Starting phenix.real_space_refine on Fri Jun 27 18:30:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y0n_33550/06_2025/7y0n_33550.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y0n_33550/06_2025/7y0n_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7y0n_33550/06_2025/7y0n_33550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y0n_33550/06_2025/7y0n_33550.map" model { file = "/net/cci-nas-00/data/ceres_data/7y0n_33550/06_2025/7y0n_33550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y0n_33550/06_2025/7y0n_33550.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 5} 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: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 5} 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: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 5} 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 33 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 dihedrals: 33 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 dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 18.05, per 1000 atoms: 0.56 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: 7.66 Conformation dependent library (CDL) restraints added in 4.0 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: 4.51 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: 20.31 Time building geometry restraints manager: 9.13 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: 18191 17.76 - 35.51: 1610 35.51 - 53.27: 248 53.27 - 71.03: 48 71.03 - 88.79: 51 Dihedral angle restraints: 20148 sinusoidal: 8433 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 20145 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: 0.01 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: 3.330 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: 0.030 Extract box with map and model: 1.360 Check model and map are aligned: 0.250 Set scattering table: 0.310 Process input model: 78.140 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.260 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: 0.020 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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 : 13.513 88.787 12507 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.051 0.002 TRP F 47 HIS 0.003 0.001 HIS B1048 PHE 0.026 0.001 PHE G 80 TYR 0.019 0.001 TYR F 111 ARG 0.008 0.001 ARG D 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 48) link_NAG-ASN : angle 1.79999 ( 144) link_BETA1-4 : bond 0.00693 ( 15) link_BETA1-4 : angle 1.16421 ( 45) hydrogen bonds : bond 0.27096 ( 970) hydrogen bonds : angle 9.17475 ( 2565) SS BOND : bond 0.00240 ( 45) SS BOND : angle 1.43389 ( 90) covalent geometry : bond 0.00391 (32706) covalent geometry : angle 0.72608 (44511) *********************** 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 : 3.713 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: 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: 0.6671 (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: 0.7206 (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: 0.8355 (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: 0.5789 time to fit residues: 195.7718 Evaluate side-chains 173 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 3.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 30.0000 chunk 302 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 203 optimal weight: 30.0000 chunk 161 optimal weight: 0.0000 chunk 312 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 chunk 232 optimal weight: 0.9980 chunk 362 optimal weight: 9.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 751 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.127472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.089585 restraints weight = 100750.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.085268 restraints weight = 75968.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.085320 restraints weight = 71074.278| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 32814 Z= 0.113 Angle : 0.551 9.123 44790 Z= 0.286 Chirality : 0.044 0.275 5205 Planarity : 0.005 0.079 5664 Dihedral : 6.075 52.106 5679 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.36 % Allowed : 5.25 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.13), residues: 3975 helix: -1.00 (0.17), residues: 717 sheet: -0.36 (0.17), residues: 951 loop : -1.52 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 47 HIS 0.002 0.000 HIS A1088 PHE 0.022 0.001 PHE I 80 TYR 0.020 0.001 TYR J 92 ARG 0.005 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 48) link_NAG-ASN : angle 1.68733 ( 144) link_BETA1-4 : bond 0.00442 ( 15) link_BETA1-4 : angle 1.08292 ( 45) hydrogen bonds : bond 0.04867 ( 970) hydrogen bonds : angle 6.34712 ( 2565) SS BOND : bond 0.00312 ( 45) SS BOND : angle 0.75323 ( 90) covalent geometry : bond 0.00236 (32706) covalent geometry : angle 0.54267 (44511) *********************** 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 205 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 5.335 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: A 400 PHE cc_start: 0.8012 (p90) cc_final: 0.7530 (p90) REVERT: A 508 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7844 (t80) REVERT: A 754 LEU cc_start: 0.9495 (tp) cc_final: 0.9088 (pp) REVERT: B 400 PHE cc_start: 0.8257 (p90) cc_final: 0.7811 (p90) REVERT: B 508 TYR cc_start: 0.8006 (m-80) cc_final: 0.7675 (t80) REVERT: C 37 VAL cc_start: 0.7507 (t) cc_final: 0.7288 (p) REVERT: C 47 TRP cc_start: 0.3716 (t60) cc_final: 0.3257 (t60) REVERT: D 377 PHE cc_start: 0.6234 (t80) cc_final: 0.5930 (t80) REVERT: D 400 PHE cc_start: 0.7930 (p90) cc_final: 0.7625 (p90) REVERT: F 47 TRP cc_start: 0.4214 (t60) cc_final: 0.3788 (t60) REVERT: G 34 MET cc_start: 0.7274 (mmt) cc_final: 0.6983 (ttp) REVERT: G 85 ARG cc_start: 0.6889 (pmt-80) cc_final: 0.6087 (pmt-80) REVERT: H 85 ARG cc_start: 0.7001 (pmt-80) cc_final: 0.6245 (pmt-80) REVERT: I 85 ARG cc_start: 0.7324 (pmt-80) cc_final: 0.6884 (pmt-80) REVERT: J 83 PHE cc_start: 0.3898 (m-80) cc_final: 0.3462 (m-80) outliers start: 12 outliers final: 1 residues processed: 199 average time/residue: 0.4970 time to fit residues: 158.2526 Evaluate side-chains 174 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 172 time to evaluate : 3.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 291 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 275 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 267 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 133 optimal weight: 9.9990 chunk 292 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 326 optimal weight: 30.0000 chunk 204 optimal weight: 30.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4177 r_free = 0.4177 target = 0.123298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.086107 restraints weight = 105445.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.081972 restraints weight = 75177.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.082030 restraints weight = 77956.975| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32814 Z= 0.146 Angle : 0.552 9.480 44790 Z= 0.284 Chirality : 0.044 0.189 5205 Planarity : 0.004 0.063 5664 Dihedral : 5.685 57.718 5679 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.71 % Allowed : 7.83 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.13), residues: 3975 helix: -0.29 (0.19), residues: 717 sheet: -0.40 (0.17), residues: 924 loop : -1.47 (0.12), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 47 HIS 0.003 0.001 HIS A1088 PHE 0.026 0.001 PHE I 80 TYR 0.023 0.001 TYR J 92 ARG 0.005 0.000 ARG I 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 48) link_NAG-ASN : angle 1.77688 ( 144) link_BETA1-4 : bond 0.00257 ( 15) link_BETA1-4 : angle 1.08852 ( 45) hydrogen bonds : bond 0.04592 ( 970) hydrogen bonds : angle 5.94268 ( 2565) SS BOND : bond 0.00211 ( 45) SS BOND : angle 0.87930 ( 90) covalent geometry : bond 0.00336 (32706) covalent geometry : angle 0.54144 (44511) *********************** 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 209 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 3.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8429 (p90) cc_final: 0.7825 (p90) REVERT: A 508 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7950 (t80) REVERT: A 754 LEU cc_start: 0.9479 (tp) cc_final: 0.9063 (pp) REVERT: B 400 PHE cc_start: 0.8655 (p90) cc_final: 0.8058 (p90) REVERT: B 508 TYR cc_start: 0.8015 (m-80) cc_final: 0.7668 (t80) REVERT: B 1132 ILE cc_start: 0.7644 (tp) cc_final: 0.7416 (tp) REVERT: C 37 VAL cc_start: 0.7665 (t) cc_final: 0.7405 (p) REVERT: D 104 TRP cc_start: 0.6985 (p90) cc_final: 0.6528 (p90) REVERT: D 377 PHE cc_start: 0.6406 (t80) cc_final: 0.5974 (t80) REVERT: D 400 PHE cc_start: 0.8549 (p90) cc_final: 0.7907 (p90) REVERT: D 402 ILE cc_start: 0.4652 (OUTLIER) cc_final: 0.4199 (pt) REVERT: D 754 LEU cc_start: 0.9422 (tp) cc_final: 0.8945 (pp) REVERT: E 3 GLN cc_start: 0.5842 (OUTLIER) cc_final: 0.5609 (tm-30) REVERT: F 37 VAL cc_start: 0.7331 (t) cc_final: 0.7075 (p) REVERT: G 34 MET cc_start: 0.7416 (mmt) cc_final: 0.7031 (ttp) REVERT: G 39 GLN cc_start: 0.6995 (tp40) cc_final: 0.6659 (mp10) REVERT: H 33 TYR cc_start: 0.7549 (m-10) cc_final: 0.7098 (m-80) REVERT: H 34 MET cc_start: 0.6749 (tpp) cc_final: 0.5697 (ttt) REVERT: H 80 PHE cc_start: 0.7734 (t80) cc_final: 0.7499 (t80) REVERT: I 80 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7759 (m-80) REVERT: J 32 TYR cc_start: 0.7452 (m-80) cc_final: 0.7229 (m-80) REVERT: J 92 TYR cc_start: 0.5426 (t80) cc_final: 0.5190 (t80) outliers start: 24 outliers final: 15 residues processed: 193 average time/residue: 0.4682 time to fit residues: 145.6047 Evaluate side-chains 195 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 3.