Starting phenix.real_space_refine on Tue Jun 24 20:49:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g76_29798/06_2025/8g76_29798.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g76_29798/06_2025/8g76_29798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g76_29798/06_2025/8g76_29798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g76_29798/06_2025/8g76_29798.map" model { file = "/net/cci-nas-00/data/ceres_data/8g76_29798/06_2025/8g76_29798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g76_29798/06_2025/8g76_29798.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 18113 2.51 5 N 4738 2.21 5 O 5589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 1.49s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28569 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 8386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1074, 8386 Classifications: {'peptide': 1074} Link IDs: {'PTRANS': 58, 'TRANS': 1015} Chain breaks: 4 Chain: "B" Number of atoms: 8415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8415 Classifications: {'peptide': 1077} Link IDs: {'PTRANS': 58, 'TRANS': 1018} Chain breaks: 4 Chain: "D" Number of atoms: 8383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8383 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 5 Chain: "E" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 881 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "H" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 881 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "I" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 881 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, '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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" 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: "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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 17.43, per 1000 atoms: 0.61 Number of scatterers: 28569 At special positions: 0 Unit cell: (160.245, 175.296, 177.067, 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 5589 8.00 N 4738 7.00 C 18113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 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 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.01 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 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-ASN " NAG A1301 " - " ASN A1134 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 603 " " NAG A1311 " - " ASN A 234 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 717 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 61 " " NAG B1310 " - " ASN B 165 " " NAG B1311 " - " ASN B 282 " " NAG C 1 " - " ASN A 801 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 282 " " NAG D1303 " - " ASN D 331 " " NAG D1304 " - " ASN D 616 " " NAG D1305 " - " ASN D 657 " " NAG D1306 " - " ASN D 709 " " NAG D1307 " - " ASN D1074 " " NAG D1308 " - " ASN D 17 " " NAG D1309 " - " ASN D 165 " " NAG D1310 " - " ASN D 343 " " NAG D1311 " - " ASN D 603 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN B 801 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN D 717 " " NAG N 1 " - " ASN D 801 " " NAG O 1 " - " ASN D1098 " " NAG P 1 " - " ASN D1134 " Time building additional restraints: 7.36 Conformation dependent library (CDL) restraints added in 3.2 seconds 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6654 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 60 sheets defined 23.6% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 257 through 261 removed outlier: 3.930A pdb=" N ALA A 260 " --> pdb=" O GLY A 257 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 261 " --> pdb=" O TRP A 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 261' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.429A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.319A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.934A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 738 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.013A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.036A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.029A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.678A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.353A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.274A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.632A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.698A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' 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 364 through 371 removed outlier: 4.279A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.655A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.264A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.786A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 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: 3.628A 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 890 Processing helix chain 'B' and resid 897 through 910 removed outlier: 4.438A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.128A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.573A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.721A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.083A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 344 removed outlier: 3.720A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 371 removed outlier: 4.141A pdb=" N LEU D 368 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 389 removed outlier: 4.238A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 411 removed outlier: 3.938A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 410 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.586A 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 619 through 623 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: 3.602A 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 884 Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 897 through 910 Processing helix chain 'D' and resid 912 through 918 removed outlier: 4.183A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.664A pdb=" N SER D 939 " --> pdb=" O GLN D 935 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 965 removed outlier: 4.421A 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 976 through 982 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.244A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D1033 " --> pdb=" O MET D1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1118 