Starting phenix.real_space_refine on Wed Feb 21 06:14:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g73_29795/02_2024/8g73_29795.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g73_29795/02_2024/8g73_29795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g73_29795/02_2024/8g73_29795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g73_29795/02_2024/8g73_29795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g73_29795/02_2024/8g73_29795.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g73_29795/02_2024/8g73_29795.pdb" } resolution = 2.5 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= -0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1380 atoms to isotropic. 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 18040 2.51 5 N 4703 2.21 5 O 5548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28420 Number of models: 1 Model: "" Number of chains: 20 Chain: "E" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} 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: "C" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} 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: "F" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 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: 15.06, per 1000 atoms: 0.53 Number of scatterers: 28420 At special positions: 0 Unit cell: (164.25, 154.76, 205.13, 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 5548 8.00 N 4703 7.00 C 18040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 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=2.04 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=2.06 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 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=1.97 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=2.02 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 G 1 " - " NAG G 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 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 G 1 " - " ASN A 801 " " 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: 11.76 Conformation dependent library (CDL) restraints added in 5.3 seconds 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6638 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 62 sheets defined 22.0% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.72 Creating SS restraints... Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 370 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: 3.681A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 759 removed outlier: 6.962A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.503A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.818A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.547A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.559A 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: 4.008A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.848A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.927A 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 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.501A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) 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: 4.198A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.738A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.730A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.161A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.747A pdb=" N LYS C 64 " --> pdb=" O ASN C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.709A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 505 Processing helix chain 'D' and resid 737 through 744 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: 3.527A 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 908 Processing helix chain 'D' and resid 912 through 919 removed outlier: 4.260A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) removed outlier: 3.600A 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: 3.737A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (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: 4.331A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR D 998 " --> pdb=" O ASP D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1147 removed outlier: 4.111A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.236A pdb=" N GLY E 10 " --> pdb=" O THR E 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.575A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.345A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.597A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.890A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 68 through 70 removed outlier: 3.671A pdb=" N ARG A 78 " --> pdb=" O HIS A 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA9, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.649A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.901A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 355 Processing sheet with id=AB3, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'A' and resid 539 through 543 Processing sheet with id=AB7, first strand: chain 'A' and resid 565 through 567 removed outlier: 7.000A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.513A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.657A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.300A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.300A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.336A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.444A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.148A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.893A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 68 through 70 removed outlier: 3.629A pdb=" N ARG B 78 " --> pdb=" O HIS B 69 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AD1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.685A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.831A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AD4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.371A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.697A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.562A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.552A pdb=" N PHE B 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.980A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.776A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.630A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.300A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.437A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AE7, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.584A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR C 104 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 28 through 30 removed outlier: 8.248A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.812A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 68 through 70 Processing sheet with id=AF2, first strand: chain 'D' and resid 84 through 85 removed outlier: 6.482A pdb=" N LEU D 141 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.617A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL D 130 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 311 through 318 removed outlier: 5.088A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 650 " --> pdb=" O PHE D 643 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE D 643 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 356 through 358 Processing sheet with id=AF6, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.647A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 376 through 380 Processing sheet with id=AF8, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AF9, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.598A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 654 through 655 removed outlier: 3.625A pdb=" N ALA D 694 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.364A pdb=" N GLN D1071 " --> pdb=" O THR D 716 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE D 718 " --> pdb=" O PRO D1069 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE D 720 " --> pdb=" O TYR D1067 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N TYR D1067 " --> pdb=" O ILE D 720 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL D 722 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL D1065 " --> pdb=" O VAL D 722 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR D 724 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU D1063 " --> pdb=" O THR D 724 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE