Starting phenix.real_space_refine on Mon May 26 21:04:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g75_29797/05_2025/8g75_29797.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g75_29797/05_2025/8g75_29797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g75_29797/05_2025/8g75_29797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g75_29797/05_2025/8g75_29797.map" model { file = "/net/cci-nas-00/data/ceres_data/8g75_29797/05_2025/8g75_29797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g75_29797/05_2025/8g75_29797.cif" } resolution = 3.4 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= 0.001 sd= 0.024 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 129 5.16 5 C 18226 2.51 5 N 4748 2.21 5 O 5608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.93s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28711 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 8367 Classifications: {'peptide': 1071} Link IDs: {'PTRANS': 57, 'TRANS': 1013} Chain breaks: 4 Chain: "B" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8382 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "D" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8382 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "E" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "G" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "F" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 17.61, per 1000 atoms: 0.61 Number of scatterers: 28711 At special positions: 0 Unit cell: (156.704, 164.672, 196.544, 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 129 16.00 O 5608 8.00 N 4748 7.00 C 18226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 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 662 " - pdb=" SG CYS A 671 " 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 15 " - pdb=" SG CYS B 136 " 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 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " 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=2.02 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " 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 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 662 " - pdb=" SG CYS D 671 " 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=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 234 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 717 " " NAG B1310 " - " ASN B1074 " " NAG C 1 " - " ASN A 801 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 282 " " NAG D1303 " - " ASN D 616 " " NAG D1304 " - " ASN D 657 " " NAG D1305 " - " ASN D 709 " " NAG D1306 " - " ASN D1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN D 717 " " NAG O 1 " - " ASN D 801 " " NAG P 1 " - " ASN D1098 " " NAG Q 1 " - " ASN D1134 " Time building additional restraints: 7.40 Conformation dependent library (CDL) restraints added in 3.4 seconds 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6692 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 56 sheets defined 22.5% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.40 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.165A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.810A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.824A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.569A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 759 removed outlier: 6.940A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.578A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.507A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.540A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.595A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.501A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (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 982 removed outlier: 3.871A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.807A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.032A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.704A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.787A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.315A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.742A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (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: 3.649A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.748A 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) Processing helix chain 'B' and resid 1140 through 1147 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 removed outlier: 3.546A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 372 removed outlier: 3.778A pdb=" N ALA D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 removed outlier: 3.614A pdb=" N LYS D 386 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 383 through 387' Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.783A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 744 removed outlier: 3.600A pdb=" N ILE D 742 " --> pdb=" O CYS D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.629A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 825 Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 886 through 891 Processing helix chain 'D' and resid 897 through 909 removed outlier: 3.749A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 919 removed outlier: 4.339A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.701A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.536A 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 977 through 982 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.441A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1147 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.922A pdb=" N TYR E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.717A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.952A pdb=" N TYR F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR F 32 " --> pdb=" O LEU F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.616A pdb=" N LYS