No H-bonds generated for 'chain 'D' and resid 1116 through 1118' Processing helix chain 'D' and resid 1140 through 1147 removed outlier: 3.675A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'I' and resid 27 through 32 removed outlier: 4.204A pdb=" N GLU I 32 " --> pdb=" O ILE I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 3.959A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.510A pdb=" N THR D 553 " --> pdb=" O ASP D 586 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU D 324 " --> pdb=" O ASN D 540 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ASN D 542 " --> pdb=" O GLU D 324 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE D 326 " --> pdb=" O ASN D 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.535A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.619A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 155 through 160 removed outlier: 7.213A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 9.674A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.983A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 593 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.867A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.510A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.589A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.249A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.016A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.708A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.689A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.502A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.068A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.745A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.353A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.617A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 68 through 69 Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.809A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.642A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.642A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.218A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.555A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE B 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.512A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.735A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.560A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'B' and resid 653 through 655 removed outlier: 6.390A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 701 through 702 removed outlier: 7.224A pdb=" N ALA B 701 " --> pdb=" O ILE D 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.591A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.017A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.016A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 27 through 30 removed outlier: 4.174A pdb=" N ALA D 27 " --> pdb=" O TRP D 64 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 264 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR D 95 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL D 90 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N HIS D 207 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N ALA D 222 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.750A pdb=" N LEU D 276 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA D 288 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LYS D 278 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 54 through 55 Processing sheet with id=AE5, first strand: chain 'D' and resid 68 through 69 removed outlier: 4.101A pdb=" N ARG D 78 " --> pdb=" O HIS D 69 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.619A pdb=" N ILE D 105 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 154 through 160 removed outlier: 3.685A pdb=" N GLU D 154 " --> pdb=" O TYR D 144 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N TYR D 160 " --> pdb=" O ASP D 138 " (cutoff:3.500A) removed outlier: 10.277A pdb=" N ASP D 138 " --> pdb=" O TYR D 160 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N LEU D 244 " --> pdb=" O PRO D 139 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU D 141 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.205A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS D 649 " --> pdb=" O TYR D 612 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE D 643 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 356 through 358 Processing sheet with id=AF1, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AF2, first strand: chain 'D' and resid 654 through 655 removed outlier: 5.944A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE D 664 " --> pdb=" O ALA D 672 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.700A pdb=" N ILE D 714 " --> pdb=" O LYS D1073 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR D1076 " --> pdb=" O SER D1097 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA D1078 " --> pdb=" O PHE D1095 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR D1105 " --> pdb=" O VAL D1094 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 718 through 728 removed outlier: 7.414A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.548A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.515A pdb=" N CYS E 22 " --> pdb=" O VAL E 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE E 68 " --> pdb=" O GLN E 81 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.720A pdb=" N GLY E 10 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER E 113 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL E 12 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG E 98 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU E 33 " --> pdb=" O ARG E 98 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N MET E 34 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.720A pdb=" N GLY E 10 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER E 113 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL E 12 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA E 97 " --> pdb=" O TYR E 103 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 11 through 13 removed outlier: 7.086A pdb=" N VAL H 12 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU H 33 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 11 through 13 removed outlier: 7.086A pdb=" N VAL H 12 " --> pdb=" O SER H 113 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.948A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 11 through 13 removed outlier: 6.857A pdb=" N VAL I 12 " --> pdb=" O SER I 113 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N MET I 34 " --> pdb=" O THR I 50 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU I 46 " --> pdb=" O HIS I 38 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 17 through 23 removed outlier: 3.502A pdb=" N LEU I 18 " --> pdb=" O MET I 82 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU I 20 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU I 80 " --> pdb=" O LEU I 20 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N CYS I 22 " --> pdb=" O VAL I 78 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE I 68 " --> pdb=" O GLN I 81 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 96 through 98 1041 hydrogen bonds defined for protein. 