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 731 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 229 LEU 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 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 731 MET Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain E residue 3 GLN 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 84 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 219 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 266 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 321 optimal weight: 0.3980 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** 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** ** H 39 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 = 0.4180 r_free = 0.4180 target = 0.124115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.086400 restraints weight = 103107.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.081778 restraints weight = 67571.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.082514 restraints weight = 80520.925| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 32814 Z= 0.125 Angle : 0.517 6.287 44790 Z= 0.265 Chirality : 0.043 0.179 5205 Planarity : 0.004 0.062 5664 Dihedral : 5.291 52.588 5679 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.86 % Allowed : 9.73 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.13), residues: 3975 helix: -0.02 (0.19), residues: 717 sheet: -0.33 (0.17), residues: 927 loop : -1.45 (0.12), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 104 HIS 0.003 0.000 HIS A1088 PHE 0.022 0.001 PHE I 80 TYR 0.028 0.001 TYR K 86 ARG 0.006 0.000 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 48) link_NAG-ASN : angle 1.71535 ( 144) link_BETA1-4 : bond 0.00280 ( 15) link_BETA1-4 : angle 1.05196 ( 45) hydrogen bonds : bond 0.03924 ( 970) hydrogen bonds : angle 5.63182 ( 2565) SS BOND : bond 0.00169 ( 45) SS BOND : angle 0.81987 ( 90) covalent geometry : bond 0.00287 (32706) covalent geometry : angle 0.50670 (44511) *********************** 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 205 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 3.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8508 (p90) cc_final: 0.7930 (p90) REVERT: A 402 ILE cc_start: 0.4393 (OUTLIER) cc_final: 0.3766 (pt) REVERT: A 505 TYR cc_start: 0.8007 (t80) cc_final: 0.7425 (t80) REVERT: A 508 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7968 (t80) REVERT: A 754 LEU cc_start: 0.9509 (tp) cc_final: 0.9092 (pp) REVERT: B 400 PHE cc_start: 0.8731 (p90) cc_final: 0.8128 (p90) REVERT: B 402 ILE cc_start: 0.4236 (OUTLIER) cc_final: 0.3339 (pt) REVERT: B 508 TYR cc_start: 0.8112 (m-80) cc_final: 0.7734 (t80) REVERT: C 37 VAL cc_start: 0.7682 (t) cc_final: 0.7453 (p) REVERT: D 377 PHE cc_start: 0.6352 (t80) cc_final: 0.5913 (t80) REVERT: D 400 PHE cc_start: 0.8707 (p90) cc_final: 0.8141 (p90) REVERT: D 754 LEU cc_start: 0.9422 (tp) cc_final: 0.8943 (pp) REVERT: E 2 MET cc_start: 0.1680 (tmm) cc_final: 0.1357 (tmm) REVERT: G 33 TYR cc_start: 0.7921 (m-10) cc_final: 0.6716 (m-10) REVERT: G 34 MET cc_start: 0.7410 (mmt) cc_final: 0.7036 (ttp) REVERT: G 39 GLN cc_start: 0.7024 (tp40) cc_final: 0.6643 (mp10) REVERT: H 80 PHE cc_start: 0.7698 (t80) cc_final: 0.7455 (t80) REVERT: I 39 GLN cc_start: 0.7089 (tp40) cc_final: 0.6536 (mp10) REVERT: I 80 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7849 (m-80) REVERT: I 90 ASP cc_start: 0.4845 (t0) cc_final: 0.3963 (m-30) REVERT: J 32 TYR cc_start: 0.7504 (m-80) cc_final: 0.7283 (m-80) REVERT: J 92 TYR cc_start: 0.5765 (t80) cc_final: 0.5440 (t80) outliers start: 29 outliers final: 10 residues processed: 188 average time/residue: 0.4553 time to fit residues: 139.5619 Evaluate side-chains 183 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 3.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 517 LEU 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 505 TYR Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain I residue 80 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 172 optimal weight: 0.8980 chunk 370 optimal weight: 30.0000 chunk 170 optimal weight: 5.9990 chunk 350 optimal weight: 0.0670 chunk 162 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 236 optimal weight: 30.0000 chunk 114 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 369 optimal weight: 30.0000 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 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 = 0.4192 r_free = 0.4192 target = 0.125549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.087781 restraints weight = 101182.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.083110 restraints weight = 71617.