D 726 " --> pdb=" O VAL D1061 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL D1061 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLY D1059 " --> pdb=" O PRO D 728 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.364A pdb=" N GLN D1071 " --> pdb=" O THR D 716 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE D 718 " --> pdb=" O PRO D1069 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE D 720 " --> pdb=" O TYR D1067 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N TYR D1067 " --> pdb=" O ILE D 720 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL D 722 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL D1065 " --> pdb=" O VAL D 722 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR D 724 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU D1063 " --> pdb=" O THR D 724 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE D 726 " --> pdb=" O VAL D1061 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL D1061 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLY D1059 " --> pdb=" O PRO D 728 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR D1076 " --> pdb=" O SER D1097 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA D1078 " --> pdb=" O PHE D1095 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.309A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.304A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AG7, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.171A pdb=" N GLY F 10 " --> pdb=" O THR F 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.547A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR F 104 " --> pdb=" O ALA F 97 " (cutoff:3.500A) 1112 hydrogen bonds defined for protein. 2994 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: 14.06 Time building geometry restraints manager: 12.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4622 1.31 - 1.44: 8165 1.44 - 1.57: 16103 1.57 - 1.70: 1 1.70 - 1.83: 168 Bond restraints: 29059 Sorted by residual: bond pdb=" N ILE D 664 " pdb=" CA ILE D 664 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.70e-03 1.69e+04 1.87e+01 bond pdb=" C PRO A 85 " pdb=" O PRO A 85 " ideal model delta sigma weight residual 1.233 1.183 0.050 1.23e-02 6.61e+03 1.66e+01 bond pdb=" N ILE A 233 " pdb=" CA ILE A 233 " ideal model delta sigma weight residual 1.456 1.500 -0.044 1.11e-02 8.12e+03 1.60e+01 bond pdb=" N VAL D 320 " pdb=" CA VAL D 320 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.13e+01 bond pdb=" N TYR D 695 " pdb=" CA TYR D 695 " ideal model delta sigma weight residual 1.455 1.502 -0.047 1.41e-02 5.03e+03 1.10e+01 ... (remaining 29054 not shown) Histogram of bond angle deviations from ideal: 98.45 - 105.65: 575 105.65 - 112.86: 15611 112.86 - 120.06: 10054 120.06 - 127.26: 13062 127.26 - 134.47: 242 Bond angle restraints: 39544 Sorted by residual: angle pdb=" C ALA D 694 " pdb=" N TYR D 695 " pdb=" CA TYR D 695 " ideal model delta sigma weight residual 122.53 110.63 11.90 1.61e+00 3.86e-01 5.46e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 119.40 -8.70 1.22e+00 6.72e-01 5.08e+01 angle pdb=" N PRO A 330 " pdb=" CA PRO A 330 " pdb=" C PRO A 330 " ideal model delta sigma weight residual 110.55 101.05 9.50 1.63e+00 3.76e-01 3.40e+01 angle pdb=" O ASP B 586 " pdb=" C ASP B 586 " pdb=" N ILE B 587 " ideal model delta sigma weight residual 123.27 117.11 6.16 1.13e+00 7.83e-01 2.98e+01 angle pdb=" CA ALA D 694 " pdb=" C ALA D 694 " pdb=" O ALA D 694 " ideal model delta sigma weight residual 120.80 114.95 5.85 1.11e+00 8.12e-01 2.78e+01 ... (remaining 39539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.75: 16724 22.75 - 45.50: 997 45.50 - 68.25: 147 68.25 - 91.00: 42 91.00 - 113.75: 4 Dihedral angle restraints: 17914 sinusoidal: 7576 harmonic: 10338 Sorted by residual: 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 -158.97 72.97 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -157.43 71.43 1 1.00e+01 1.00e-02 6.54e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -132.45 46.45 1 1.00e+01 1.00e-02 2.99e+01 ... (remaining 17911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.275: 4585 0.275 - 0.551: 16 0.551 - 0.826: 1 0.826 - 1.101: 1 1.101 - 1.377: 1 Chirality restraints: 4604 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.11e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.99e+01 ... (remaining 4601 not shown) Planarity restraints: 5109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " -0.351 2.00e-02 2.50e+03 3.03e-01 1.14e+03 pdb=" C7 NAG A1306 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " -0.118 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " 0.539 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " -0.153 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1304 " 0.345 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG B1304 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG B1304 " 0.090 2.00e-02 2.50e+03 pdb=" N2 NAG B1304 " -0.529 2.00e-02 2.50e+03 pdb=" O7 NAG B1304 " 0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.295 2.00e-02 2.50e+03 2.45e-01 7.49e+02 pdb=" C7 NAG A1301 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " -0.196 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.409 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " -0.000 2.00e-02 2.50e+03 ... (remaining 5106 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 49 2.16 - 2.85: 9703 2.85 - 3.53: 37249 3.53 - 4.22: 66557 4.22 - 4.90: 113327 Nonbonded interactions: 226885 Sorted by model distance: nonbonded pdb=" CZ TYR A 351 " pdb=" OD1 ASN A 422 " model vdw 1.478 3.260 nonbonded pdb=" O SER D 373 " pdb=" CD1 TRP D 436 " model vdw 1.498 3.260 nonbonded pdb=" O ASP D 398 " pdb=" CA VAL D 511 " model vdw 1.524 3.470 nonbonded pdb=" N PHE D 400 " pdb=" O VAL D 510 " model vdw 1.564 2.520 nonbonded pdb=" CZ3 TRP D 436 " pdb=" O ASN D 437 " model vdw 1.634 3.340 ... (remaining 226880 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 'E' selection = chain 'F' } ncs_group { reference = chain 'G' 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' } 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: 5.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.020 Extract box with map and model: 22.180 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 80.340 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 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 : 0.006 0.064 29059 Z= 0.369 Angle : 0.857 11.900 39544 Z= 0.521 Chirality : 0.065 1.377 4604 Planarity : 0.011 0.303 5073 Dihedral : 14.230 113.751 11153 Min Nonbonded Distance : 1.478 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.77 % Favored : 96.00 % Rotamer: Outliers : 1.29 % Allowed : 13.41 % Favored : 85.30 % Cbeta Deviations : 0.06 % 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: -0.65 (0.13), residues: 3526 helix: 0.85 (0.20), residues: 682 sheet: 0.11 (0.17), residues: 842 loop : -1.15 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 353 HIS 0.016 0.001 HIS D1083 PHE 0.059 0.002 PHE D 400 TYR 0.073 0.002 TYR B 423 ARG 0.008 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 299 time to evaluate : 2.885 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: E 34 MET cc_start: 0.0951 (mmm) cc_final: 0.0232 (pmm) REVERT: E 47 MET cc_start: -0.0113 (mmm) cc_final: -0.0494 (tmm) REVERT: A 40 ASP cc_start: 0.7158 (m-30) cc_final: 0.6871 (m-30) REVERT: A 153 MET cc_start: 0.0999 (ptp) cc_final: 0.0492 (pmm) REVERT: A 207 HIS cc_start: 0.6185 (m170) cc_final: 0.5824 (t-90) REVERT: A 229 LEU cc_start: 0.6104 (OUTLIER) cc_final: 0.5719 (tt) REVERT: A 779 GLN cc_start: 0.7557 (tt0) cc_final: 0.6910 (tp40) REVERT: A 868 GLU cc_start: 0.7057 (pp20) cc_final: 0.6184 (mm-30) REVERT: A 900 MET cc_start: 0.8469 (ttm) cc_final: 0.8220 (mtp) REVERT: A 990 GLU cc_start: 0.7958 (mt-10) cc_final: 0.6970 (mp0) REVERT: A 1038 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7811 (ttmt) REVERT: A 1091 ARG cc_start: 0.7947 (mtt180) cc_final: 0.7624 (mtt-85) REVERT: A 1141 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6690 (tp) REVERT: B 153 MET cc_start: 0.0666 (ptt) cc_final: -0.0188 (mtp) REVERT: B 177 MET cc_start: 0.0743 (mmp) cc_final: 0.0442 (mmm) REVERT: B 211 ASN cc_start: 0.3091 (OUTLIER) cc_final: 0.2379 (m-40) REVERT: B 564 GLN cc_start: 0.6026 (OUTLIER) cc_final: 0.5810 (mm110) REVERT: B 606 ASN cc_start: 0.6433 (p0) cc_final: 0.5967 (m110) REVERT: B 747 THR cc_start: 0.7613 (m) cc_final: 0.7399 (t) REVERT: B 780 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7155 (pt0) REVERT: B 787 GLN cc_start: 0.7611 (mt0) cc_final: 0.7374 (tt0) REVERT: B 912 THR cc_start: 0.8797 (m) cc_final: 0.8498 (p) REVERT: B 963 VAL cc_start: 0.7332 (t) cc_final: 0.7040 (p) REVERT: B 995 ARG cc_start: 0.7736 (mtt180) cc_final: 0.7488 (mtp180) REVERT: B 1125 ASN cc_start: 0.5897 (m-40) cc_final: 0.4978 (p0) REVERT: C 47 MET cc_start: 0.0779 (ttp) cc_final: 0.0492 (mpt) REVERT: C 82 MET cc_start: -0.1760 (mmp) cc_final: -0.2361 (ptm) REVERT: D 190 ARG cc_start: 0.5836 (OUTLIER) cc_final: 0.5371 (mtp85) REVERT: D 319 ARG cc_start: 0.7520 (ptp-170) cc_final: 0.7275 (mtp180) REVERT: D 675 GLN cc_start: 0.5916 (mt0) cc_final: 0.5630 (tt0) REVERT: D 780 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7254 (pt0) REVERT: D 820 ASP cc_start: 0.6688 (m-30) cc_final: 0.6389 (m-30) REVERT: D 1005 GLN cc_start: 0.7797 (mt0) cc_final: 0.7502 (mt0) REVERT: D 1010 GLN cc_start: 0.7274 (tp40) cc_final: 0.6554 (pt0) REVERT: D 1017 GLU cc_start: 0.7516 (tt0) cc_final: 0.7299 (tt0) REVERT: D 1038 LYS cc_start: 0.7752 (ttmm) cc_final: 0.7291 (mmtp) REVERT: F 34 MET cc_start: 0.3157 (ttt) cc_final: 0.2936 (ttt) outliers start: 40 outliers final: 20 residues processed: 332 average time/residue: 1.1667 time to fit residues: 466.4163 Evaluate side-chains 224 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 199 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 643 PHE Chi-restraints excluded: chain D residue 659 SER Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 0.0980 chunk 268 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 180 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 chunk 277 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 321 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 ASN A 49 HIS A 69 HIS A 121 ASN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 641 ASN A 856 ASN A 935 GLN A 954 GLN A 965 GLN A1002 GLN A1005 GLN A1101 HIS A1113 GLN B 69 HIS B 188 ASN B 207 HIS B 245 HIS B 314 GLN B 607 GLN B 613 GLN B 641 ASN B 764 ASN B 804 GLN B 914 ASN B1002 GLN B1048 HIS B1101 HIS B1113 GLN C 32 ASN C 44 GLN D 69 HIS D 121 ASN D 613 GLN D 655 HIS D 901 GLN D 955 ASN D1002 GLN D1048 HIS D1071 GLN ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1119 ASN F 32 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 29059 Z= 0.367 Angle : 0.739 10.088 39544 Z= 0.380 Chirality : 0.053 0.745 4604 Planarity : 0.006 0.063 5073 Dihedral : 7.363 94.653 4850 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 4.13 % Allowed : 13.12 % Favored : 82.76 % 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: -0.60 (0.13), residues: 3526 helix: 1.16 (0.20), residues: 709 sheet: -0.05 (0.17), residues: 890 loop : -1.18 (0.13), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP D 436 HIS 0.012 0.002 HIS D1083 PHE 0.051 0.003 PHE D 400 TYR 0.054 0.003 TYR A1067 ARG 0.013 0.001 ARG F 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 230 time to evaluate : 3.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.6361 (OUTLIER) cc_final: 0.5561 (mt) REVERT: A 129 LYS cc_start: 0.6275 (mttm) cc_final: 0.5734 (ptmm) REVERT: A 153 MET cc_start: 0.0811 (ptp) cc_final: 0.0238 (pmm) REVERT: A 177 MET cc_start: 0.1260 (mtp) cc_final: 0.0424 (mtp) REVERT: A 190 ARG cc_start: 0.5746 (OUTLIER) cc_final: 0.3928 (mmt180) REVERT: A 200 TYR cc_start: 0.6681 (OUTLIER) cc_final: 0.5560 (m-80) REVERT: A 356 LYS cc_start: 0.3733 (ptmt) cc_final: 0.3341 (ptmm) REVERT: A 532 ASN cc_start: 0.7635 (OUTLIER) cc_final: 0.7249 (t0) REVERT: A 565 PHE cc_start: 0.6887 (m-10) cc_final: 0.6625 (m-80) REVERT: A 596 SER cc_start: 0.8543 (t) cc_final: 0.8265 (m) REVERT: A 646 ARG cc_start: 0.7097 (mtt180) cc_final: 0.6783 (mtp-110) REVERT: A 758 SER cc_start: 0.7812 (m) cc_final: 0.7535 (p) REVERT: A 779 GLN cc_start: 0.7463 (tt0) cc_final: 0.6907 (tp40) REVERT: A 790 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7806 (mtpt) REVERT: A 825 LYS cc_start: 0.7847 (mmtt) cc_final: 0.7276 (mtpt) REVERT: A 868 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6342 (pp20) REVERT: A 964 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.6729 (mptp) REVERT: A 1029 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8489 (tpp) REVERT: A 1038 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7940 (mttt) REVERT: A 1091 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7577 (mtt-85) REVERT: A 1125 ASN cc_start: 0.6655 (m-40) cc_final: 0.6068 (p0) REVERT: B 195 LYS cc_start: 0.5841 (mtpt) cc_final: 0.5439 (mtmm) REVERT: B 211 ASN cc_start: 0.3278 (OUTLIER) cc_final: 0.2598 (m-40) REVERT: B 319 ARG cc_start: 0.7744 (ttm170) cc_final: 0.7344 (mtp180) REVERT: B 422 ASN cc_start: -0.1060 (OUTLIER) cc_final: -0.1353 (t0) REVERT: B 564 GLN cc_start: 0.6133 (tp40) cc_final: 0.5760 (mm110) REVERT: B 787 GLN cc_start: 0.7896 (mt0) cc_final: 0.7520 (mp10) REVERT: B 858 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8106 (mt) REVERT: B 912 THR cc_start: 0.8605 (m) cc_final: 0.8378 (p) REVERT: B 935 GLN cc_start: 0.6686 (OUTLIER) cc_final: 0.6224 (mm-40) REVERT: B 939 SER cc_start: 0.6909 (OUTLIER) cc_final: 0.6646 (m) REVERT: B 954 GLN cc_start: 0.7532 (mt0) cc_final: 0.7329 (mt0) REVERT: B 994 ASP cc_start: 0.7638 (m-30) cc_final: 0.7057 (t70) REVERT: B 995 ARG cc_start: 0.7489 (mtt180) cc_final: 0.7191 (mtp180) REVERT: B 1045 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7399 (tmtt) REVERT: B 1125 ASN cc_start: 0.6759 (m-40) cc_final: 0.6327 (p0) REVERT: D 153 MET cc_start: 0.0693 (ttt) cc_final: -0.0411 (mtp) REVERT: D 190 ARG cc_start: 0.6045 (mpp80) cc_final: 0.5424 (mtp85) REVERT: D 319 ARG cc_start: 0.7067 (ptp-170) cc_final: 0.6835 (mtp85) REVERT: D 734 THR cc_start: 0.8397 (m) cc_final: 0.7949 (p) REVERT: D 780 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7236 (pt0) REVERT: D 820 ASP cc_start: 0.7245 (m-30) cc_final: 0.6943 (m-30) REVERT: D 950 ASP cc_start: 0.7196 (m-30) cc_final: 0.6993 (m-30) REVERT: D 994 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7178 (t0) REVERT: D 1002 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.7014 (tt0) REVERT: D 1005 GLN cc_start: 0.7949 (mt0) cc_final: 0.7729 (mt0) REVERT: D 1010 GLN cc_start: 0.7465 (tp40) cc_final: 0.6784 (tm-30) REVERT: D 1017 GLU cc_start: 0.7508 (tt0) cc_final: 0.7265 (tt0) REVERT: D 1038 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7424 (mmtp) REVERT: D 1050 MET cc_start: 0.9196 (ptm) cc_final: 0.8945 (ptp) REVERT: F 34 MET cc_start: 0.3133 (OUTLIER) cc_final: 0.2876 (ttt) outliers start: 128 outliers final: 49 residues processed: 329 average time/residue: 1.0902 time to fit residues: 438.2964 Evaluate side-chains 269 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 201 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 940 SER Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1002 GLN Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1127 ASP Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 50 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 178 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 267 optimal weight: 0.5980 chunk 218 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 322 optimal weight: 0.5980 chunk 347 optimal weight: 7.9990 chunk 286 optimal weight: 4.9990 chunk 319 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 258 optimal weight: 20.