622 8.074 44790 Z= 0.319 Chirality : 0.045 0.196 5205 Planarity : 0.005 0.067 5664 Dihedral : 4.821 21.961 4356 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.57 % Allowed : 10.88 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.68 (0.13), residues: 3975 helix: -0.39 (0.19), residues: 720 sheet: -0.58 (0.17), residues: 957 loop : -1.62 (0.12), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 102 TYR 0.027 0.002 TYR K 86 PHE 0.023 0.002 PHE I 80 TRP 0.038 0.002 TRP A 104 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 (32706) covalent geometry : angle 0.61080 / 0.32 (44511) SS BOND : bond 0.00219 / 0.15 ( 45) SS BOND : angle 0.96555 / 0.59 ( 90) hydrogen bonds : bond 0.04689 / 3.11 ( 970) hydrogen bonds : angle 6.11613 / 4.13 ( 2565) link_BETA1-4 : bond 0.00256 / 0.15 ( 15) link_BETA1-4 : angle 1.13583 / 0.76 ( 45) link_NAG-ASN : bond 0.00371 / 0.23 ( 48) link_NAG-ASN : angle 2.00263 / 1.30 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.7538 (p90) cc_final: 0.7276 (p90) REVERT: A 402 ILE cc_start: 0.3691 (OUTLIER) cc_final: 0.3294 (pt) REVERT: A 754 LEU cc_start: 0.9296 (tp) cc_final: 0.9019 (pp) REVERT: B 400 PHE cc_start: 0.7602 (p90) cc_final: 0.7278 (p90) REVERT: C 37 VAL cc_start: 0.6982 (t) cc_final: 0.6724 (p) REVERT: D 377 PHE cc_start: 0.5989 (OUTLIER) cc_final: 0.5398 (t80) REVERT: D 400 PHE cc_start: 0.7668 (p90) cc_final: 0.7335 (p90) REVERT: I 90 ASP cc_start: 0.4423 (t0) cc_final: 0.4078 (m-30) outliers start: 53 outliers final: 34 residues processed: 208 average time/residue: 0.2072 time to fit residues: 69.8200 Evaluate side-chains 199 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 67 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 340 optimal weight: 0.0270 chunk 108 optimal weight: 10.0000 chunk 158 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 249 optimal weight: 30.0000 chunk 182 optimal weight: 6.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 965 GLN E 3 GLN ** H 39 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 = 0.4185 r_free = 0.4185 target = 0.123818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.083714 restraints weight = 103677.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.080288 restraints weight = 68721.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.081079 restraints weight = 63107.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.081243 restraints weight = 53750.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.081337 restraints weight = 49831.042| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32814 Z= 0.096 Angle : 0.515 7.525 44790 Z= 0.263 Chirality : 0.043 0.187 5205 Planarity : 0.004 0.051 5664 Dihedral : 4.368 20.529 4356 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.19 % Allowed : 12.54 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.45 (0.13), residues: 3975 helix: -0.11 (0.19), residues: 735 sheet: -0.44 (0.18), residues: 918 loop : -1.50 (0.12), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 85 TYR 0.019 0.001 TYR L 92 PHE 0.021 0.001 PHE A 515 TRP 0.023 0.001 TRP A 104 HIS 0.002 0.000 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (32706) covalent geometry : angle 0.50576 / 0.26 (44511) SS BOND : bond 0.00166 / 0.13 ( 45) SS BOND : angle 0.73597 / 0.44 ( 90) hydrogen bonds : bond 0.03695 / 2.46 ( 970) hydrogen bonds : angle 5.51432 / 3.72 ( 2565) link_BETA1-4 : bond 0.00358 / 0.21 ( 15) link_BETA1-4 : angle 0.92111 / 0.61 ( 45) link_NAG-ASN : bond 0.00272 / 0.16 ( 48) link_NAG-ASN : angle 1.71623 / 1.10 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8527 (p90) cc_final: 0.8052 (p90) REVERT: A 505 TYR cc_start: 0.7237 (t80) cc_final: 0.6855 (t80) REVERT: A 754 LEU cc_start: 0.9468 (tp) cc_final: 0.9047 (pp) REVERT: B 400 PHE cc_start: 0.8557 (p90) cc_final: 0.8101 (p90) REVERT: C 37 VAL cc_start: 0.7623 (t) cc_final: 0.7312 (p) REVERT: C 48 MET cc_start: -0.1088 (ptt) cc_final: -0.1401 (ptt) REVERT: D 400 PHE cc_start: 0.8598 (p90) cc_final: 0.8192 (p90) REVERT: E 47 TRP cc_start: 0.4211 (t60) cc_final: 0.3086 (t60) REVERT: G 33 TYR cc_start: 0.7022 (m-10) cc_final: 0.6751 (m-10) REVERT: H 34 MET cc_start: 0.6664 (tpp) cc_final: 0.6342 (tpt) REVERT: I 90 ASP cc_start: 0.4693 (t0) cc_final: 0.4092 (m-30) REVERT: J 32 TYR cc_start: 0.7553 (m-80) cc_final: 0.7291 (m-80) outliers start: 40 outliers final: 19 residues processed: 198 average time/residue: 0.1973 time to fit residues: 63.7071 Evaluate side-chains 181 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 904 TYR Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain I residue 80 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 347 optimal weight: 9.9990 chunk 170 optimal weight: 0.8980 chunk 200 optimal weight: 50.0000 chunk 61 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 396 optimal weight: 40.0000 chunk 281 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 106 optimal weight: 0.1980 chunk 184 optimal weight: 0.4980 chunk 284 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 ASN D 935 GLN E 3 GLN ** H 39 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 = 0.4317 r_free = 0.4317 target = 0.129720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.098533 restraints weight = 119247.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.097021 restraints weight = 111411.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.096629 restraints weight = 97289.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.096261 restraints weight = 74448.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.096334 restraints weight = 72335.022| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32814 Z= 0.123 Angle : 0.518 8.251 44790 Z= 0.263 Chirality : 0.043 0.179 5205 Planarity : 0.004 0.053 5664 Dihedral : 4.292 20.090 4356 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 1.45 % Allowed : 12.75 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.39 (0.13), residues: 3975 helix: 0.02 (0.19), residues: 735 sheet: -0.48 (0.17), residues: 948 loop : -1.47 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 59 TYR 0.018 0.001 TYR L 92 PHE 0.014 0.001 PHE D 515 TRP 0.025 0.001 TRP A 104 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (32706) covalent geometry : angle 0.50800 / 0.26 (44511) SS BOND : bond 0.00160 / 0.11 ( 45) SS BOND : angle 0.72032 / 0.43 ( 90) hydrogen bonds : bond 0.03640 / 2.42 ( 970) hydrogen bonds : angle 5.43473 / 3.66 ( 2565) link_BETA1-4 : bond 0.00291 / 0.17 ( 15) link_BETA1-4 : angle 0.99788 / 0.67 ( 45) link_NAG-ASN : bond 0.00229 / 0.13 ( 48) link_NAG-ASN : angle 1.70730 / 1.11 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.3862 (OUTLIER) cc_final: 0.3349 (pt) REVERT: A 505 TYR cc_start: 0.6150 (t80) cc_final: 0.5885 (t80) REVERT: A 754 LEU cc_start: 0.9248 (tp) cc_final: 0.8991 (pp) REVERT: C 37 VAL cc_start: 0.6843 (t) cc_final: 0.6562 (p) REVERT: D 377 PHE cc_start: 0.5948 (OUTLIER) cc_final: 0.5462 (t80) REVERT: D 754 LEU cc_start: 0.9165 (tt) cc_final: 0.8878 (pp) REVERT: H 33 TYR cc_start: 0.5918 (m-80) cc_final: 0.5402 (m-80) outliers start: 49 outliers final: 26 residues processed: 197 average time/residue: 0.2059 time to fit residues: 66.4779 Evaluate side-chains 188 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 904 TYR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I residue 80 PHE Chi-restraints excluded: chain I residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 289 optimal weight: 0.8980 chunk 343 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 125 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 113 optimal weight: 0.0370 chunk 173 optimal weight: 0.4980 chunk 292 optimal weight: 6.9990 overall best weight: 2.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.129082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.098414 restraints weight = 119385.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.096335 restraints weight = 125311.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.096855 restraints weight = 106341.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.095920 restraints weight = 84092.