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.083685 restraints weight = 71392.509| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 32814 Z= 0.097 Angle : 0.490 7.664 44790 Z= 0.251 Chirality : 0.043 0.178 5205 Planarity : 0.004 0.053 5664 Dihedral : 4.937 56.347 5679 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.19 % Allowed : 10.53 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.13), residues: 3975 helix: 0.08 (0.19), residues: 735 sheet: -0.35 (0.17), residues: 942 loop : -1.36 (0.13), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 47 HIS 0.002 0.000 HIS B1088 PHE 0.018 0.001 PHE I 80 TYR 0.029 0.001 TYR K 92 ARG 0.004 0.000 ARG H 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 48) link_NAG-ASN : angle 1.63769 ( 144) link_BETA1-4 : bond 0.00334 ( 15) link_BETA1-4 : angle 0.99597 ( 45) hydrogen bonds : bond 0.03548 ( 970) hydrogen bonds : angle 5.36374 ( 2565) SS BOND : bond 0.00170 ( 45) SS BOND : angle 0.70688 ( 90) covalent geometry : bond 0.00218 (32706) covalent geometry : angle 0.48053 (44511) *********************** 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 216 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 3.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8320 (p90) cc_final: 0.7854 (p90) REVERT: A 402 ILE cc_start: 0.4485 (OUTLIER) cc_final: 0.3723 (pt) REVERT: A 505 TYR cc_start: 0.7913 (t80) cc_final: 0.7362 (t80) REVERT: A 508 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.7927 (t80) REVERT: A 754 LEU cc_start: 0.9450 (tp) cc_final: 0.9056 (pp) REVERT: B 400 PHE cc_start: 0.8611 (p90) cc_final: 0.8108 (p90) REVERT: B 402 ILE cc_start: 0.4104 (OUTLIER) cc_final: 0.3006 (pt) REVERT: B 508 TYR cc_start: 0.8037 (m-80) cc_final: 0.7726 (t80) REVERT: C 37 VAL cc_start: 0.7483 (t) cc_final: 0.7192 (p) REVERT: C 48 MET cc_start: -0.1234 (ptt) cc_final: -0.1466 (ptt) REVERT: D 377 PHE cc_start: 0.6302 (t80) cc_final: 0.5913 (t80) REVERT: D 400 PHE cc_start: 0.8434 (p90) cc_final: 0.8075 (p90) REVERT: D 483 VAL cc_start: -0.2454 (OUTLIER) cc_final: -0.2684 (m) REVERT: D 754 LEU cc_start: 0.9419 (tp) cc_final: 0.8971 (pp) REVERT: F 37 VAL cc_start: 0.7384 (t) cc_final: 0.7176 (p) REVERT: G 34 MET cc_start: 0.7322 (mmt) cc_final: 0.7027 (ttt) REVERT: G 39 GLN cc_start: 0.6874 (tp40) cc_final: 0.6585 (mp10) REVERT: H 33 TYR cc_start: 0.7088 (m-80) cc_final: 0.6841 (m-10) REVERT: H 52 ASN cc_start: 0.7426 (m110) cc_final: 0.6889 (m110) REVERT: I 39 GLN cc_start: 0.6629 (tp40) cc_final: 0.6293 (mp10) REVERT: I 80 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: I 90 ASP cc_start: 0.4664 (t0) cc_final: 0.4055 (m-30) REVERT: J 83 PHE cc_start: 0.3868 (m-80) cc_final: 0.3442 (m-80) outliers start: 40 outliers final: 20 residues processed: 199 average time/residue: 0.4251 time to fit residues: 138.7452 Evaluate side-chains 194 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE 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 738 CYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 489 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 900 MET 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 483 VAL 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 G residue 91 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain I residue 80 PHE Chi-restraints excluded: chain K residue 92 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 243 optimal weight: 9.9990 chunk 299 optimal weight: 0.3980 chunk 261 optimal weight: 5.9990 chunk 301 optimal weight: 0.7980 chunk 310 optimal weight: 8.9990 chunk 238 optimal weight: 20.0000 chunk 162 optimal weight: 0.4980 chunk 267 optimal weight: 7.9990 chunk 228 optimal weight: 2.9990 chunk 147 optimal weight: 0.3980 chunk 376 optimal weight: 50.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 965 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 = 0.4199 r_free = 0.4199 target = 0.127610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.090007 restraints weight = 99034.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.084214 restraints weight = 70945.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.084609 restraints weight = 83282.054| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 32814 Z= 0.096 Angle : 0.482 7.365 44790 Z= 0.246 Chirality : 0.042 0.176 5205 Planarity : 0.004 0.052 5664 Dihedral : 4.632 44.779 5679 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.04 % Allowed : 11.68 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.13), residues: 3975 helix: 0.26 (0.20), residues: 735 sheet: -0.33 (0.17), residues: 972 loop : -1.31 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 47 HIS 0.002 0.000 HIS A1088 PHE 0.015 0.001 PHE H 80 TYR 0.019 0.001 TYR K 92 ARG 0.003 0.000 ARG H 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 48) link_NAG-ASN : angle 1.60063 ( 144) link_BETA1-4 : bond 0.00327 ( 15) link_BETA1-4 : angle 0.98156 ( 45) hydrogen bonds : bond 0.03369 ( 970) hydrogen bonds : angle 5.20148 ( 2565) SS BOND : bond 0.00154 ( 45) SS BOND : angle 0.69216 ( 90) covalent geometry : bond 0.00218 (32706) covalent geometry : angle 0.47326 (44511) *********************** 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 211 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 3.