F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.216A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.738A pdb=" N ARG D 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY D 566 " --> pdb=" O ASP D 574 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.780A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 68 through 70 removed outlier: 3.782A pdb=" N ARG A 78 " --> pdb=" O HIS A 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.587A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.662A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.852A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.405A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 355 through 358 removed outlier: 4.164A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.573A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.512A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.552A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.647A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.367A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.350A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.006A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.765A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 68 through 70 removed outlier: 3.682A pdb=" N ARG B 78 " --> pdb=" O HIS B 69 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.654A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.773A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.975A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 326 through 328 removed outlier: 3.883A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE B 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.635A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.526A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.020A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.652A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.653A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.389A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.478A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 28 through 30 removed outlier: 7.990A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.741A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 68 through 69 removed outlier: 3.588A pdb=" N ARG D 78 " --> pdb=" O HIS D 69 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 84 through 85 removed outlier: 12.725A pdb=" N PHE D 135 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 12.622A pdb=" N THR D 240 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 10.689A pdb=" N ASN D 137 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 10.188A pdb=" N LEU D 242 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LEU D 244 " --> pdb=" O PRO D 139 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU D 141 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 10.148A pdb=" N ASP D 138 " --> pdb=" O TYR D 160 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N TYR D 160 " --> pdb=" O ASP D 138 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE D 140 " --> pdb=" O ARG D 158 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.594A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER D 172 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL D 130 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 3.815A 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 318 removed outlier: 5.206A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY D 593 " --> pdb=" O PHE D 318 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS D 649 " --> pdb=" O TYR D 612 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE D 643 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 356 through 358 Processing sheet with id=AE4, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.681A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 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 removed outlier: 3.680A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.644A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 711 through 715 removed outlier: 4.145A pdb=" N THR D1076 " --> pdb=" O SER D1097 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA D1078 " --> pdb=" O PHE D1095 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 718 through 728 removed outlier: 3.625A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.330A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.296A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AF4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.394A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG E 38 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLY E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.394A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AF7, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.737A pdb=" N VAL G 93 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ARG G 38 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLY G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AF9, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.562A pdb=" N SER F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG F 38 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLY F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 10 through 12 1153 hydrogen bonds defined for protein. 3090 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: 13.37 Time building geometry restraints manager: 8.