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 188 ASN A 207 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A 914 ASN A 935 GLN A 954 GLN A1005 GLN A1119 ASN B 207 HIS B 245 HIS B 532 ASN B 641 ASN B 658 ASN B 901 GLN B1002 GLN D 121 ASN D 613 GLN D 675 GLN D 762 GLN ** D 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 GLN ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1125 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29059 Z= 0.217 Angle : 0.591 9.964 39544 Z= 0.305 Chirality : 0.047 0.650 4604 Planarity : 0.005 0.056 5073 Dihedral : 5.945 63.430 4818 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.12 % Favored : 96.77 % Rotamer: Outliers : 3.48 % Allowed : 14.08 % Favored : 82.44 % 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: -0.41 (0.14), residues: 3526 helix: 1.56 (0.20), residues: 715 sheet: 0.07 (0.17), residues: 878 loop : -1.17 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 353 HIS 0.008 0.001 HIS D1083 PHE 0.033 0.002 PHE D 400 TYR 0.034 0.002 TYR A1067 ARG 0.006 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 209 time to evaluate : 3.227 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: E 80 LEU cc_start: 0.0891 (OUTLIER) cc_final: 0.0645 (mt) REVERT: A 100 ILE cc_start: 0.6345 (OUTLIER) cc_final: 0.5582 (mt) REVERT: A 153 MET cc_start: 0.0990 (ptp) cc_final: 0.0291 (pmm) REVERT: A 177 MET cc_start: 0.1346 (OUTLIER) cc_final: 0.0491 (mtp) REVERT: A 190 ARG cc_start: 0.5564 (OUTLIER) cc_final: 0.4080 (mmt180) REVERT: A 200 TYR cc_start: 0.6743 (OUTLIER) cc_final: 0.5546 (m-80) REVERT: A 202 LYS cc_start: 0.6812 (mttt) cc_final: 0.6429 (mttp) REVERT: A 396 TYR cc_start: 0.4443 (OUTLIER) cc_final: 0.3533 (p90) REVERT: A 529 LYS cc_start: 0.7716 (mmmm) cc_final: 0.7254 (mmmt) REVERT: A 532 ASN cc_start: 0.7665 (OUTLIER) cc_final: 0.7298 (t0) REVERT: A 536 ASN cc_start: 0.6659 (OUTLIER) cc_final: 0.6158 (t0) REVERT: A 565 PHE cc_start: 0.7074 (m-10) cc_final: 0.6821 (m-80) REVERT: A 646 ARG cc_start: 0.7103 (mtt180) cc_final: 0.6725 (mtp-110) REVERT: A 758 SER cc_start: 0.7722 (m) cc_final: 0.7493 (p) REVERT: A 779 GLN cc_start: 0.7464 (tt0) cc_final: 0.6938 (tp40) REVERT: A 790 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8087 (mtpt) REVERT: A 825 LYS cc_start: 0.7813 (mmtt) cc_final: 0.7281 (mtpt) REVERT: A 964 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.6716 (mptp) REVERT: A 990 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: A 1029 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8281 (tpp) REVERT: A 1038 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7964 (mttt) REVERT: A 1091 ARG cc_start: 0.8088 (mtt180) cc_final: 0.7604 (mtt-85) REVERT: A 1125 ASN cc_start: 0.6808 (m-40) cc_final: 0.6434 (p0) REVERT: A 1138 TYR cc_start: 0.7678 (t80) cc_final: 0.7476 (t80) REVERT: B 195 LYS cc_start: 0.5835 (mtpt) cc_final: 0.5433 (mtmm) REVERT: B 211 ASN cc_start: 0.3445 (OUTLIER) cc_final: 0.2791 (m-40) REVERT: B 319 ARG cc_start: 0.7851 (ttm170) cc_final: 0.7336 (mtp180) REVERT: B 422 ASN cc_start: -0.1084 (OUTLIER) cc_final: -0.1323 (t0) REVERT: B 564 GLN cc_start: 0.6216 (tp40) cc_final: 0.5905 (mm110) REVERT: B 780 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7252 (tt0) REVERT: B 787 GLN cc_start: 0.7895 (mt0) cc_final: 0.7551 (mp10) REVERT: B 858 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8100 (mt) REVERT: B 935 GLN cc_start: 0.6708 (OUTLIER) cc_final: 0.6496 (mm110) REVERT: B 994 ASP cc_start: 0.7682 (m-30) cc_final: 0.7070 (t70) REVERT: B 995 ARG cc_start: 0.7466 (mtt180) cc_final: 0.7174 (mtp180) REVERT: B 1045 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7495 (tmtt) REVERT: B 1125 ASN cc_start: 0.7083 (m-40) cc_final: 0.6683 (p0) REVERT: D 45 SER cc_start: 0.7626 (OUTLIER) cc_final: 0.7084 (t) REVERT: D 47 VAL cc_start: 0.6577 (p) cc_final: 0.6317 (m) REVERT: D 153 MET cc_start: 0.0613 (ttt) cc_final: -0.0451 (mtp) REVERT: D 190 ARG cc_start: 0.6048 (mpp80) cc_final: 0.5540 (mtp180) REVERT: D 439 ASN cc_start: 0.3003 (OUTLIER) cc_final: 0.2592 (t0) REVERT: D 613 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8092 (mt0) REVERT: D 734 THR cc_start: 0.8312 (m) cc_final: 0.7897 (p) REVERT: D 780 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7248 (pt0) REVERT: D 950 ASP cc_start: 0.7229 (m-30) cc_final: 0.6969 (m-30) REVERT: D 994 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7237 (t0) REVERT: D 1002 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6850 (tt0) REVERT: D 1005 GLN cc_start: 0.7860 (mt0) cc_final: 0.7517 (mt0) REVERT: D 1010 GLN cc_start: 0.7432 (tp40) cc_final: 0.6711 (tm-30) REVERT: D 1017 GLU cc_start: 0.7433 (tt0) cc_final: 0.7147 (tt0) REVERT: D 1038 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7406 (mmtp) REVERT: D 1113 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7978 (mm110) REVERT: F 34 MET cc_start: 0.1890 (OUTLIER) cc_final: 0.1684 (ttm) outliers start: 108 outliers final: 41 residues processed: 287 average time/residue: 1.1851 time to fit residues: 412.1091 Evaluate side-chains 262 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 195 time to evaluate : 3.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 439 ASN Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 613 GLN Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 940 SER Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1002 GLN Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain D residue 1127 ASP Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 78 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 318 optimal weight: 2.9990 chunk 242 optimal weight: 20.0000 chunk 167 optimal weight: 30.0000 chunk 35 optimal weight: 8.9990 chunk 153 optimal weight: 0.4980 chunk 216 optimal weight: 2.9990 chunk 323 optimal weight: 3.9990 chunk 342 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 306 optimal weight: 5.9990 chunk 92 optimal weight: 0.0030 overall best weight: 1.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 935 GLN A1005 GLN B 207 HIS B 245 HIS B 606 ASN B 613 GLN B 641 ASN B 914 ASN B 954 GLN D 121 ASN D 370 ASN D 437 ASN D 563 GLN D 607 GLN D 613 GLN D 804 GLN D 935 GLN D1002 GLN ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1125 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29059 Z= 0.258 Angle : 0.606 9.343 39544 Z= 0.310 Chirality : 0.048 0.619 4604 Planarity : 0.004 0.056 5073 Dihedral : 5.441 57.437 4815 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.46 % Favored : 96.40 % Rotamer: Outliers : 4.29 % Allowed : 13.63 % Favored : 82.08 % 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: -0.41 (0.14), residues: 3526 helix: 1.66 (0.20), residues: 705 sheet: -0.15 (0.16), residues: 959 loop : -1.12 (0.13), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 104 HIS 0.012 0.001 HIS D1083 PHE 0.030 0.002 PHE D 400 TYR 0.034 0.002 TYR A1067 ARG 0.004 0.000 ARG D 577 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 200 time to evaluate : 3.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 80 LEU cc_start: 0.0965 (OUTLIER) cc_final: 0.0706 (mt) REVERT: A 100 ILE cc_start: 0.6360 (OUTLIER) cc_final: 0.5671 (mt) REVERT: A 130 VAL cc_start: 0.5897 (OUTLIER) cc_final: 0.5657 (p) REVERT: A 190 ARG cc_start: 0.5583 (OUTLIER) cc_final: 0.4136 (mmt180) REVERT: A 200 TYR cc_start: 0.6728 (OUTLIER) cc_final: 0.5597 (m-80) REVERT: A 202 LYS cc_start: 0.6805 (mttt) cc_final: 0.6455 (mttp) REVERT: A 332 ILE cc_start: 0.5428 (OUTLIER) cc_final: 0.5118 (mp) REVERT: A 396 TYR cc_start: 0.4424 (OUTLIER) cc_final: 0.3470 (p90) REVERT: A 529 LYS cc_start: 0.7659 (mmmm) cc_final: 0.7219 (mmmt) REVERT: A 532 ASN cc_start: 0.7658 (OUTLIER) cc_final: 0.7270 (t0) REVERT: A 565 PHE cc_start: 0.7237 (m-10) cc_final: 0.6986 (m-80) REVERT: A 646 ARG cc_start: 0.7198 (mtt180) cc_final: 0.6771 (mtp-110) REVERT: A 762 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.7192 (mt0) REVERT: A 779 GLN cc_start: 0.7488 (tt0) cc_final: 0.6981 (tp40) REVERT: A 790 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8085 (mtpt) REVERT: A 825 LYS cc_start: 0.7837 (mmtt) cc_final: 0.7305 (mtpt) REVERT: A 964 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.6699 (mptp) REVERT: A 1029 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8275 (tpp) REVERT: A 1038 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7819 (mtpt) REVERT: A 1091 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7533 (mtt-85) REVERT: A 1125 ASN cc_start: 0.7022 (m-40) cc_final: 0.6708 (p0) REVERT: A 1141 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6882 (tp) REVERT: B 195 LYS cc_start: 0.5999 (mtpt) cc_final: 0.5595 (mtmm) REVERT: B 211 ASN cc_start: 0.3434 (OUTLIER) cc_final: 0.2782 (m-40) REVERT: B 319 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7358 (mtp180) REVERT: B 422 ASN cc_start: -0.1018 (OUTLIER) cc_final: -0.1242 (t0) REVERT: B 564 GLN cc_start: 0.6274 (OUTLIER) cc_final: 0.5955 (mm110) REVERT: B 651 ILE cc_start: 0.8695 (mt) cc_final: 0.8427 (mm) REVERT: B 780 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7317 (tt0) REVERT: B 787 GLN cc_start: 0.7916 (mt0) cc_final: 0.7622 (mp10) REVERT: B 994 ASP cc_start: 0.7706 (m-30) cc_final: 0.7086 (t70) REVERT: B 995 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7186 (mtp180) REVERT: B 1045 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7526 (tmtt) REVERT: B 1125 ASN cc_start: 0.7233 (m-40) cc_final: 0.6805 (p0) REVERT: D 45 SER cc_start: 0.7774 (OUTLIER) cc_final: 0.7200 (t) REVERT: D 47 VAL cc_start: 0.6689 (p) cc_final: 0.6442 (m) REVERT: D 153 MET cc_start: 0.0474 (ttt) cc_final: -0.0958 (mtm) REVERT: D 190 ARG cc_start: 0.6010 (mpp80) cc_final: 0.5473 (mtp180) REVERT: D 439 ASN cc_start: 0.2990 (OUTLIER) cc_final: 0.2575 (t0) REVERT: D 734 THR cc_start: 0.8425 (m) cc_final: 0.8075 (p) REVERT: D 780 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7255 (pt0) REVERT: D 814 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.6630 (pptt) REVERT: D 916 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7748 (tt) REVERT: D 950 ASP cc_start: 0.7286 (m-30) cc_final: 0.7010 (m-30) REVERT: D 954 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7699 (mt0) REVERT: D 994 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7287 (t0) REVERT: D 1010 GLN cc_start: 0.7452 (tp40) cc_final: 0.6749 (tm-30) REVERT: D 1017 GLU cc_start: 0.7471 (tt0) cc_final: 0.7181 (tt0) REVERT: D 1038 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7427 (mmtp) REVERT: D 1113 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7796 (mm110) outliers start: 133 outliers final: 51 residues processed: 296 average time/residue: 1.2149 time to fit residues: 436.1642 Evaluate side-chains 261 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 184 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 439 ASN Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 748 GLU Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 814 LYS Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 940 SER Chi-restraints excluded: chain D residue 954 GLN Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain D residue 1127 ASP Chi-restraints excluded: chain F residue 78 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 284 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 254 optimal weight: 9.9990 chunk 141 optimal weight: 0.0470 chunk 291 optimal weight: 7.9990 chunk 236 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 174 optimal weight: 3.9990 chunk 307 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A1005 GLN B 207 HIS B 613 GLN B 641 ASN B 954 GLN D 607 GLN D 955 ASN D1005 GLN ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29059 Z= 0.198 Angle : 0.561 9.975 39544 Z= 0.287 Chirality : 0.046 0.573 4604 Planarity : 0.004 0.055 5073 Dihedral : 5.116 58.967 4814 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.06 % Favored : 96.82 % Rotamer: Outliers : 3.54 % Allowed : 14.31 % Favored : 82.15 % 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: -0.33 (0.14), residues: 3526 helix: 1.81 (0.20), residues: 704 sheet: -0.06 (0.16), residues: 948 loop : -1.11 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 64 HIS 0.009 0.001 HIS D1083 PHE 0.050 0.001 PHE B 400 TYR 0.025 0.001 TYR A1067 ARG 0.008 0.000 ARG D 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 191 time to evaluate : 3.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.6258 (OUTLIER) cc_final: 0.5638 (mt) REVERT: A 129 LYS cc_start: 0.6112 (mttm) cc_final: 0.5658 (ptmm) REVERT: A 153 MET cc_start: 0.1201 (OUTLIER) cc_final: 0.0928 (tpp) REVERT: A 190 ARG cc_start: 0.5576 (OUTLIER) cc_final: 0.4178 (mmt180) REVERT: A 200 TYR cc_start: 0.6756 (OUTLIER) cc_final: 0.5540 (m-80) REVERT: A 202 LYS cc_start: 0.6786 (mttt) cc_final: 0.6461 (mttp) REVERT: A 332 ILE cc_start: 0.5586 (OUTLIER) cc_final: 0.5216 (mp) REVERT: A 396 TYR cc_start: 0.4334 (OUTLIER) cc_final: 0.3507 (p90) REVERT: A 529 LYS cc_start: 0.7597 (mmmm) cc_final: 0.7188 (mmmt) REVERT: A 532 ASN cc_start: 0.7653 (OUTLIER) cc_final: 0.7269 (t0) REVERT: A 565 PHE cc_start: 0.7268 (m-10) cc_final: 0.7061 (m-80) REVERT: A 646 ARG cc_start: 0.7164 (mtt180) cc_final: 0.6623 (mtp-110) REVERT: A 655 HIS cc_start: 0.7186 (t70) cc_final: 0.6656 (t70) REVERT: A 779 GLN cc_start: 0.7463 (tt0) cc_final: 0.7132 (tp40) REVERT: A 790 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8103 (mtpt) REVERT: A 825 LYS cc_start: 0.7784 (mmtt) cc_final: 0.7281 (mtpt) REVERT: A 964 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.6683 (mptp) REVERT: A 1029 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8315 (tpp) REVERT: A 1038 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7825 (mtpt) REVERT: A 1091 ARG cc_start: 0.8015 (mtt180) cc_final: 0.7506 (mtt-85) REVERT: A 1125 ASN cc_start: 0.7116 (m-40) cc_final: 0.6816 (p0) REVERT: B 51 THR cc_start: 0.7767 (p) cc_final: 0.7306 (t) REVERT: B 53 ASP cc_start: 0.7285 (m-30) cc_final: 0.6675 (m-30) REVERT: B 195 LYS cc_start: 0.5997 (mtpt) cc_final: 0.5571 (mtmm) REVERT: B 564 GLN cc_start: 0.6301 (OUTLIER) cc_final: 0.5978 (mm110) REVERT: B 651 ILE cc_start: 0.8697 (mt) cc_final: 0.8444 (mm) REVERT: B 780 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7300 (tt0) REVERT: B 787 GLN cc_start: 0.7918 (mt0) cc_final: 0.7619 (mp10) REVERT: B 858 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8221 (mt) REVERT: B 994 ASP cc_start: 0.7691 (m-30) cc_final: 0.7043 (t70) REVERT: B 995 ARG cc_start: 0.7461 (mtt180) cc_final: 0.7163 (mtp180) REVERT: B 1045 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7539 (tmtt) REVERT: B 1125 ASN cc_start: 0.7274 (m-40) cc_final: 0.6886 (p0) REVERT: D 45 SER cc_start: 0.7780 (OUTLIER) cc_final: 0.7280 (p) REVERT: D 47 VAL cc_start: 0.6747 (p) cc_final: 0.6510 (m) REVERT: D 153 MET cc_start: 0.0442 (ttt) cc_final: -0.0608 (mtp) REVERT: D 190 ARG cc_start: 0.6001 (mpp80) cc_final: 0.5494 (mtp180) REVERT: D 439 ASN cc_start: 0.3041 (OUTLIER) cc_final: 0.2592 (t0) REVERT: D 558 LYS cc_start: 0.7282 (mttt) cc_final: 0.6985 (tmmt) REVERT: D 656 VAL cc_start: 0.7215 (p) cc_final: 0.6984 (m) REVERT: D 780 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7218 (pt0) REVERT: D 814 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.6700 (pptt) REVERT: D 916 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7678 (tt) REVERT: D 950 ASP cc_start: 0.7284 (m-30) cc_final: 0.6989 (m-30) REVERT: D 994 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7228 (t0) REVERT: D 1010 GLN cc_start: 0.7462 (tp40) cc_final: 0.6740 (tm-30) REVERT: D 1017 GLU cc_start: 0.7445 (tt0) cc_final: 0.7159 (tt0) REVERT: D 1038 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7424 (mmtp) REVERT: D 1050 MET cc_start: 0.9183 (ptm) cc_final: 0.8880 (ptp) REVERT: D 1113 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7785 (mm110) outliers start: 110 outliers final: 46 residues processed: 277 average time/residue: 1.1522 time to fit residues: 386.0316 Evaluate side-chains 246 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 179 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 439 ASN Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 748 GLU Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 814 LYS Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 940 SER Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain F residue 78 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 115 optimal weight: 3.9990 chunk 308 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 chunk 84 optimal weight: 0.0570 chunk 342 optimal weight: 0.7980 chunk 284 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 179 optimal weight: 8.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 613 GLN B 641 ASN B 954 GLN B1002 GLN D 935 GLN D1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29059 Z= 0.260 Angle : 0.589 9.518 39544 Z= 0.303 Chirality : 0.047 0.562 4604 Planarity : 0.004 0.056 5073 Dihedral : 5.198 55.729 4812 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.66 % Favored : 96.23 % Rotamer: Outliers : 3.90 % Allowed : 13.99 % Favored : 82.11 % 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: -0.36 (0.14), residues: 3526 helix: 1.70 (0.20), residues: 703 sheet: -0.04 (0.16), residues: 950 loop : -1.12 (0.13), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 353 HIS 0.009 0.001 HIS D1083 PHE 0.038 0.002 PHE B 400 TYR 0.031 0.002 TYR A1067 ARG 0.006 0.000 ARG D 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 191 time to evaluate : 3.