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8474 (p90) cc_final: 0.8037 (p90) REVERT: A 402 ILE cc_start: 0.4694 (OUTLIER) cc_final: 0.3798 (pt) REVERT: A 505 TYR cc_start: 0.8148 (t80) cc_final: 0.7540 (t80) REVERT: A 508 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.8028 (t80) REVERT: A 754 LEU cc_start: 0.9453 (tp) cc_final: 0.9034 (pp) REVERT: B 400 PHE cc_start: 0.8642 (p90) cc_final: 0.8239 (p90) REVERT: B 508 TYR cc_start: 0.8250 (m-80) cc_final: 0.7860 (t80) REVERT: C 37 VAL cc_start: 0.7614 (t) cc_final: 0.7335 (p) REVERT: D 377 PHE cc_start: 0.6517 (t80) cc_final: 0.6096 (t80) REVERT: D 400 PHE cc_start: 0.8612 (p90) cc_final: 0.8285 (p90) REVERT: D 483 VAL cc_start: -0.2169 (OUTLIER) cc_final: -0.2404 (m) REVERT: D 754 LEU cc_start: 0.9419 (tp) cc_final: 0.8996 (pp) REVERT: F 37 VAL cc_start: 0.7511 (t) cc_final: 0.7283 (p) REVERT: G 34 MET cc_start: 0.7406 (mmt) cc_final: 0.7087 (ttt) REVERT: G 39 GLN cc_start: 0.7086 (tp40) cc_final: 0.6725 (mp10) REVERT: H 33 TYR cc_start: 0.7137 (m-80) cc_final: 0.6694 (m-10) REVERT: H 34 MET cc_start: 0.6765 (tpp) cc_final: 0.6447 (tpt) REVERT: H 52 ASN cc_start: 0.7426 (m110) cc_final: 0.6791 (m110) REVERT: I 39 GLN cc_start: 0.6853 (tp40) cc_final: 0.6407 (mp10) REVERT: I 80 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7718 (m-80) REVERT: I 90 ASP cc_start: 0.4810 (t0) cc_final: 0.4097 (m-30) REVERT: J 32 TYR cc_start: 0.7541 (m-80) cc_final: 0.7230 (m-80) REVERT: J 83 PHE cc_start: 0.3677 (m-80) cc_final: 0.3324 (m-80) outliers start: 35 outliers final: 22 residues processed: 196 average time/residue: 0.4334 time to fit residues: 138.6001 Evaluate side-chains 198 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 3.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 508 TYR 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 1104 VAL 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 768 THR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 2 MET 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 904 TYR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain I residue 80 PHE Chi-restraints excluded: chain I residue 121 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 197 optimal weight: 5.9990 chunk 299 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 27 optimal weight: 20.0000 chunk 77 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 67 optimal weight: 0.0030 chunk 283 optimal weight: 0.0070 chunk 152 optimal weight: 8.9990 overall best weight: 0.5008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1119 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.127580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.088652 restraints weight = 100087.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.085017 restraints weight = 65179.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.085655 restraints weight = 74589.412| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 32814 Z= 0.079 Angle : 0.470 8.757 44790 Z= 0.238 Chirality : 0.042 0.176 5205 Planarity : 0.003 0.050 5664 Dihedral : 4.352 44.420 5679 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.10 % Allowed : 12.28 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.13), residues: 3975 helix: 0.46 (0.20), residues: 735 sheet: -0.29 (0.17), residues: 990 loop : -1.26 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 47 HIS 0.001 0.000 HIS B1088 PHE 0.020 0.001 PHE A 515 TYR 0.017 0.001 TYR F 27 ARG 0.003 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 48) link_NAG-ASN : angle 1.53744 ( 144) link_BETA1-4 : bond 0.00388 ( 15) link_BETA1-4 : angle 0.92982 ( 45) hydrogen bonds : bond 0.03106 ( 970) hydrogen bonds : angle 5.01722 ( 2565) SS BOND : bond 0.00141 ( 45) SS BOND : angle 0.63096 ( 90) covalent geometry : bond 0.00171 (32706) covalent geometry : angle 0.46145 (44511) *********************** 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: 37 poor density : 183 time to evaluate : 3.