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.096175 restraints weight = 79057.540| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32814 Z= 0.161 Angle : 0.552 7.337 44790 Z= 0.280 Chirality : 0.044 0.253 5205 Planarity : 0.004 0.055 5664 Dihedral : 4.403 20.293 4356 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 1.69 % Allowed : 13.46 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.42 (0.13), residues: 3975 helix: -0.01 (0.19), residues: 735 sheet: -0.56 (0.17), residues: 987 loop : -1.45 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 59 TYR 0.020 0.001 TYR K 92 PHE 0.033 0.001 PHE A 400 TRP 0.027 0.002 TRP A 104 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (32706) covalent geometry : angle 0.54267 / 0.28 (44511) SS BOND : bond 0.00169 / 0.12 ( 45) SS BOND : angle 0.75893 / 0.46 ( 90) hydrogen bonds : bond 0.03864 / 2.57 ( 970) hydrogen bonds : angle 5.48784 / 3.70 ( 2565) link_BETA1-4 : bond 0.00264 / 0.15 ( 15) link_BETA1-4 : angle 1.05023 / 0.71 ( 45) link_NAG-ASN : bond 0.00258 / 0.16 ( 48) link_NAG-ASN : angle 1.77589 / 1.16 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 163 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.7195 (p90) cc_final: 0.6889 (p90) REVERT: A 505 TYR cc_start: 0.6196 (t80) cc_final: 0.5936 (t80) REVERT: A 754 LEU cc_start: 0.9245 (tp) cc_final: 0.9000 (pp) REVERT: B 400 PHE cc_start: 0.7095 (p90) cc_final: 0.6870 (p90) REVERT: C 37 VAL cc_start: 0.6766 (t) cc_final: 0.6555 (p) REVERT: D 377 PHE cc_start: 0.6011 (OUTLIER) cc_final: 0.5568 (t80) REVERT: D 400 PHE cc_start: 0.7284 (p90) cc_final: 0.7077 (p90) REVERT: D 483 VAL cc_start: -0.3524 (OUTLIER) cc_final: -0.3750 (m) REVERT: D 754 LEU cc_start: 0.9170 (tt) cc_final: 0.8849 (pp) outliers start: 57 outliers final: 34 residues processed: 204 average time/residue: 0.2109 time to fit residues: 70.4667 Evaluate side-chains 196 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I residue 80 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 56 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 392 optimal weight: 40.0000 chunk 204 optimal weight: 0.8980 chunk 311 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 351 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.129600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.098640 restraints weight = 119206.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.096920 restraints weight = 116556.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.097344 restraints weight = 99279.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.096089 restraints weight = 81384.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.096199 restraints weight = 88453.368| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32814 Z= 0.123 Angle : 0.526 8.641 44790 Z= 0.267 Chirality : 0.044 0.194 5205 Planarity : 0.004 0.056 5664 Dihedral : 4.308 19.922 4356 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.25 % Allowed : 14.06 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.36 (0.13), residues: 3975 helix: 0.09 (0.19), residues: 735 sheet: -0.59 (0.17), residues: 987 loop : -1.40 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 102 TYR 0.019 0.001 TYR K 92 PHE 0.020 0.001 PHE A 400 TRP 0.028 0.002 TRP F 47 HIS 0.003 0.000 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (32706) covalent geometry : angle 0.51671 / 0.26 (44511) SS BOND : bond 0.00160 / 0.12 ( 45) SS BOND : angle 0.71975 / 0.43 ( 90) hydrogen bonds : bond 0.03640 / 2.43 ( 970) hydrogen bonds : angle 5.34599 / 3.60 ( 2565) link_BETA1-4 : bond 0.00292 / 0.17 ( 15) link_BETA1-4 : angle 0.98342 / 0.66 ( 45) link_NAG-ASN : bond 0.00229 / 0.13 ( 48) link_NAG-ASN : angle 1.70194 / 1.11 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 TYR cc_start: 0.6292 (t80) cc_final: 0.6011 (t80) REVERT: A 754 LEU cc_start: 0.9240 (tp) cc_final: 0.8994 (pp) REVERT: B 873 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.8455 (m-10) REVERT: C 37 VAL cc_start: 0.6791 (t) cc_final: 0.6579 (p) REVERT: D 377 PHE cc_start: 0.6003 (OUTLIER) cc_final: 0.5601 (t80) REVERT: D 483 VAL cc_start: -0.3487 (OUTLIER) cc_final: -0.3709 (m) REVERT: D 754 LEU cc_start: 0.9158 (tt) cc_final: 0.8855 (pp) REVERT: I 34 MET cc_start: 0.5369 (tpt) cc_final: 0.4625 (tpt) outliers start: 42 outliers final: 30 residues processed: 189 average time/residue: 0.2023 time to fit residues: 62.8738 Evaluate side-chains 192 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I residue 80 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 351 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 395 optimal weight: 30.0000 chunk 362 optimal weight: 2.9990 chunk 280 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 349 optimal weight: 6.9990 chunk 135 optimal weight: 30.0000 chunk 37 optimal weight: 0.8980 chunk 358 optimal weight: 30.