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8742 1.34 - 1.46: 7711 1.46 - 1.59: 12759 1.59 - 1.72: 0 1.72 - 1.85: 162 Bond restraints: 29374 Sorted by residual: bond pdb=" N ARG A 577 " pdb=" CA ARG A 577 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.18e-02 7.18e+03 1.00e+01 bond pdb=" C1 NAG D1303 " pdb=" O5 NAG D1303 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.69e+00 bond pdb=" N VAL B 320 " pdb=" CA VAL B 320 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 9.14e+00 bond pdb=" N LYS B 811 " pdb=" CA LYS B 811 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.04e-02 9.25e+03 8.75e+00 bond pdb=" N VAL B1104 " pdb=" CA VAL B1104 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.19e-02 7.06e+03 7.10e+00 ... (remaining 29369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 39192 2.28 - 4.55: 703 4.55 - 6.83: 58 6.83 - 9.11: 17 9.11 - 11.39: 6 Bond angle restraints: 39976 Sorted by residual: angle pdb=" CA PRO B1143 " pdb=" N PRO B1143 " pdb=" CD PRO B1143 " ideal model delta sigma weight residual 112.00 103.38 8.62 1.40e+00 5.10e-01 3.79e+01 angle pdb=" CA TRP D 436 " pdb=" CB TRP D 436 " pdb=" CG TRP D 436 " ideal model delta sigma weight residual 113.60 122.91 -9.31 1.90e+00 2.77e-01 2.40e+01 angle pdb=" CA CYS A 760 " pdb=" CB CYS A 760 " pdb=" SG CYS A 760 " ideal model delta sigma weight residual 114.40 123.35 -8.95 2.30e+00 1.89e-01 1.51e+01 angle pdb=" N GLY A 485 " pdb=" CA GLY A 485 " pdb=" C GLY A 485 " ideal model delta sigma weight residual 113.18 122.26 -9.08 2.37e+00 1.78e-01 1.47e+01 angle pdb=" C TRP E 104 " pdb=" N TYR E 105 " pdb=" CA TYR E 105 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 ... (remaining 39971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 15958 17.94 - 35.89: 1582 35.89 - 53.83: 431 53.83 - 71.77: 66 71.77 - 89.72: 33 Dihedral angle restraints: 18070 sinusoidal: 7636 harmonic: 10434 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 7.59 85.41 1 1.00e+01 1.00e-02 8.83e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 170.19 -77.19 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -162.99 76.99 1 1.00e+01 1.00e-02 7.44e+01 ... (remaining 18067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 4537 0.126 - 0.251: 71 0.251 - 0.377: 9 0.377 - 0.503: 0 0.503 - 0.628: 2 Chirality restraints: 4619 Sorted by residual: chirality pdb=" C1 NAG D1302 " pdb=" ND2 ASN D 282 " pdb=" C2 NAG D1302 " pdb=" O5 NAG D1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.87e+00 chirality pdb=" C1 NAG D1303 " pdb=" ND2 ASN D 616 " pdb=" C2 NAG D1303 " pdb=" O5 NAG D1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.96 0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.72 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 4616 not shown) Planarity restraints: 5169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1309 " -0.062 2.00e-02 2.50e+03 5.11e-02 3.27e+01 pdb=" C7 NAG A1309 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG A1309 " -0.046 2.00e-02 2.50e+03 pdb=" N2 NAG A1309 " 0.082 2.00e-02 2.50e+03 pdb=" O7 NAG A1309 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B1142 " 0.060 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO B1143 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO B1143 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B1143 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 400 " 0.030 2.00e-02 2.50e+03 2.60e-02 1.19e+01 pdb=" CG PHE D 400 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE D 400 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE D 400 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 400 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE D 400 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE D 400 " 0.008 2.00e-02 2.50e+03 ... (remaining 5166 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 230 2.59 - 3.17: 23753 3.17 - 3.75: 43519 3.75 - 4.32: 60537 4.32 - 4.90: 99210 Nonbonded interactions: 227249 Sorted by model distance: nonbonded pdb=" NZ LYS A 417 " pdb=" OH TYR A 495 " model vdw 2.017 3.120 nonbonded pdb=" OG1 THR D 323 " pdb=" OE1 GLU D 324 " model vdw 2.102 3.040 nonbonded pdb=" O SER G 52 " pdb=" NH2 ARG G 72 " model vdw 2.105 3.120 nonbonded pdb=" OD1 ASN B 616 " pdb=" N CYS B 617 " model vdw 2.110 3.120 nonbonded pdb=" OH TYR B 37 " pdb=" OD1 ASP B 53 " model vdw 2.116 3.040 ... (remaining 227244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 1147 or resid 1301 through 1306)) selection = (chain 'B' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147 or resid 1301 through 1306)) selection = (chain 'D' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147 or resid 1301 through 1306)) } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.120 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 65.910 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 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 0.062 29463 Z= 0.206 Angle : 0.752 20.858 40201 Z= 0.377 Chirality : 0.050 0.628 4619 Planarity : 0.006 0.096 5133 Dihedral : 15.318 89.718 11252 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.37 % Favored : 96.49 % Rotamer: Outliers : 0.61 % Allowed : 19.09 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.13), residues: 3562 helix: 0.95 (0.20), residues: 687 sheet: 0.47 (0.17), residues: 811 loop : -0.87 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 104 HIS 0.006 0.001 HIS A 655 PHE 0.058 0.002 PHE D 400 TYR 0.049 0.002 TYR A 453 ARG 0.011 0.001 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00859 ( 36) link_NAG-ASN : angle 5.33529 ( 108) link_BETA1-4 : bond 0.00378 ( 11) link_BETA1-4 : angle 1.58501 ( 33) hydrogen bonds : bond 0.23665 ( 1129) hydrogen bonds : angle 8.52813 ( 3090) SS BOND : bond 0.00364 ( 42) SS BOND : angle 1.39840 ( 84) covalent geometry : bond 0.00408 (29374) covalent geometry : angle 0.69735 (39976) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 220 time to evaluate : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.6198 (p0) cc_final: 0.5973 (p0) REVERT: A 821 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8273 (tm) REVERT: B 900 MET cc_start: 0.8477 (ttm) cc_final: 0.8255 (mtm) REVERT: D 153 MET cc_start: 0.0085 (ptp) cc_final: -0.1163 (pmm) REVERT: D 602 THR cc_start: 0.7495 (p) cc_final: 0.7288 (p) outliers start: 19 outliers final: 8 residues processed: 233 average time/residue: 0.3581 time to fit residues: 140.2928 Evaluate side-chains 208 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 199 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 616 