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.7915 (t80) cc_final: 0.7481 (t80) REVERT: A 400 PHE cc_start: 0.8361 (p90) cc_final: 0.8046 (p90) REVERT: A 402 ILE cc_start: 0.4474 (OUTLIER) cc_final: 0.3545 (pt) REVERT: A 505 TYR cc_start: 0.8066 (t80) cc_final: 0.7453 (t80) REVERT: A 508 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7988 (t80) REVERT: A 754 LEU cc_start: 0.9419 (tp) cc_final: 0.9046 (pp) REVERT: B 400 PHE cc_start: 0.8556 (p90) cc_final: 0.8141 (p90) REVERT: B 402 ILE cc_start: 0.4393 (OUTLIER) cc_final: 0.3111 (pt) REVERT: B 508 TYR cc_start: 0.8166 (m-80) cc_final: 0.7839 (t80) REVERT: C 37 VAL cc_start: 0.7482 (t) cc_final: 0.7246 (p) REVERT: D 377 PHE cc_start: 0.6505 (OUTLIER) cc_final: 0.6086 (t80) REVERT: D 400 PHE cc_start: 0.8539 (p90) cc_final: 0.8267 (p90) REVERT: D 483 VAL cc_start: -0.2725 (OUTLIER) cc_final: -0.2932 (m) REVERT: D 508 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.7486 (t80) REVERT: D 754 LEU cc_start: 0.9388 (tp) cc_final: 0.8967 (pp) REVERT: F 2 MET cc_start: 0.2241 (tpt) cc_final: 0.1636 (tpt) REVERT: F 37 VAL cc_start: 0.7539 (t) cc_final: 0.7311 (p) REVERT: G 34 MET cc_start: 0.7443 (mmt) cc_final: 0.7118 (ttt) REVERT: G 39 GLN cc_start: 0.6933 (tp40) cc_final: 0.6633 (mp10) REVERT: H 33 TYR cc_start: 0.7096 (m-80) cc_final: 0.6813 (m-80) REVERT: H 52 ASN cc_start: 0.7327 (m110) cc_final: 0.6882 (p0) REVERT: I 39 GLN cc_start: 0.6717 (tp40) cc_final: 0.6327 (mp10) REVERT: I 80 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7697 (m-80) REVERT: I 90 ASP cc_start: 0.4650 (t0) cc_final: 0.4072 (m-30) REVERT: J 32 TYR cc_start: 0.7399 (m-80) cc_final: 0.7064 (m-80) REVERT: J 83 PHE cc_start: 0.3675 (m-80) cc_final: 0.3334 (m-80) outliers start: 37 outliers final: 22 residues processed: 204 average time/residue: 0.4520 time to fit residues: 150.5597 Evaluate side-chains 203 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 402 ILE 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 768 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 483 VAL Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 508 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 G residue 91 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 307 optimal weight: 0.7980 chunk 42 optimal weight: 0.0770 chunk 93 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 276 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 314 optimal weight: 40.0000 chunk 305 optimal weight: 7.9990 chunk 394 optimal weight: 0.0060 chunk 332 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 overall best weight: 0.5354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 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 = 0.4204 r_free = 0.4204 target = 0.126285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.089551 restraints weight = 102290.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.085063 restraints weight = 69759.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.085433 restraints weight = 78310.526| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2212 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= 0.080 Angle : 0.479 9.813 44790 Z= 0.240 Chirality : 0.042 0.174 5205 Planarity : 0.003 0.050 5664 Dihedral : 4.227 44.173 5679 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.19 % Allowed : 12.75 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.13), residues: 3975 helix: 0.57 (0.20), residues: 735 sheet: -0.33 (0.17), residues: 1023 loop : -1.17 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 47 HIS 0.001 0.000 HIS B1088 PHE 0.017 0.001 PHE A 515 TYR 0.015 0.001 TYR L 92 ARG 0.004 0.000 ARG H 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 48) link_NAG-ASN : angle 1.51904 ( 144) link_BETA1-4 : bond 0.00364 ( 15) link_BETA1-4 : angle 0.92488 ( 45) hydrogen bonds : bond 0.03046 ( 970) hydrogen bonds : angle 4.93429 ( 2565) SS BOND : bond 0.00137 ( 45) SS BOND : angle 0.60974 ( 90) covalent geometry : bond 0.00177 (32706) covalent geometry : angle 0.47063 (44511) *********************** 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 217 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 3.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.7906 (t80) cc_final: 0.7462 (t80) REVERT: A 400 PHE cc_start: 0.8410 (p90) cc_final: 0.8121 (p90) REVERT: A 402 ILE cc_start: 0.4472 (OUTLIER) cc_final: 0.3161 (pt) REVERT: A 505 TYR cc_start: 0.8066 (t80) cc_final: 0.7445 (t80) REVERT: A 508 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7983 (t80) REVERT: A 754 LEU cc_start: 0.9416 (tp) cc_final: 0.9045 (pp) REVERT: B 400 PHE cc_start: 0.8539 (p90) cc_final: 0.8259 (p90) REVERT: B 402 ILE cc_start: 0.4352 (OUTLIER) cc_final: 0.3091 (pt) REVERT: B 508 TYR cc_start: 0.8178 (m-80) cc_final: 0.7837 (t80) REVERT: C 37 VAL cc_start: 0.7479 (t) cc_final: 0.7242 (p) REVERT: D 377 PHE cc_start: 0.6507 (OUTLIER) cc_final: 0.6139 (t80) REVERT: D 400 PHE cc_start: 0.8499 (p90) cc_final: 0.8248 (p90) REVERT: D 508 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.7507 (t80) REVERT: D 754 LEU cc_start: 0.9371 (tp) cc_final: 0.8967 (pp) REVERT: F 37 VAL cc_start: 0.7555 (t) cc_final: 0.7318 (p) REVERT: G 34 MET cc_start: 0.7454 (mmt) cc_final: 0.7121 (ttt) REVERT: G 39 GLN cc_start: 0.6950 (tp40) cc_final: 0.6641 (mp10) REVERT: H 33 TYR cc_start: 0.7043 (m-80) cc_final: 0.6803 (m-80) REVERT: H 52 ASN cc_start: 0.7346 (m110) cc_final: 0.6884 (p0) REVERT: I 39 GLN cc_start: 0.6707 (tp40) cc_final: 0.6303 (mp10) REVERT: I 80 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7733 (m-80) REVERT: I 90 ASP cc_start: 0.4623 (t0) cc_final: 0.4069 (m-30) REVERT: J 32 TYR cc_start: 0.7382 (m-80) cc_final: 0.7002 (m-80) REVERT: J 83 PHE cc_start: 0.3662 (m-80) cc_final: 0.3321 (m-80) outliers start: 40 outliers final: 25 residues processed: 201 average time/residue: 0.4548 time to fit residues: 150.3526 Evaluate side-chains 204 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 402 ILE 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 B residue 1104 VAL Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 508 TYR Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain G residue 91 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 H residue 113 TYR 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 277 optimal weight: 0.7980 chunk 362 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 343 optimal weight: 0.0980 chunk 170 optimal weight: 0.5980 chunk 389 optimal weight: 20.0000 chunk 18 optimal weight: 0.3980 chunk 230 optimal weight: 0.9990 chunk 355 optimal weight: 20.0000 chunk 200 optimal weight: 50.0000 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 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 = 0.4261 r_free = 0.4261 target = 0.125220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.087498 restraints weight = 111538.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.084786 restraints weight = 66154.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.085646 restraints weight = 60855.953| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 32814 Z= 0.081 Angle : 0.475 8.410 44790 Z= 0.239 Chirality : 0.042 0.173 5205 Planarity : 0.003 0.050 5664 Dihedral : 4.122 43.945 5679 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.01 % Allowed : 13.17 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.13), residues: 3975 helix: 0.66 (0.20), residues: 735 sheet: -0.26 (0.17), residues: 1020 loop : -1.15 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 47 HIS 0.001 0.000 HIS D1088 PHE 0.014 0.001 PHE B 515 TYR 0.014 0.001 TYR L 92 ARG 0.005 0.000 ARG H 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 48) link_NAG-ASN : angle 1.49945 ( 144) link_BETA1-4 : bond 0.00379 ( 15) link_BETA1-4 : angle 0.92985 ( 45) hydrogen bonds : bond 0.02993 ( 970) hydrogen bonds : angle 4.86583 ( 2565) SS BOND : bond 0.00141 ( 45) SS BOND : angle 0.60850 ( 90) covalent geometry : bond 0.00179 (32706) covalent geometry : angle 0.46676 (44511) *********************** 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 207 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 4.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.7971 (t80) cc_final: 0.7509 (t80) REVERT: A 400 PHE cc_start: 0.8521 (p90) cc_final: 0.8178 (p90) REVERT: A 402 ILE cc_start: 0.4546 (OUTLIER) cc_final: 0.3131 (pt) REVERT: A 505 TYR cc_start: 0.8087 (t80) cc_final: 0.7452 (t80) REVERT: A 508 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7950 (t80) REVERT: A 754 LEU cc_start: 0.9429 (tp) cc_final: 0.9038 (pp) REVERT: B 400 PHE cc_start: 0.8622 (p90) cc_final: 0.8312 (p90) REVERT: B 402 ILE cc_start: 0.4271 (OUTLIER) cc_final: 0.2975 (pt) REVERT: B 508 TYR cc_start: 0.8191 (m-80) cc_final: 0.7899 (t80) REVERT: C 37 VAL cc_start: 0.7512 (t) cc_final: 0.7278 (p) REVERT: D 400 PHE cc_start: 0.8713 (p90) cc_final: 0.8398 (p90) REVERT: D 495 TYR cc_start: 0.6928 (m-10) cc_final: 0.6727 (m-10) REVERT: D 508 TYR cc_start: 0.7939 (OUTLIER) cc_final: 0.7670 (t80) REVERT: D 754 LEU cc_start: 0.9360 (tp) cc_final: 0.8949 (pp) REVERT: F 37 VAL cc_start: 0.7566 (t) cc_final: 0.7328 (p) REVERT: G 34 MET cc_start: 0.7489 (mmt) cc_final: 0.7144 (ttt) REVERT: G 39 GLN cc_start: 0.7129 (tp40) cc_final: 0.6749 (mp10) REVERT: H 33 TYR cc_start: 0.7058 (m-80) cc_final: 0.6695 (m-80) REVERT: H 34 MET cc_start: 0.6720 (tpp) cc_final: 0.6275 (tpt) REVERT: H 52 ASN cc_start: 0.7354 (m110) cc_final: 0.6868 (p0) REVERT: I 34 MET cc_start: 0.6157 (tpt) cc_final: 0.5276 (tpt) REVERT: I 39 GLN cc_start: 0.6890 (tp40) cc_final: 0.6307 (mp10) REVERT: I 80 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7668 (m-80) REVERT: I 90 ASP cc_start: 0.4448 (t0) cc_final: 0.3906 (m-30) REVERT: J 32 TYR cc_start: 0.7357 (m-80) cc_final: 0.7011 (m-80) REVERT: J 83 PHE cc_start: 0.3650 (m-80) cc_final: 0.3297 (m-80) outliers start: 34 outliers final: 27 residues processed: 192 average time/residue: 0.4576 time to fit residues: 142.5015 Evaluate side-chains 204 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 3.