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.129196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3685 r_free = 0.3685 target = 0.091423 restraints weight = 118669.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.085517 restraints weight = 90475.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.085878 restraints weight = 96839.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.086286 restraints weight = 86022.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.086354 restraints weight = 75522.523| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32814 Z= 0.147 Angle : 0.545 7.935 44790 Z= 0.275 Chirality : 0.044 0.187 5205 Planarity : 0.004 0.057 5664 Dihedral : 4.352 19.927 4356 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 1.51 % Allowed : 14.21 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.38 (0.13), residues: 3975 helix: 0.08 (0.19), residues: 735 sheet: -0.58 (0.17), residues: 990 loop : -1.42 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 102 TYR 0.015 0.001 TYR A 365 PHE 0.020 0.001 PHE D 400 TRP 0.032 0.002 TRP F 47 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (32706) covalent geometry : angle 0.53567 / 0.27 (44511) SS BOND : bond 0.00175 / 0.13 ( 45) SS BOND : angle 0.73417 / 0.44 ( 90) hydrogen bonds : bond 0.03736 / 2.49 ( 970) hydrogen bonds : angle 5.37160 / 3.61 ( 2565) link_BETA1-4 : bond 0.00267 / 0.15 ( 15) link_BETA1-4 : angle 1.04659 / 0.70 ( 45) link_NAG-ASN : bond 0.00246 / 0.14 ( 48) link_NAG-ASN : angle 1.73924 / 1.14 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 162 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8497 (m-80) cc_final: 0.8112 (m-80) REVERT: A 505 TYR cc_start: 0.7801 (t80) cc_final: 0.7397 (t80) REVERT: A 754 LEU cc_start: 0.9390 (tp) cc_final: 0.9056 (pp) REVERT: B 505 TYR cc_start: 0.7715 (t80) cc_final: 0.7358 (t80) REVERT: B 873 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.8507 (m-10) REVERT: D 377 PHE cc_start: 0.6613 (OUTLIER) cc_final: 0.6220 (t80) REVERT: D 483 VAL cc_start: -0.2761 (OUTLIER) cc_final: -0.2984 (m) REVERT: D 712 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7723 (tp) REVERT: D 754 LEU cc_start: 0.9307 (tt) cc_final: 0.8921 (pp) REVERT: I 34 MET cc_start: 0.6320 (tpt) cc_final: 0.5682 (tpt) REVERT: I 83 MET cc_start: 0.7290 (pmm) cc_final: 0.7037 (pmm) REVERT: J 32 TYR cc_start: 0.7876 (m-80) cc_final: 0.7661 (m-80) outliers start: 51 outliers final: 40 residues processed: 198 average time/residue: 0.1922 time to fit residues: 63.1723 Evaluate side-chains 203 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I residue 80 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 6 optimal weight: 6.9990 chunk 305 optimal weight: 4.9990 chunk 383 optimal weight: 20.0000 chunk 289 optimal weight: 0.9980 chunk 299 optimal weight: 0.8980 chunk 377 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 278 optimal weight: 0.5980 chunk 261 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 320 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.129363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3716 r_free = 0.3716 target = 0.092904 restraints weight = 118897.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.086105 restraints weight = 93525.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.086733 restraints weight = 98613.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.087033 restraints weight = 84848.