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 4.9990 chunk 270 optimal weight: 2.9990 chunk 150 optimal weight: 50.0000 chunk 92 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 144 optimal weight: 30.0000 chunk 279 optimal weight: 6.9990 chunk 108 optimal weight: 0.0970 chunk 170 optimal weight: 0.1980 chunk 208 optimal weight: 2.9990 chunk 324 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 856 ASN A 926 GLN A 935 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.228277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.181970 restraints weight = 45051.817| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 3.92 r_work: 0.3745 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 29463 Z= 0.199 Angle : 0.724 21.521 40201 Z= 0.365 Chirality : 0.049 0.540 4619 Planarity : 0.005 0.085 5133 Dihedral : 6.379 58.577 4874 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.59 % Favored : 96.29 % Rotamer: Outliers : 2.65 % Allowed : 16.82 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.13), residues: 3562 helix: 1.60 (0.20), residues: 676 sheet: 0.31 (0.17), residues: 834 loop : -1.09 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 436 HIS 0.006 0.001 HIS B1064 PHE 0.034 0.002 PHE D 400 TYR 0.028 0.002 TYR A 351 ARG 0.007 0.001 ARG D 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00919 ( 36) link_NAG-ASN : angle 4.48760 ( 108) link_BETA1-4 : bond 0.00308 ( 11) link_BETA1-4 : angle 1.21422 ( 33) hydrogen bonds : bond 0.05812 ( 1129) hydrogen bonds : angle 6.13788 ( 3090) SS BOND : bond 0.00544 ( 42) SS BOND : angle 1.55114 ( 84) covalent geometry : bond 0.00454 (29374) covalent geometry : angle 0.68280 (39976) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 217 time to evaluate : 3.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1470 (OUTLIER) cc_final: -0.0217 (mmm) REVERT: B 153 MET cc_start: 0.3200 (tpt) cc_final: 0.0105 (ptp) REVERT: B 269 TYR cc_start: 0.7813 (m-10) cc_final: 0.7598 (m-10) REVERT: B 1081 ILE cc_start: 0.8508 (mt) cc_final: 0.8173 (mt) REVERT: D 153 MET cc_start: -0.0028 (ptp) cc_final: -0.1473 (pmm) REVERT: D 822 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8694 (mm) REVERT: D 950 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8069 (t0) REVERT: D 967 SER cc_start: 0.8976 (OUTLIER) cc_final: 0.8747 (m) REVERT: D 985 ASP cc_start: 0.6790 (t0) cc_final: 0.6445 (m-30) REVERT: E 125 VAL cc_start: 0.1562 (OUTLIER) cc_final: 0.1243 (t) outliers start: 83 outliers final: 32 residues processed: 283 average time/residue: 0.3409 time to fit residues: 164.0110 Evaluate side-chains 215 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 950 ASP Chi-restraints excluded: chain D residue 967 SER Chi-restraints excluded: chain D residue 1037 SER Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain G residue 94 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 302 optimal weight: 4.9990 chunk 291 optimal weight: 0.0470 chunk 342 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 273 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 138 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 chunk 330 optimal weight: 10.0000 chunk 308 optimal weight: 1.9990 chunk 266 optimal weight: 0.7980 overall best weight: 1.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 784 GLN D 935 GLN ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.218849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.170901 restraints weight = 43697.251| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 3.92 r_work: 0.3669 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29463 Z= 0.151 Angle : 0.624 21.154 40201 Z= 0.315 Chirality : 0.046 0.481 4619 Planarity : 0.005 0.055 5133 Dihedral : 5.388 55.451 4863 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.00 % Favored : 96.88 % Rotamer: Outliers : 2.49 % Allowed : 17.30 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.14), residues: 3562 helix: 1.89 (0.20), residues: 700 sheet: 0.44 (0.17), residues: 803 loop : -1.08 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 436 HIS 0.011 0.001 HIS D1083 PHE 0.048 0.002 PHE D 400 TYR 0.029 0.001 TYR A 351 ARG 0.009 0.001 ARG D 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00736 ( 36) link_NAG-ASN : angle 3.82608 ( 108) link_BETA1-4 : bond 0.00324 ( 11) link_BETA1-4 : angle 1.23863 ( 33) hydrogen bonds : bond 0.05507 ( 1129) hydrogen bonds : angle 5.71757 ( 3090) SS BOND : bond 0.00512 ( 42) SS BOND : angle 1.15868 ( 84) covalent geometry : bond 0.00344 (29374) covalent geometry : angle 0.59014 (39976) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 211 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.7490 (tp40) cc_final: 0.7073 (tp40) REVERT: A 351 TYR cc_start: 0.6020 (t80) cc_final: 0.4710 (t80) REVERT: A 753 LEU cc_start: 0.7271 (tp) cc_final: 0.6887 (tp) REVERT: A 983 ARG cc_start: 0.6495 (tpt90) cc_final: 0.6190 (tmm-80) REVERT: B 160 TYR cc_start: 0.6857 (p90) cc_final: 0.6461 (p90) REVERT: B 269 TYR cc_start: 0.7859 (m-10) cc_final: 0.7621 (m-10) REVERT: B 1081 ILE cc_start: 0.8684 (mt) cc_final: 0.8440 (mt) REVERT: D 153 MET cc_start: -0.0352 (ptp) cc_final: -0.1530 (pmm) REVERT: D 200 TYR cc_start: 0.6371 (m-80) cc_final: 0.6110 (m-80) REVERT: D 565 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7425 (m-80) REVERT: D 786 LYS cc_start: 0.7527 (pttm) cc_final: 0.7000 (mmtp) REVERT: D 985 ASP cc_start: 0.7176 (t0) cc_final: 0.6925 (m-30) outliers start: 78 outliers final: 38 residues processed: 275 average time/residue: 0.3329 time to fit residues: 154.2947 Evaluate side-chains 217 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 83 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 82 optimal weight: 0.5980 chunk 124 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 353 optimal weight: 20.0000 chunk 348 optimal weight: 0.9990 chunk 277 optimal weight: 2.