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 402 ILE 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 768 THR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 508 TYR Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain G residue 91 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 H residue 113 TYR 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 219 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 387 optimal weight: 9.9990 chunk 279 optimal weight: 2.9990 chunk 369 optimal weight: 0.9980 chunk 276 optimal weight: 4.9990 chunk 263 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 35 optimal weight: 30.0000 chunk 201 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1119 ASN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.129140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.097891 restraints weight = 119461.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.095268 restraints weight = 129423.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.095362 restraints weight = 113752.950| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 32814 Z= 0.194 Angle : 0.582 9.587 44790 Z= 0.294 Chirality : 0.045 0.182 5205 Planarity : 0.004 0.050 5664 Dihedral : 4.767 43.971 5679 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.83 % Allowed : 13.52 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.13), residues: 3975 helix: 0.22 (0.19), residues: 735 sheet: -0.38 (0.17), residues: 1005 loop : -1.25 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 104 HIS 0.003 0.001 HIS B1048 PHE 0.014 0.001 PHE B 515 TYR 0.022 0.001 TYR A1047 ARG 0.006 0.001 ARG H 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 48) link_NAG-ASN : angle 1.83847 ( 144) link_BETA1-4 : bond 0.00244 ( 15) link_BETA1-4 : angle 1.18384 ( 45) hydrogen bonds : bond 0.04003 ( 970) hydrogen bonds : angle 5.34848 ( 2565) SS BOND : bond 0.00190 ( 45) SS BOND : angle 0.85904 ( 90) covalent geometry : bond 0.00457 (32706) covalent geometry : angle 0.57210 (44511) ********************** 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 200 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 3.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 TYR cc_start: 0.6957 (t80) cc_final: 0.6745 (t80) REVERT: D 754 LEU cc_start: 0.9086 (tp) cc_final: 0.8858 (pp) REVERT: F 37 VAL cc_start: 0.6866 (t) cc_final: 0.6663 (p) REVERT: G 33 TYR cc_start: 0.7116 (m-10) cc_final: 0.6180 (m-10) REVERT: H 52 ASN cc_start: 0.7321 (m110) cc_final: 0.6163 (m110) REVERT: I 34 MET cc_start: 0.5070 (tpt) cc_final: 0.4564 (tpt) outliers start: 28 outliers final: 20 residues processed: 190 average time/residue: 0.4599 time to fit residues: 141.9558 Evaluate side-chains 184 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 3.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 1104 VAL 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 B residue 1104 VAL Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain G residue 91 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 381 optimal weight: 40.0000 chunk 338 optimal weight: 7.9990 chunk 195 optimal weight: 3.9990 chunk 308 optimal weight: 4.9990 chunk 201 optimal weight: 40.0000 chunk 47 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 263 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 chunk 126 optimal weight: 8.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN G 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.128886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 122)---------------| | r_work = 0.3699 r_free = 0.3699 target = 0.092121 restraints weight = 119270.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.084987 restraints weight = 91544.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.085085 restraints weight = 104475.366| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 32814 Z= 0.210 Angle : 0.597 9.280 44790 Z= 0.302 Chirality : 0.046 0.301 5205 Planarity : 0.004 0.046 5664 Dihedral : 5.045 44.129 5679 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.86 % Allowed : 14.12 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.13), residues: 3975 helix: 0.09 (0.19), residues: 735 sheet: -0.41 (0.17), residues: 984 loop : -1.38 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 104 HIS 0.003 0.001 HIS A1088 PHE 0.018 0.002 PHE D 374 TYR 0.018 0.001 TYR A1047 ARG 0.007 0.001 ARG G 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 48) link_NAG-ASN : angle 1.87947 ( 144) link_BETA1-4 : bond 0.00251 ( 15) link_BETA1-4 : angle 1.15978 ( 45) hydrogen bonds : bond 0.04000 ( 970) hydrogen bonds : angle 5.42561 ( 2565) SS BOND : bond 0.00191 ( 45) SS BOND : angle 0.86216 ( 90) covalent geometry : bond 0.00492 (32706) covalent geometry : angle 0.58663 (44511) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10291.57 seconds wall clock time: 183 minutes 19.04 seconds (10999.04 seconds total)