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6175 (mttm) cc_final: 0.5752 (ptmm) REVERT: A 153 MET cc_start: 0.1044 (OUTLIER) cc_final: -0.0157 (mpp) REVERT: A 190 ARG cc_start: 0.5586 (OUTLIER) cc_final: 0.4180 (mmt180) REVERT: A 200 TYR cc_start: 0.6716 (OUTLIER) cc_final: 0.6304 (t80) REVERT: A 202 LYS cc_start: 0.6788 (mttt) cc_final: 0.6282 (mttp) REVERT: A 332 ILE cc_start: 0.5663 (OUTLIER) cc_final: 0.5407 (mm) REVERT: A 396 TYR cc_start: 0.4402 (OUTLIER) cc_final: 0.3612 (p90) REVERT: A 529 LYS cc_start: 0.7677 (mmmm) cc_final: 0.7235 (mmmt) REVERT: A 532 ASN cc_start: 0.7689 (OUTLIER) cc_final: 0.7291 (t0) REVERT: A 565 PHE cc_start: 0.7427 (m-10) cc_final: 0.7221 (m-80) REVERT: A 646 ARG cc_start: 0.7164 (mtt180) cc_final: 0.6609 (mtp-110) REVERT: A 779 GLN cc_start: 0.7458 (tt0) cc_final: 0.7161 (tp40) REVERT: A 790 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8072 (mtpt) REVERT: A 825 LYS cc_start: 0.7833 (mmtt) cc_final: 0.7353 (mtpt) REVERT: A 868 GLU cc_start: 0.6935 (pp20) cc_final: 0.6197 (mp0) REVERT: A 964 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.6613 (mptp) REVERT: A 1029 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8264 (tpp) REVERT: A 1038 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7832 (mtpt) REVERT: A 1091 ARG cc_start: 0.8027 (mtt180) cc_final: 0.7480 (mtt-85) REVERT: A 1125 ASN cc_start: 0.7248 (m-40) cc_final: 0.6994 (p0) REVERT: B 51 THR cc_start: 0.7727 (OUTLIER) cc_final: 0.7262 (t) REVERT: B 53 ASP cc_start: 0.7246 (m-30) cc_final: 0.6609 (m-30) REVERT: B 195 LYS cc_start: 0.6070 (mtpt) cc_final: 0.5640 (mtmm) REVERT: B 211 ASN cc_start: 0.3355 (OUTLIER) cc_final: 0.3074 (m-40) REVERT: B 319 ARG cc_start: 0.7852 (ttm170) cc_final: 0.7256 (mtp180) REVERT: B 564 GLN cc_start: 0.6333 (OUTLIER) cc_final: 0.5958 (mm110) REVERT: B 651 ILE cc_start: 0.8714 (mt) cc_final: 0.8476 (mm) REVERT: B 654 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6628 (tm-30) REVERT: B 735 SER cc_start: 0.7328 (t) cc_final: 0.6953 (p) REVERT: B 780 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7335 (tt0) REVERT: B 787 GLN cc_start: 0.7964 (mt0) cc_final: 0.7687 (mp10) REVERT: B 995 ARG cc_start: 0.7557 (mtt180) cc_final: 0.7212 (mtp180) REVERT: B 1045 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7628 (tmtt) REVERT: B 1125 ASN cc_start: 0.7244 (m-40) cc_final: 0.6929 (p0) REVERT: D 45 SER cc_start: 0.7855 (OUTLIER) cc_final: 0.7326 (p) REVERT: D 47 VAL cc_start: 0.6837 (p) cc_final: 0.6581 (m) REVERT: D 153 MET cc_start: 0.0437 (ttt) cc_final: -0.0937 (mtm) REVERT: D 266 TYR cc_start: 0.6854 (OUTLIER) cc_final: 0.6596 (m-80) REVERT: D 302 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8664 (t) REVERT: D 439 ASN cc_start: 0.2879 (OUTLIER) cc_final: 0.2417 (t0) REVERT: D 558 LYS cc_start: 0.7359 (mttt) cc_final: 0.7019 (tmmt) REVERT: D 656 VAL cc_start: 0.7187 (p) cc_final: 0.6985 (m) REVERT: D 780 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7200 (pt0) REVERT: D 814 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.6633 (pptt) REVERT: D 916 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7785 (tt) REVERT: D 950 ASP cc_start: 0.7324 (m-30) cc_final: 0.6966 (m-30) REVERT: D 954 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7701 (mt0) REVERT: D 994 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7272 (t0) REVERT: D 1010 GLN cc_start: 0.7464 (tp40) cc_final: 0.6719 (tm-30) REVERT: D 1017 GLU cc_start: 0.7497 (tt0) cc_final: 0.7207 (tt0) REVERT: D 1038 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7430 (mmtp) REVERT: D 1050 MET cc_start: 0.9150 (ptm) cc_final: 0.8891 (ptp) REVERT: D 1113 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7800 (mm110) outliers start: 121 outliers final: 58 residues processed: 279 average time/residue: 1.3009 time to fit residues: 440.5846 Evaluate side-chains 269 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 186 time to evaluate : 3.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 439 ASN Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 748 GLU Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 814 LYS Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 939 SER Chi-restraints excluded: chain D residue 940 SER Chi-restraints excluded: chain D residue 954 GLN Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1055 SER Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain D residue 1127 ASP Chi-restraints excluded: chain F residue 78 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 330 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 195 optimal weight: 3.9990 chunk 250 optimal weight: 0.0020 chunk 193 optimal weight: 0.0970 chunk 288 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 341 optimal weight: 2.9990 chunk 213 optimal weight: 0.6980 chunk 208 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 ASN A 121 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 321 GLN B 641 ASN D 935 GLN D1125 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29059 Z= 0.148 Angle : 0.523 10.933 39544 Z= 0.268 Chirality : 0.044 0.509 4604 Planarity : 0.004 0.055 5073 Dihedral : 4.845 54.426 4812 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.01 % Favored : 96.88 % Rotamer: Outliers : 2.77 % Allowed : 15.28 % Favored : 81.95 % 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: -0.19 (0.14), residues: 3526 helix: 2.06 (0.20), residues: 703 sheet: 0.03 (0.16), residues: 935 loop : -1.08 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 353 HIS 0.007 0.001 HIS D1083 PHE 0.034 0.001 PHE B 400 TYR 0.024 0.001 TYR A1138 ARG 0.004 0.000 ARG D 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 204 time to evaluate : 2.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6119 (mttm) cc_final: 0.5720 (ptmm) REVERT: A 153 MET cc_start: 0.0925 (OUTLIER) cc_final: -0.0336 (mpp) REVERT: A 190 ARG cc_start: 0.5540 (OUTLIER) cc_final: 0.4130 (mmt180) REVERT: A 200 TYR cc_start: 0.6747 (OUTLIER) cc_final: 0.6353 (t80) REVERT: A 202 LYS cc_start: 0.6719 (mttt) cc_final: 0.6251 (mttp) REVERT: A 332 ILE cc_start: 0.5586 (OUTLIER) cc_final: 0.5374 (mm) REVERT: A 356 LYS cc_start: 0.4985 (OUTLIER) cc_final: 0.4711 (ptmm) REVERT: A 529 LYS cc_start: 0.7649 (mmmm) cc_final: 0.7228 (mmmt) REVERT: A 646 ARG cc_start: 0.7083 (mtt180) cc_final: 0.6517 (mtp-110) REVERT: A 779 GLN cc_start: 0.7378 (tt0) cc_final: 0.7124 (tp40) REVERT: A 780 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6908 (mp0) REVERT: A 790 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8186 (mtpt) REVERT: A 825 LYS cc_start: 0.7787 (mmtt) cc_final: 0.7316 (mtpt) REVERT: A 868 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6147 (mp0) REVERT: A 964 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7140 (mtpt) REVERT: A 1038 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7786 (mtpt) REVERT: A 1125 ASN cc_start: 0.7194 (m-40) cc_final: 0.6947 (p0) REVERT: B 51 THR cc_start: 0.7751 (p) cc_final: 0.7378 (t) REVERT: B 195 LYS cc_start: 0.6036 (mtpt) cc_final: 0.5628 (mtmm) REVERT: B 211 ASN cc_start: 0.3418 (OUTLIER) cc_final: 0.3132 (m-40) REVERT: B 319 ARG cc_start: 0.7828 (ttm170) cc_final: 0.7211 (mtp180) REVERT: B 564 GLN cc_start: 0.6338 (OUTLIER) cc_final: 0.6113 (mm110) REVERT: B 651 ILE cc_start: 0.8705 (mt) cc_final: 0.8470 (mm) REVERT: B 654 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6610 (tm-30) REVERT: B 735 SER cc_start: 0.7379 (t) cc_final: 0.6979 (p) REVERT: B 780 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7308 (tt0) REVERT: B 787 GLN cc_start: 0.7943 (mt0) cc_final: 0.7714 (mp10) REVERT: B 995 ARG cc_start: 0.7421 (mtt180) cc_final: 0.7141 (mtp180) REVERT: B 1045 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.6936 (ttpp) REVERT: B 1125 ASN cc_start: 0.7268 (m-40) cc_final: 0.6898 (p0) REVERT: D 45 SER cc_start: 0.7774 (p) cc_final: 0.7296 (p) REVERT: D 47 VAL cc_start: 0.6773 (p) cc_final: 0.6558 (m) REVERT: D 153 MET cc_start: 0.0423 (ttt) cc_final: -0.0954 (mtm) REVERT: D 266 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.6510 (m-80) REVERT: D 317 ASN cc_start: 0.7534 (OUTLIER) cc_final: 0.7133 (p0) REVERT: D 439 ASN cc_start: 0.2863 (OUTLIER) cc_final: 0.2401 (t0) REVERT: D 558 LYS cc_start: 0.7318 (mttt) cc_final: 0.6997 (tmmt) REVERT: D 814 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.6701 (pptt) REVERT: D 935 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.7058 (tt0) REVERT: D 949 GLN cc_start: 0.7114 (mm-40) cc_final: 0.6351 (mt0) REVERT: D 950 ASP cc_start: 0.7290 (m-30) cc_final: 0.6930 (m-30) REVERT: D 954 GLN cc_start: 0.7898 (mt0) cc_final: 0.7669 (mt0) REVERT: D 977 LEU cc_start: 0.8022 (mt) cc_final: 0.7800 (mt) REVERT: D 994 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7169 (t0) REVERT: D 1010 GLN cc_start: 0.7455 (tp40) cc_final: 0.6723 (tm-30) REVERT: D 1017 GLU cc_start: 0.7400 (tt0) cc_final: 0.7112 (tt0) REVERT: D 1038 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7399 (mmtp) REVERT: D 1050 MET cc_start: 0.9116 (ptm) cc_final: 0.8833 (ptp) REVERT: D 1125 ASN cc_start: 0.7683 (m-40) cc_final: 0.7394 (t0) outliers start: 86 outliers final: 34 residues processed: 268 average time/residue: 1.1870 time to fit residues: 