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 99 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN D 99 ASN D 437 ASN ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.215113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.165738 restraints weight = 43121.178| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 4.29 r_work: 0.3597 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29463 Z= 0.154 Angle : 0.633 20.870 40201 Z= 0.319 Chirality : 0.047 0.454 4619 Planarity : 0.005 0.056 5133 Dihedral : 5.195 56.905 4862 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.62 % Favored : 96.27 % Rotamer: Outliers : 3.49 % Allowed : 16.98 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.14), residues: 3562 helix: 1.99 (0.20), residues: 693 sheet: 0.37 (0.17), residues: 803 loop : -1.08 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 436 HIS 0.005 0.001 HIS D1083 PHE 0.048 0.002 PHE D 400 TYR 0.025 0.002 TYR D1138 ARG 0.015 0.001 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00771 ( 36) link_NAG-ASN : angle 3.69914 ( 108) link_BETA1-4 : bond 0.00271 ( 11) link_BETA1-4 : angle 1.30143 ( 33) hydrogen bonds : bond 0.04742 ( 1129) hydrogen bonds : angle 5.43737 ( 3090) SS BOND : bond 0.00432 ( 42) SS BOND : angle 1.47152 ( 84) covalent geometry : bond 0.00350 (29374) covalent geometry : angle 0.60008 (39976) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 185 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.7088 (m-80) cc_final: 0.6825 (m-80) REVERT: A 753 LEU cc_start: 0.7669 (tp) cc_final: 0.7377 (tp) REVERT: A 921 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8377 (mttt) REVERT: A 983 ARG cc_start: 0.6714 (tpt90) cc_final: 0.6490 (ttt180) REVERT: B 160 TYR cc_start: 0.6835 (p90) cc_final: 0.6382 (p90) REVERT: B 269 TYR cc_start: 0.7943 (m-10) cc_final: 0.7381 (m-10) REVERT: B 978 ASN cc_start: 0.8272 (m-40) cc_final: 0.7971 (m-40) REVERT: D 153 MET cc_start: -0.0566 (ptp) cc_final: -0.1569 (pmm) REVERT: D 200 TYR cc_start: 0.6629 (m-80) cc_final: 0.6336 (m-80) REVERT: D 565 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.7404 (m-80) REVERT: D 823 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7554 (m-80) REVERT: D 984 LEU cc_start: 0.7709 (mm) cc_final: 0.7486 (mp) REVERT: D 985 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7190 (m-30) REVERT: E 125 VAL cc_start: 0.0785 (OUTLIER) cc_final: 0.0461 (t) REVERT: G 83 MET cc_start: 0.0031 (mpp) cc_final: -0.0790 (tpt) outliers start: 109 outliers final: 58 residues processed: 276 average time/residue: 0.3602 time to fit residues: 166.9553 Evaluate side-chains 226 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 163 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 949 GLN Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 94 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 95 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 244 optimal weight: 3.9990 chunk 246 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 334 optimal weight: 8.9990 chunk 249 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 301 optimal weight: 0.6980 chunk 103 optimal weight: 0.2980 chunk 104 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 935 GLN D 954 GLN ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.209447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.159405 restraints weight = 42620.777| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.76 r_work: 0.3640 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 29463 Z= 0.166 Angle : 0.631 20.637 40201 Z= 0.317 Chirality : 0.046 0.429 4619 Planarity : 0.005 0.055 5133 Dihedral : 5.215 59.562 4862 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.40 % Favored : 96.55 % Rotamer: Outliers : 3.01 % Allowed : 18.04 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.14), residues: 3562 helix: 2.01 (0.20), residues: 693 sheet: 0.47 (0.17), residues: 833 loop : -1.06 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 436 HIS 0.006 0.001 HIS D1083 PHE 0.034 0.002 PHE D 400 TYR 0.026 0.001 TYR A 351 ARG 0.008 0.001 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00660 ( 36) link_NAG-ASN : angle 3.52420 ( 108) link_BETA1-4 : bond 0.00303 ( 11) link_BETA1-4 : angle 1.16142 ( 33) hydrogen bonds : bond 0.05278 ( 1129) hydrogen bonds : angle 5.41259 ( 3090) SS BOND : bond 0.00348 ( 42) SS BOND : angle 1.30833 ( 84) covalent geometry : bond 0.00393 (29374) covalent geometry : angle 0.60186 (39976) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 178 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.7257 (tp40) cc_final: 0.6365 (mm-40) REVERT: A 338 PHE cc_start: 0.7193 (m-80) cc_final: 0.6888 (m-80) REVERT: A 484 GLU cc_start: 0.3432 (OUTLIER) cc_final: 0.2785 (tp30) REVERT: A 584 ILE cc_start: 0.7164 (OUTLIER) cc_final: 0.6922 (pp) REVERT: A 753 LEU cc_start: 0.8200 (tp) cc_final: 0.7976 (tp) REVERT: A 960 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7823 (m-40) REVERT: A 984 LEU cc_start: 0.6171 (mt) cc_final: 0.5774 (mt) REVERT: A 1138 TYR cc_start: 0.7777 (t80) cc_final: 0.7554 (t80) REVERT: B 131 CYS cc_start: 0.1769 (OUTLIER) cc_final: 0.1503 (m) REVERT: B 160 TYR cc_start: 0.6562 (p90) cc_final: 0.6159 (p90) REVERT: B 269 TYR cc_start: 0.8027 (m-10) cc_final: 0.7591 (m-10) REVERT: D 153 MET cc_start: -0.0564 (ptp) cc_final: -0.1091 (pmm) REVERT: D 200 TYR cc_start: 0.6535 (m-80) cc_final: 0.6313 (m-80) REVERT: D 565 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.7179 (m-80) REVERT: D 823 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7603 (m-80) REVERT: D 900 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8251 (mtt) REVERT: G 83 MET cc_start: -0.0350 (mpp) cc_final: -0.1037 (tpt) outliers start: 94 outliers final: 56 residues processed: 255 average time/residue: 0.3337 time to fit residues: 143.9692 Evaluate side-chains 218 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 155 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 1037 SER Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 114 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 