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.087155 restraints weight = 75895.399| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 32814 Z= 0.141 Angle : 0.543 9.149 44790 Z= 0.275 Chirality : 0.044 0.189 5205 Planarity : 0.004 0.058 5664 Dihedral : 4.336 19.908 4356 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.36 % Allowed : 14.74 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.36 (0.13), residues: 3975 helix: 0.12 (0.19), residues: 735 sheet: -0.58 (0.17), residues: 987 loop : -1.42 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 59 TYR 0.029 0.001 TYR F 111 PHE 0.017 0.001 PHE D 400 TRP 0.035 0.002 TRP E 47 HIS 0.003 0.000 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (32706) covalent geometry : angle 0.53398 / 0.27 (44511) SS BOND : bond 0.00157 / 0.11 ( 45) SS BOND : angle 0.71673 / 0.44 ( 90) hydrogen bonds : bond 0.03692 / 2.47 ( 970) hydrogen bonds : angle 5.31362 / 3.57 ( 2565) link_BETA1-4 : bond 0.00278 / 0.16 ( 15) link_BETA1-4 : angle 1.01625 / 0.69 ( 45) link_NAG-ASN : bond 0.00234 / 0.13 ( 48) link_NAG-ASN : angle 1.71817 / 1.12 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7950 Ramachandran restraints generated. 3975 Oldfield, 0 Emsley, 3975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8483 (m-80) cc_final: 0.8074 (m-80) REVERT: A 505 TYR cc_start: 0.7735 (t80) cc_final: 0.7326 (t80) REVERT: A 754 LEU cc_start: 0.9371 (tp) cc_final: 0.9049 (pp) REVERT: B 505 TYR cc_start: 0.7659 (t80) cc_final: 0.7262 (t80) REVERT: B 873 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.8510 (m-10) REVERT: D 377 PHE cc_start: 0.6648 (OUTLIER) cc_final: 0.6245 (t80) REVERT: D 483 VAL cc_start: -0.3050 (OUTLIER) cc_final: -0.3259 (m) REVERT: D 754 LEU cc_start: 0.9281 (tt) cc_final: 0.8904 (pp) REVERT: I 33 TYR cc_start: 0.7570 (m-80) cc_final: 0.7207 (t80) REVERT: I 34 MET cc_start: 0.6027 (tpt) cc_final: 0.5571 (tpt) REVERT: I 83 MET cc_start: 0.7081 (pmm) cc_final: 0.6793 (pmm) REVERT: I 105 PHE cc_start: 0.7611 (m-10) cc_final: 0.7243 (t80) REVERT: J 32 TYR cc_start: 0.7848 (m-80) cc_final: 0.7616 (m-80) outliers start: 46 outliers final: 39 residues processed: 197 average time/residue: 0.1966 time to fit residues: 64.0823 Evaluate side-chains 203 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 380 TYR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I residue 80 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 150 optimal weight: 0.9990 chunk 374 optimal weight: 10.0000 chunk 269 optimal weight: 4.9990 chunk 219 optimal weight: 0.9980 chunk 125 optimal weight: 20.0000 chunk 96 optimal weight: 0.1980 chunk 35 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 chunk 396 optimal weight: 50.0000 chunk 197 optimal weight: 0.6980 chunk 369 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.130637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3739 r_free = 0.3739 target = 0.093804 restraints weight = 119303.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.088119 restraints weight = 89012.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.088726 restraints weight = 88882.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.089147 restraints weight = 77862.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.089191 restraints weight = 69442.203| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32814 Z= 0.090 Angle : 0.512 8.106 44790 Z= 0.258 Chirality : 0.043 0.200 5205 Planarity : 0.004 0.058 5664 Dihedral : 4.087 19.017 4356 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.19 % Allowed : 14.95 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.21 (0.13), residues: 3975 helix: 0.35 (0.20), residues: 735 sheet: -0.58 (0.17), residues: 1023 loop : -1.32 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 59 TYR 0.018 0.001 TYR G 60 PHE 0.029 0.001 PHE A 347 TRP 0.031 0.001 TRP F 47 HIS 0.002 0.000 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (32706) covalent geometry : angle 0.50356 / 0.26 (44511) SS BOND : bond 0.00152 / 0.11 ( 45) SS BOND : angle 0.64937 / 0.39 ( 90) hydrogen bonds : bond 0.03228 / 2.17 ( 970) hydrogen bonds : angle 5.04190 / 3.39 ( 2565) link_BETA1-4 : bond 0.00387 / 0.22 ( 15) link_BETA1-4 : angle 0.93844 / 0.63 ( 45) link_NAG-ASN : bond 0.00272 / 0.16 ( 48) link_NAG-ASN : angle 1.57163 / 1.02 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5178.02 seconds wall clock time: 90 minutes 32.17 seconds (5432.17 seconds total)