385.6418 Evaluate side-chains 236 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 182 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 439 ASN Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 748 GLU Chi-restraints excluded: chain D residue 814 LYS Chi-restraints excluded: chain D residue 935 GLN Chi-restraints excluded: chain D residue 940 SER Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain F residue 78 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 211 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 168 optimal weight: 0.0870 chunk 31 optimal weight: 0.0670 chunk 268 optimal weight: 8.9990 overall best weight: 1.3700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 321 GLN B 641 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29059 Z= 0.214 Angle : 0.555 11.028 39544 Z= 0.284 Chirality : 0.046 0.505 4604 Planarity : 0.004 0.055 5073 Dihedral : 4.927 53.379 4812 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.37 % Favored : 96.51 % Rotamer: Outliers : 2.61 % Allowed : 15.66 % Favored : 81.73 % 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: -0.20 (0.14), residues: 3526 helix: 1.95 (0.20), residues: 705 sheet: 0.03 (0.16), residues: 951 loop : -1.05 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 353 HIS 0.007 0.001 HIS D1083 PHE 0.030 0.001 PHE B 400 TYR 0.027 0.001 TYR A1067 ARG 0.004 0.000 ARG D 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 183 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6134 (mttm) cc_final: 0.5738 (ptmm) REVERT: A 153 MET cc_start: 0.0902 (OUTLIER) cc_final: -0.0393 (mpp) REVERT: A 190 ARG cc_start: 0.5548 (OUTLIER) cc_final: 0.4129 (mmt180) REVERT: A 200 TYR cc_start: 0.6747 (OUTLIER) cc_final: 0.6310 (t80) REVERT: A 202 LYS cc_start: 0.6766 (mttt) cc_final: 0.6197 (mttp) REVERT: A 396 TYR cc_start: 0.4609 (OUTLIER) cc_final: 0.3933 (p90) REVERT: A 529 LYS cc_start: 0.7661 (mmmm) cc_final: 0.7232 (mmmt) REVERT: A 537 LYS cc_start: 0.6855 (ttmt) cc_final: 0.6398 (ttpt) REVERT: A 646 ARG cc_start: 0.7069 (mtt180) cc_final: 0.6508 (mtp-110) REVERT: A 779 GLN cc_start: 0.7361 (tt0) cc_final: 0.7112 (tp40) REVERT: A 790 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8142 (mtpt) REVERT: A 825 LYS cc_start: 0.7810 (mmtt) cc_final: 0.7338 (mtpt) REVERT: A 868 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6155 (mp0) REVERT: A 964 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7240 (mtpt) REVERT: A 1038 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7813 (mtpt) REVERT: A 1125 ASN cc_start: 0.7259 (m-40) cc_final: 0.6970 (p0) REVERT: B 51 THR cc_start: 0.7680 (p) cc_final: 0.7373 (t) REVERT: B 195 LYS cc_start: 0.6094 (mtpt) cc_final: 0.5658 (mtmm) REVERT: B 211 ASN cc_start: 0.3609 (OUTLIER) cc_final: 0.3303 (m-40) REVERT: B 319 ARG cc_start: 0.7834 (ttm170) cc_final: 0.7223 (mtp180) REVERT: B 564 GLN cc_start: 0.6339 (OUTLIER) cc_final: 0.6081 (mm110) REVERT: B 651 ILE cc_start: 0.8676 (mt) cc_final: 0.8441 (mm) REVERT: B 654 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6674 (tm-30) REVERT: B 735 SER cc_start: 0.7393 (t) cc_final: 0.7005 (p) REVERT: B 780 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7301 (tt0) REVERT: B 787 GLN cc_start: 0.7963 (mt0) cc_final: 0.7714 (mp10) REVERT: B 995 ARG cc_start: 0.7503 (mtt180) cc_final: 0.7167 (mtp180) REVERT: B 1045 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7493 (tmtt) REVERT: B 1125 ASN cc_start: 0.7311 (m-40) cc_final: 0.6940 (p0) REVERT: D 45 SER cc_start: 0.7837 (p) cc_final: 0.7339 (p) REVERT: D 47 VAL cc_start: 0.6803 (p) cc_final: 0.6572 (m) REVERT: D 153 MET cc_start: 0.0441 (ttt) cc_final: -0.0941 (mtm) REVERT: D 266 TYR cc_start: 0.6868 (OUTLIER) cc_final: 0.6604 (m-80) REVERT: D 317 ASN cc_start: 0.7559 (OUTLIER) cc_final: 0.7178 (p0) REVERT: D 326 ILE cc_start: 0.6373 (tt) cc_final: 0.6005 (tt) REVERT: D 439 ASN cc_start: 0.2776 (OUTLIER) cc_final: 0.2301 (t0) REVERT: D 558 LYS cc_start: 0.7329 (mttt) cc_final: 0.7028 (tmmt) REVERT: D 814 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.6680 (pptt) REVERT: D 950 ASP cc_start: 0.7281 (m-30) cc_final: 0.6904 (m-30) REVERT: D 954 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7691 (mt0) REVERT: D 994 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7176 (t0) REVERT: D 1010 GLN cc_start: 0.7458 (tp40) cc_final: 0.6725 (tm-30) REVERT: D 1017 GLU cc_start: 0.7431 (tt0) cc_final: 0.7152 (tt0) REVERT: D 1038 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7439 (mmtp) REVERT: D 1050 MET cc_start: 0.9167 (ptm) cc_final: 0.8888 (ptp) REVERT: D 1113 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7960 (mm110) outliers start: 81 outliers final: 46 residues processed: 240 average time/residue: 1.2477 time to fit residues: 359.9968 Evaluate side-chains 248 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 182 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 439 ASN Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 748 GLU Chi-restraints excluded: chain D residue 814 LYS Chi-restraints excluded: chain D residue 954 GLN Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain D residue 1127 ASP Chi-restraints excluded: chain F residue 78 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 310 optimal weight: 3.9990 chunk 326 optimal weight: 0.7980 chunk 298 optimal weight: 1.9990 chunk 317 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 249 optimal weight: 0.0670 chunk 97 optimal weight: 1.9990 chunk 287 optimal weight: 6.9990 chunk 300 optimal weight: 2.9990 chunk 316 optimal weight: 2.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 ASN A 121 ASN A 394 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 321 GLN B 641 ASN D 764 ASN D 935 GLN D1125 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29059 Z= 0.196 Angle : 0.547 10.880 39544 Z= 0.279 Chirality : 0.045 0.489 4604 Planarity : 0.004 0.054 5073 Dihedral : 4.965 52.245 4812 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.20 % Favored : 96.68 % Rotamer: Outliers : 2.61 % Allowed : 15.92 % Favored : 81.47 % 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: -0.14 (0.14), residues: 3526 helix: 2.01 (0.20), residues: 704 sheet: 0.07 (0.16), residues: 945 loop : -1.02 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 353 HIS 0.007 0.001 HIS D1083 PHE 0.027 0.001 PHE B 400 TYR 0.028 0.001 TYR A1067 ARG 0.006 0.000 ARG D 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 191 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6083 (mttm) cc_final: 0.5710 (ptmm) REVERT: A 153 MET cc_start: 0.0833 (OUTLIER) cc_final: -0.0553 (mpp) REVERT: A 190 ARG cc_start: 0.5542 (OUTLIER) cc_final: 0.4110 (mmt180) REVERT: A 200 TYR cc_start: 0.6803 (OUTLIER) cc_final: 0.6424 (t80) REVERT: A 202 LYS cc_start: 0.6774 (mttt) cc_final: 0.6298 (mttp) REVERT: A 396 TYR cc_start: 0.4565 (OUTLIER) cc_final: 0.3894 (p90) REVERT: A 529 LYS cc_start: 0.7650 (mmmm) cc_final: 0.7233 (mmmt) REVERT: A 537 LYS cc_start: 0.6889 (ttmt) cc_final: 0.6446 (ttpt) REVERT: A 646 ARG cc_start: 0.7070 (mtt180) cc_final: 0.6510 (mtp-110) REVERT: A 734 THR cc_start: 0.8138 (m) cc_final: 0.7735 (p) REVERT: A 779 GLN cc_start: 0.7366 (tt0) cc_final: 0.7142 (tp40) REVERT: A 780 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6984 (mp0) REVERT: A 790 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8137 (mtpt) REVERT: A 825 LYS cc_start: 0.7781 (mmtt) cc_final: 0.7291 (mtpt) REVERT: A 868 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6134 (mp0) REVERT: A 964 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7220 (mtpt) REVERT: A 1038 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7846 (mtpt) REVERT: A 1125 ASN cc_start: 0.7313 (m-40) cc_final: 0.6992 (p0) REVERT: B 51 THR cc_start: 0.7666 (p) cc_final: 0.7368 (t) REVERT: B 195 LYS cc_start: 0.6161 (mtpt) cc_final: 0.5645 (mtmm) REVERT: B 211 ASN cc_start: 0.3588 (OUTLIER) cc_final: 0.3306 (m-40) REVERT: B 319 ARG cc_start: 0.7820 (ttm170) cc_final: 0.7207 (mtp180) REVERT: B 564 GLN cc_start: 0.6368 (OUTLIER) cc_final: 0.6112 (mm110) REVERT: B 651 ILE cc_start: 0.8707 (mt) cc_final: 0.8471 (mm) REVERT: B 654 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6702 (tm-30) REVERT: B 735 SER cc_start: 0.7336 (t) cc_final: 0.6954 (p) REVERT: B 780 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7290 (tt0) REVERT: B 787 GLN cc_start: 0.7969 (mt0) cc_final: 0.7718 (mp10) REVERT: B 820 ASP cc_start: 0.7379 (m-30) cc_final: 0.7073 (m-30) REVERT: B 995 ARG cc_start: 0.7491 (mtt180) cc_final: 0.7165 (mtp180) REVERT: B 1045 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7474 (tmtt) REVERT: B 1125 ASN cc_start: 0.7328 (m-40) cc_final: 0.6956 (p0) REVERT: D 45 SER cc_start: 0.7827 (p) cc_final: 0.7309 (p) REVERT: D 47 VAL cc_start: 0.6817 (p) cc_final: 0.6576 (m) REVERT: D 153 MET cc_start: 0.0496 (ttt) cc_final: -0.1017 (mtm) REVERT: D 266 TYR cc_start: 0.6811 (OUTLIER) cc_final: 0.6531 (m-80) REVERT: D 302 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8651 (t) REVERT: D 317 ASN cc_start: 0.7578 (OUTLIER) cc_final: 0.7197 (p0) REVERT: D 326 ILE cc_start: 0.6391 (tt) cc_final: 0.6052 (tt) REVERT: D 439 ASN cc_start: 0.2882 (OUTLIER) cc_final: 0.2261 (t0) REVERT: D 558 LYS cc_start: 0.7360 (mttt) cc_final: 0.7051 (tmmt) REVERT: D 814 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.6712 (pptt) REVERT: D 935 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7399 (tm-30) REVERT: D 949 GLN cc_start: 0.7068 (mm-40) cc_final: 0.6354 (mt0) REVERT: D 950 ASP cc_start: 0.7283 (m-30) cc_final: 0.6906 (m-30) REVERT: D 954 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7641 (mt0) REVERT: D 994 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7184 (t0) REVERT: D 1010 GLN cc_start: 0.7465 (tp40) cc_final: 0.6697 (tm-30) REVERT: D 1017 GLU cc_start: 0.7446 (tt0) cc_final: 0.7169 (tt0) REVERT: D 1038 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7486 (mmtp) REVERT: D 1050 MET cc_start: 0.9146 (ptm) cc_final: 0.8842 (ptp) REVERT: D 1113 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7886 (mm110) outliers start: 81 outliers final: 47 residues processed: 250 average time/residue: 1.1654 time to fit residues: 354.7917 Evaluate side-chains 252 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 183 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 439 ASN Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 748 GLU Chi-restraints excluded: chain D residue 814 LYS Chi-restraints excluded: chain D residue 935 GLN Chi-restraints excluded: chain D residue 954 GLN Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain D residue 1127 ASP Chi-restraints excluded: chain F residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 208 optimal weight: 6.9990 chunk 336 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 159 optimal weight: 20.0000 chunk 233 optimal weight: 8.9990 chunk 352 optimal weight: 7.9990 chunk 324 optimal weight: 5.9990 chunk 280 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 321 GLN B 762 GLN B 907 ASN ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1125 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 29059 Z= 0.355 Angle : 0.640 11.255 39544 Z= 0.328 Chirality : 0.049 0.503 4604 Planarity : 0.005 0.054 5073 Dihedral : 5.424 54.113 4812 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.20 % Favored : 95.69 % Rotamer: Outliers : 2.67 % Allowed : 15.98 % Favored : 81.34 % 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: -0.35 (0.14), residues: 3526 helix: 1.62 (0.20), residues: 704 sheet: 0.04 (0.16), residues: 944 loop : -1.12 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 353 HIS 0.008 0.001 HIS D1083 PHE 0.027 0.002 PHE D 192 TYR 0.041 0.002 TYR A1067 ARG 0.005 0.001 ARG A 815 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 194 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6127 (mttm) cc_final: 0.5715 (ptmm) REVERT: A 153 MET cc_start: 0.0642 (OUTLIER) cc_final: -0.0551 (mpp) REVERT: A 190 ARG cc_start: 0.5594 (OUTLIER) cc_final: 0.4212 (mmt180) REVERT: A 200 TYR cc_start: 0.6835 (OUTLIER) cc_final: 0.6501 (t80) REVERT: A 396 TYR cc_start: 0.4564 (OUTLIER) cc_final: 0.3922 (p90) REVERT: A 529 LYS cc_start: 0.7681 (mmmm) cc_final: 0.7200 (mmmt) REVERT: A 537 LYS cc_start: 0.6927 (ttmt) cc_final: 0.6530 (ttpt) REVERT: A 646 ARG cc_start: 0.7221 (mtt180) cc_final: 0.6662 (mtp180) REVERT: A 779 GLN cc_start: 0.7503 (tt0) cc_final: 0.7179 (tp40) REVERT: A 790 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8088 (mtpt) REVERT: A 825 LYS cc_start: 0.7809 (mmtt) cc_final: 0.7342 (mtpt) REVERT: A 868 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6136 (mp0) REVERT: A 964 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.6680 (mptp) REVERT: A 1038 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.7892 (mtpt) REVERT: A 1125 ASN cc_start: 0.7379 (m-40) cc_final: 0.7090 (p0) REVERT: B 51 THR cc_start: 0.7687 (OUTLIER) cc_final: 0.7395 (t) REVERT: B 195 LYS cc_start: 0.6178 (mtpt) cc_final: 0.5776 (mtmm) REVERT: B 211 ASN cc_start: 0.3865 (OUTLIER) cc_final: 0.3579 (m-40) REVERT: B 319 ARG cc_start: 0.7851 (ttm170) cc_final: 0.7279 (mtp180) REVERT: B 564 GLN cc_start: 0.6338 (OUTLIER) cc_final: 0.5955 (mm110) REVERT: B 651 ILE cc_start: 0.8726 (mt) cc_final: 0.8490 (mm) REVERT: B 654 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6750 (tm-30) REVERT: B 735 SER cc_start: 0.7335 (t) cc_final: 0.6960 (p) REVERT: B 780 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7281 (tt0) REVERT: B 787 GLN cc_start: 0.8017 (mt0) cc_final: 0.7752 (mp10) REVERT: B 995 ARG cc_start: 0.7586 (mtt180) cc_final: 0.7218 (mtp180) REVERT: B 1045 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7634 (tmtt) REVERT: B 1125 ASN cc_start: 0.7395 (m-40) cc_final: 0.6970 (p0) REVERT: D 45 SER cc_start: 0.7927 (p) cc_final: 0.7384 (p) REVERT: D 47 VAL cc_start: 0.6838 (p) cc_final: 0.6552 (m) REVERT: D 153 MET cc_start: 0.0556 (ttt) cc_final: -0.0919 (mtm) REVERT: D 266 TYR cc_start: 0.6890 (OUTLIER) cc_final: 0.6556 (m-80) REVERT: D 439 ASN cc_start: 0.2835 (OUTLIER) cc_final: 0.2238 (t0) REVERT: D 558 LYS cc_start: 0.7414 (mttt) cc_final: 0.7080 (tmtt) REVERT: D 814 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.6621 (pptt) REVERT: D 935 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7355 (tm-30) REVERT: D 950 ASP cc_start: 0.7423 (m-30) cc_final: 0.7119 (m-30) REVERT: D 954 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7666 (mt0) REVERT: D 983 ARG cc_start: 0.7345 (mtp85) cc_final: 0.7117 (mtp85) REVERT: D 994 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7250 (t0) REVERT: D 1010 GLN cc_start: 0.7454 (tp40) cc_final: 0.6749 (tm-30) REVERT: D 1017 GLU cc_start: 0.7533 (tt0) cc_final: 0.7249 (tt0) REVERT: D 1038 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7638 (ttmm) REVERT: D 1050 MET cc_start: 0.9181 (ptm) cc_final: 0.8903 (ptp) REVERT: D 1113 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7969 (mm110) outliers start: 83 outliers final: 52 residues processed: 251 average time/residue: 1.1569 time to fit residues: 350.7138 Evaluate side-chains 264 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 191 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 439 ASN Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 748 GLU Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 814 LYS Chi-restraints excluded: chain D residue 935 GLN Chi-restraints excluded: chain D residue 954 GLN Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1038 LYS Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain D residue 1127 ASP Chi-restraints excluded: chain F residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 223 optimal weight: 0.6980 chunk 299 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 258 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 281 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 chunk 288 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS B 207 HIS B 321 GLN B 907 ASN D 935 GLN D 957 GLN D1125 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.237676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.162478 restraints weight = 35979.124| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.94 r_work: 0.3636 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 29059 Z= 0.212 Angle : 0.561 10.965 39544 Z= 0.287 Chirality : 0.046 0.496 4604 Planarity : 0.004 0.055 5073 Dihedral : 5.139 54.847 4812 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.32 % Favored : 96.57 % Rotamer: Outliers : 2.61 % Allowed : 16.44 % Favored : 80.95 % 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: -0.22 (0.14), residues: 3526 helix: 1.86 (0.20), residues: 702 sheet: 0.07 (0.16), residues: 944 loop : -1.06 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 64 HIS 0.008 0.001 HIS D1083 PHE 0.026 0.001 PHE B 400 TYR 0.034 0.001 TYR A1067 ARG 0.004 0.000 ARG D 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10776.66 seconds wall clock time: 193 minutes 49.17 seconds (11629.17 seconds total)