329 optimal weight: 5.9990 chunk 140 optimal weight: 20.0000 chunk 136 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 183 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 300 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 690 GLN B 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 GLN ** D1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1083 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.209441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.159210 restraints weight = 42615.879| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.79 r_work: 0.3624 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29463 Z= 0.136 Angle : 0.598 20.393 40201 Z= 0.299 Chirality : 0.046 0.438 4619 Planarity : 0.004 0.057 5133 Dihedral : 4.985 56.049 4860 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 2.94 % Allowed : 18.36 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.04 (0.14), residues: 3562 helix: 2.20 (0.21), residues: 680 sheet: 0.40 (0.17), residues: 833 loop : -1.03 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 436 HIS 0.011 0.001 HIS D1083 PHE 0.026 0.001 PHE D 400 TYR 0.022 0.001 TYR B 674 ARG 0.004 0.000 ARG G 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00666 ( 36) link_NAG-ASN : angle 3.47489 ( 108) link_BETA1-4 : bond 0.00282 ( 11) link_BETA1-4 : angle 1.18942 ( 33) hydrogen bonds : bond 0.04610 ( 1129) hydrogen bonds : angle 5.29189 ( 3090) SS BOND : bond 0.00286 ( 42) SS BOND : angle 1.54810 ( 84) covalent geometry : bond 0.00320 (29374) covalent geometry : angle 0.56645 (39976) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 170 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 VAL cc_start: 0.6757 (OUTLIER) cc_final: 0.6543 (p) REVERT: A 134 GLN cc_start: 0.7334 (tp40) cc_final: 0.7128 (tp40) REVERT: A 403 ARG cc_start: 0.5970 (mtm110) cc_final: 0.5364 (mtm110) REVERT: A 484 GLU cc_start: 0.3451 (OUTLIER) cc_final: 0.2789 (tp30) REVERT: A 584 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7108 (pp) REVERT: A 752 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8227 (mp) REVERT: A 753 LEU cc_start: 0.8264 (tp) cc_final: 0.8062 (tp) REVERT: A 921 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8364 (mttt) REVERT: A 960 ASN cc_start: 0.8210 (t0) cc_final: 0.7861 (m-40) REVERT: A 1138 TYR cc_start: 0.7684 (t80) cc_final: 0.7466 (t80) REVERT: B 131 CYS cc_start: 0.1869 (OUTLIER) cc_final: 0.1514 (m) REVERT: B 160 TYR cc_start: 0.6648 (p90) cc_final: 0.6234 (p90) REVERT: B 210 ILE cc_start: 0.6806 (OUTLIER) cc_final: 0.6522 (tp) REVERT: B 269 TYR cc_start: 0.8004 (m-10) cc_final: 0.7698 (m-10) REVERT: D 153 MET cc_start: -0.0809 (ptp) cc_final: -0.1238 (pmm) REVERT: D 200 TYR cc_start: 0.6573 (m-80) cc_final: 0.6309 (m-80) REVERT: D 565 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.7089 (m-80) REVERT: D 673 SER cc_start: 0.8538 (p) cc_final: 0.8064 (m) REVERT: D 786 LYS cc_start: 0.7707 (pttm) cc_final: 0.7029 (mmtp) REVERT: D 823 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7671 (m-80) REVERT: D 900 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8259 (mtt) outliers start: 92 outliers final: 61 residues processed: 240 average time/residue: 0.3381 time to fit residues: 137.2718 Evaluate side-chains 227 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 156 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 423 TYR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 661 GLU Chi-restraints excluded: chain D residue 784 GLN Chi-restraints excluded: chain D residue 804 GLN Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 949 GLN Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 221 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 141 optimal weight: 30.0000 chunk 17 optimal weight: 5.9990 chunk 35 optimal weight: 0.3980 chunk 23 optimal weight: 40.0000 chunk 109 optimal weight: 4.9990 chunk 46 optimal weight: 30.0000 chunk 30 optimal weight: 6.9990 chunk 283 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN D 655 HIS D 949 GLN D 954 GLN E 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.199922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.128999 restraints weight = 42341.470| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 3.24 r_work: 0.3354 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 29463 Z= 0.347 Angle : 0.817 21.382 40201 Z= 0.415 Chirality : 0.053 0.490 4619 Planarity : 0.006 0.062 5133 Dihedral : 6.014 56.278 4860 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.50 % Favored : 94.44 % Rotamer: Outliers : 3.74 % Allowed : 17.78 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.64 (0.14), residues: 3562 helix: 1.33 (0.20), residues: 671 sheet: 0.11 (0.16), residues: 899 loop : -1.34 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 436 HIS 0.010 0.002 HIS A1058 PHE 0.025 0.003 PHE B 92 TYR 0.027 0.002 TYR B 279 ARG 0.007 0.001 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00958 ( 36) link_NAG-ASN : angle 4.02767 ( 108) link_BETA1-4 : bond 0.00470 ( 11) link_BETA1-4 : angle 1.55494 ( 33) hydrogen bonds : bond 0.07405 ( 1129) hydrogen bonds : angle 5.88176 ( 3090) SS BOND : bond 0.00453 ( 42) SS BOND : angle 2.04681 ( 84) covalent geometry : bond 0.00836 (29374) covalent geometry : angle 0.78551 (39976) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 156 time to evaluate : 2.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.7364 (tp40) cc_final: 0.7053 (tp40) REVERT: A 200 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.7550 (t80) REVERT: A 239 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.7136 (tt0) REVERT: A 347 PHE cc_start: 0.6179 (m-80) cc_final: 0.5809 (m-80) REVERT: A 484 GLU cc_start: 0.3205 (OUTLIER) cc_final: 0.2749 (tp30) REVERT: A 787 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: A 1138 TYR cc_start: 0.7925 (t80) cc_final: 0.7723 (t80) REVERT: B 131 CYS cc_start: 0.2138 (OUTLIER) cc_final: 0.1680 (m) REVERT: B 160 TYR cc_start: 0.6910 (p90) cc_final: 0.6309 (p90) REVERT: B 200 TYR cc_start: 0.6535 (OUTLIER) cc_final: 0.6296 (t80) REVERT: B 210 ILE cc_start: 0.7127 (OUTLIER) cc_final: 0.6784 (tp) REVERT: B 269 TYR cc_start: 0.8430 (m-10) cc_final: 0.7960 (m-10) REVERT: B 369 TYR cc_start: 0.0465 (OUTLIER) cc_final: 0.0155 (m-80) REVERT: B 1138 TYR cc_start: 0.7581 (t80) cc_final: 0.6981 (m-80) REVERT: D 153 MET cc_start: -0.0860 (ptp) cc_final: -0.1377 (pmm) REVERT: D 565 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7420 (m-80) REVERT: D 673 SER cc_start: 0.8814 (p) cc_final: 0.8320 (m) REVERT: D 900 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8652 (mtm) REVERT: F 100 GLU cc_start: 0.2023 (OUTLIER) cc_final: -0.0161 (mp0) outliers start: 117 outliers final: 65 residues processed: 255 average time/residue: 0.3496 time to fit residues: 149.8547 Evaluate side-chains 219 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 143 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 661 GLU Chi-restraints excluded: chain D residue 784 GLN Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 100 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 107 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 219 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 222 optimal weight: 0.3980 chunk 108 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 chunk 267 optimal weight: 0.9990 chunk 250 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B 52 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.206422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.153305 restraints weight = 42680.916| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.73 r_work: 0.3596 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29463 Z= 0.121 Angle : 0.614 20.064 40201 Z= 0.309 Chirality : 0.046 0.474 4619 Planarity : 0.005 0.059 5133 Dihedral : 5.272 55.790 4860 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 2.24 % Allowed : 19.03 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.14), residues: 3562 helix: 2.11 (0.21), residues: 667 sheet: 0.21 (0.17), residues: 846 loop : -1.12 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 104 HIS 0.010 0.001 HIS D1083 PHE 0.023 0.002 PHE B 490 TYR 0.024 0.001 TYR D1138 ARG 0.005 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00664 ( 36) link_NAG-ASN : angle 3.47964 ( 108) link_BETA1-4 : bond 0.00359 ( 11) link_BETA1-4 : angle 1.20253 ( 33) hydrogen bonds : bond 0.04708 ( 1129) hydrogen bonds : angle 5.34254 ( 3090) SS BOND : bond 0.00484 ( 42) SS BOND : angle 2.07644 ( 84) covalent geometry : bond 0.00270 (29374) covalent geometry : angle 0.57932 (39976) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 162 time to evaluate : 3.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 VAL cc_start: 0.7059 (OUTLIER) cc_final: 0.6853 (p) REVERT: A 200 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.7342 (t80) REVERT: A 484 GLU cc_start: 0.3522 (OUTLIER) cc_final: 0.2973 (tp30) REVERT: A 921 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8322 (mttt) REVERT: B 131 CYS cc_start: 0.1902 (OUTLIER) cc_final: 0.1519 (m) REVERT: B 160 TYR cc_start: 0.6542 (p90) cc_final: 0.6068 (p90) REVERT: B 210 ILE cc_start: 0.7113 (OUTLIER) cc_final: 0.6783 (tp) REVERT: B 269 TYR cc_start: 0.8130 (m-10) cc_final: 0.7830 (m-80) REVERT: B 369 TYR cc_start: 0.0600 (OUTLIER) cc_final: 0.0324 (m-80) REVERT: D 200 TYR cc_start: 0.6677 (m-80) cc_final: 0.6346 (m-80) REVERT: D 265 TYR cc_start: 0.7140 (p90) cc_final: 0.6826 (p90) REVERT: D 673 SER cc_start: 0.8519 (p) cc_final: 0.8120 (m) REVERT: D 900 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8329 (mtp) outliers start: 70 outliers final: 47 residues processed: 217 average time/residue: 0.3591 time to fit residues: 133.4221 Evaluate side-chains 201 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 146 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 661 GLU Chi-restraints excluded: chain D residue 784 GLN Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 94 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 190 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 140 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 690 GLN B 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN D 901 GLN D 954 GLN ** D1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.202123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.130253 restraints weight = 42378.334| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 3.44 r_work: 0.3418 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 29463 Z= 0.194 Angle : 0.663 20.176 40201 Z= 0.333 Chirality : 0.047 0.476 4619 Planarity : 0.005 0.061 5133 Dihedral : 5.323 56.509 4860 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.86 % Favored : 95.09 % Rotamer: Outliers : 2.33 % Allowed : 19.12 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.14), residues: 3562 helix: 1.98 (0.20), residues: 667 sheet: 0.30 (0.17), residues: 857 loop : -1.19 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 436 HIS 0.008 0.002 HIS D1083 PHE 0.020 0.002 PHE B 490 TYR 0.025 0.001 TYR A1138 ARG 0.006 0.001 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00680 ( 36) link_NAG-ASN : angle 3.58709 ( 108) link_BETA1-4 : bond 0.00306 ( 11) link_BETA1-4 : angle 1.27305 ( 33) hydrogen bonds : bond 0.05564 ( 1129) hydrogen bonds : angle 5.42619 ( 3090) SS BOND : bond 0.00346 ( 42) SS BOND : angle 2.24313 ( 84) covalent geometry : bond 0.00470 (29374) covalent geometry : angle 0.62907 (39976) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 146 time to evaluate : 3.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.7226 (tp40) cc_final: 0.6157 (mm-40) REVERT: A 200 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.7612 (t80) REVERT: A 484 GLU cc_start: 0.3559 (OUTLIER) cc_final: 0.3152 (tp30) REVERT: A 921 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8577 (mttt) REVERT: B 131 CYS cc_start: 0.2163 (OUTLIER) cc_final: 0.1696 (m) REVERT: B 160 TYR cc_start: 0.6895 (p90) cc_final: 0.6336 (p90) REVERT: B 210 ILE cc_start: 0.7079 (OUTLIER) cc_final: 0.6728 (tp) REVERT: B 269 TYR cc_start: 0.8361 (m-10) cc_final: 0.8067 (m-10) REVERT: B 369 TYR cc_start: 0.0573 (OUTLIER) cc_final: 0.0269 (m-80) REVERT: D 200 TYR cc_start: 0.7112 (m-80) cc_final: 0.6611 (m-80) REVERT: D 265 TYR cc_start: 0.7050 (p90) cc_final: 0.6717 (p90) REVERT: D 673 SER cc_start: 0.8738 (p) cc_final: 0.8222 (m) outliers start: 73 outliers final: 57 residues processed: 209 average time/residue: 0.3728 time to fit residues: 132.5987 Evaluate side-chains 205 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 142 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 661 GLU Chi-restraints excluded: chain D residue 745 ASP Chi-restraints excluded: chain D residue 784 GLN Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 32 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 300 optimal weight: 0.8980 chunk 338 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 254 optimal weight: 30.0000 chunk 18 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 284 optimal weight: 4.9990 chunk 221 optimal weight: 8.9990 chunk 171 optimal weight: 4.9990 chunk 295 optimal weight: 0.7980 chunk 267 optimal weight: 4.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 GLN D 954 GLN ** D1002 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 = 0.4497 r_free = 0.4497 target = 0.206111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.138204 restraints weight = 42413.692| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.77 r_work: 0.3435 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 29463 Z= 0.210 Angle : 0.673 20.060 40201 Z= 0.339 Chirality : 0.048 0.501 4619 Planarity : 0.005 0.061 5133 Dihedral : 5.505 58.586 4860 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.60 % Favored : 95.34 % Rotamer: Outliers : 2.49 % Allowed : 18.96 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.14), residues: 3562 helix: 1.92 (0.20), residues: 668 sheet: 0.16 (0.17), residues: 837 loop : -1.24 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 436 HIS 0.008 0.002 HIS D1083 PHE 0.035 0.002 PHE D 392 TYR 0.021 0.001 TYR A 351 ARG 0.008 0.001 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00653 ( 36) link_NAG-ASN : angle 3.58174 ( 108) link_BETA1-4 : bond 0.00310 ( 11) link_BETA1-4 : angle 1.25446 ( 33) hydrogen bonds : bond 0.05721 ( 1129) hydrogen bonds : angle 5.49973 ( 3090) SS BOND : bond 0.00436 ( 42) SS BOND : angle 2.17246 ( 84) covalent geometry : bond 0.00509 (29374) covalent geometry : angle 0.63966 (39976) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 157 time to evaluate : 2.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.7531 (t80) REVERT: A 423 TYR cc_start: 0.4898 (OUTLIER) cc_final: 0.3661 (t80) REVERT: A 484 GLU cc_start: 0.3532 (OUTLIER) cc_final: 0.3136 (tp30) REVERT: A 556 ASN cc_start: 0.7569 (p0) cc_final: 0.7073 (t0) REVERT: B 131 CYS cc_start: 0.1883 (OUTLIER) cc_final: 0.1412 (m) REVERT: B 160 TYR cc_start: 0.6821 (p90) cc_final: 0.6226 (p90) REVERT: B 200 TYR cc_start: 0.6740 (OUTLIER) cc_final: 0.6538 (t80) REVERT: B 210 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6815 (tp) REVERT: B 269 TYR cc_start: 0.8282 (m-10) cc_final: 0.7982 (m-10) REVERT: B 369 TYR cc_start: 0.0464 (OUTLIER) cc_final: 0.0151 (m-80) REVERT: B 1138 TYR cc_start: 0.7573 (t80) cc_final: 0.7178 (m-80) REVERT: D 200 TYR cc_start: 0.7182 (m-80) cc_final: 0.6663 (m-80) REVERT: D 265 TYR cc_start: 0.6978 (p90) cc_final: 0.6712 (p90) REVERT: D 673 SER cc_start: 0.8715 (p) cc_final: 0.8258 (m) outliers start: 78 outliers final: 59 residues processed: 224 average time/residue: 0.3540 time to fit residues: 136.0967 Evaluate side-chains 214 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 148 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 423 TYR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 661 GLU Chi-restraints excluded: chain D residue 745 ASP Chi-restraints excluded: chain D residue 784 GLN Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 32 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 90 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 208 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 250 optimal weight: 7.9990 chunk 237 optimal weight: 20.0000 chunk 303 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 chunk 198 optimal weight: 0.8980 chunk 347 optimal weight: 4.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 245 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN D 954 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.198810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.129414 restraints weight = 42341.611| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.01 r_work: 0.3358 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.6828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 29463 Z= 0.272 Angle : 0.750 20.408 40201 Z= 0.379 Chirality : 0.051 0.547 4619 Planarity : 0.005 0.061 5133 Dihedral : 5.996 59.975 4860 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.32 % Favored : 93.63 % Rotamer: Outliers : 2.43 % Allowed : 19.28 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.73 (0.14), residues: 3562 helix: 1.63 (0.20), residues: 664 sheet: -0.15 (0.17), residues: 893 loop : -1.43 (0.13), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 353 HIS 0.008 0.002 HIS D1083 PHE 0.023 0.002 PHE B 306 TYR 0.031 0.002 TYR A1138 ARG 0.007 0.001 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00712 ( 36) link_NAG-ASN : angle 3.79203 ( 108) link_BETA1-4 : bond 0.00331 ( 11) link_BETA1-4 : angle 1.43989 ( 33) hydrogen bonds : bond 0.06666 ( 1129) hydrogen bonds : angle 5.74152 ( 3090) SS BOND : bond 0.00467 ( 42) SS BOND : angle 2.35305 ( 84) covalent geometry : bond 0.00666 (29374) covalent geometry : angle 0.71693 (39976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14349.15 seconds wall clock time: 249 minutes 11.18 seconds (14951.18 seconds total)