2820 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: 14.08 Time building geometry restraints manager: 8.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9124 1.34 - 1.46: 7009 1.46 - 1.58: 12917 1.58 - 1.70: 0 1.70 - 1.83: 165 Bond restraints: 29215 Sorted by residual: bond pdb=" N PRO B 892 " pdb=" CD PRO B 892 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.16e+01 bond pdb=" N LEU A 216 " pdb=" CA LEU A 216 " ideal model delta sigma weight residual 1.453 1.488 -0.034 1.16e-02 7.43e+03 8.75e+00 bond pdb=" N ILE A 692 " pdb=" CA ILE A 692 " ideal model delta sigma weight residual 1.459 1.491 -0.033 1.20e-02 6.94e+03 7.39e+00 bond pdb=" N ILE B 692 " pdb=" CA ILE B 692 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.21e-02 6.83e+03 7.36e+00 bond pdb=" N LEU A 212 " pdb=" CA LEU A 212 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.27e+00 ... (remaining 29210 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 39220 2.44 - 4.89: 470 4.89 - 7.33: 49 7.33 - 9.77: 10 9.77 - 12.21: 5 Bond angle restraints: 39754 Sorted by residual: angle pdb=" CA PRO B 892 " pdb=" N PRO B 892 " pdb=" CD PRO B 892 " ideal model delta sigma weight residual 112.00 99.79 12.21 1.40e+00 5.10e-01 7.61e+01 angle pdb=" CB LYS B 462 " pdb=" CG LYS B 462 " pdb=" CD LYS B 462 " ideal model delta sigma weight residual 111.30 120.99 -9.69 2.30e+00 1.89e-01 1.78e+01 angle pdb=" CA GLN A 414 " pdb=" CB GLN A 414 " pdb=" CG GLN A 414 " ideal model delta sigma weight residual 114.10 121.98 -7.88 2.00e+00 2.50e-01 1.55e+01 angle pdb=" CA MET B 902 " pdb=" C MET B 902 " pdb=" N ALA B 903 " ideal model delta sigma weight residual 117.07 121.27 -4.20 1.14e+00 7.69e-01 1.35e+01 angle pdb=" CA LYS B 304 " pdb=" CB LYS B 304 " pdb=" CG LYS B 304 " ideal model delta sigma weight residual 114.10 121.36 -7.26 2.00e+00 2.50e-01 1.32e+01 ... (remaining 39749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 16160 17.91 - 35.83: 1490 35.83 - 53.74: 351 53.74 - 71.66: 68 71.66 - 89.57: 21 Dihedral angle restraints: 18090 sinusoidal: 7730 harmonic: 10360 Sorted by residual: dihedral pdb=" CB CYS D 617 " pdb=" SG CYS D 617 " pdb=" SG CYS D 649 " pdb=" CB CYS D 649 " ideal model delta sinusoidal sigma weight residual 93.00 15.96 77.04 1 1.00e+01 1.00e-02 7.45e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 167.63 -74.63 1 1.00e+01 1.00e-02 7.05e+01 dihedral pdb=" CB CYS D1082 " pdb=" SG CYS D1082 " pdb=" SG CYS D1126 " pdb=" CB CYS D1126 " ideal model delta sinusoidal sigma weight residual -86.00 -39.58 -46.42 1 1.00e+01 1.00e-02 2.98e+01 ... (remaining 18087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4256 0.090 - 0.180: 366 0.180 - 0.270: 9 0.270 - 0.360: 1 0.360 - 0.450: 2 Chirality restraints: 4634 Sorted by residual: chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.07e+00 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 -2.36 -0.04 2.00e-02 2.50e+03 4.56e+00 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.40e+00 ... (remaining 4631 not shown) Planarity restraints: 5126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.055 2.00e-02 2.50e+03 6.05e-02 4.57e+01 pdb=" CG ASN A 234 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.091 2.00e-02 2.50e+03 pdb=" C1 NAG A1311 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 891 " -0.107 5.00e-02 4.00e+02 1.50e-01 3.59e+01 pdb=" N PRO B 892 " 0.259 5.00e-02 4.00e+02 pdb=" CA PRO B 892 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO B 892 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 411 " 0.045 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO A 412 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " 0.037 5.00e-02 4.00e+02 ... (remaining 5123 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 351 2.56 - 3.14: 23451 3.14 - 3.73: 44656 3.73 - 4.31: 59330 4.31 - 4.90: 97175 Nonbonded interactions: 224963 Sorted by model distance: nonbonded pdb=" OE2 GLU B 654 " pdb=" OE1 GLN B 690 " model vdw 1.971 3.040 nonbonded pdb=" CG GLU B 654 " pdb=" CG GLN B 690 " model vdw 2.030 3.840 nonbonded pdb=" OE2 GLU B 654 " pdb=" CD GLN B 690 " model vdw 2.039 3.270 nonbonded pdb=" O ASN A 74 " pdb=" OG SER A 254 " model vdw 2.126 3.040 nonbonded pdb=" OG SER A 359 " pdb=" OD1 ASN A 394 " model vdw 2.131 3.040 ... (remaining 224958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 172 or resid 186 through 249 or resid 254 throu \ gh 1147 or resid 1301 through 1311)) selection = (chain 'B' and (resid 14 through 172 or resid 186 through 249 or resid 254 throu \ gh 623 or resid 634 through 676 or resid 690 through 827 or resid 855 through 11 \ 47 or resid 1301 through 1311)) selection = (chain 'D' and (resid 14 through 623 or resid 634 through 676 or resid 690 throu \ gh 827 or resid 855 through 1147 or resid 1301 through 1311)) } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.300 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 67.330 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 29312 Z= 0.214 Angle : 0.697 19.421 40001 Z= 0.341 Chirality : 0.046 0.450 4634 Planarity : 0.004 0.150 5083 Dihedral : 14.488 89.573 11304 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.56 % Favored : 95.29 % Rotamer: Outliers : 0.42 % Allowed : 20.12 % Favored : 79.46 % 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: -0.47 (0.14), residues: 3528 helix: 2.07 (0.20), residues: 677 sheet: -0.37 (0.18), residues: 824 loop : -1.15 (0.14), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 104 HIS 0.006 0.001 HIS H 96 PHE 0.025 0.001 PHE E 29 TYR 0.018 0.001 TYR A 505 ARG 0.007 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.01717 ( 43) link_NAG-ASN : angle 4.00107 ( 129) link_BETA1-4 : bond 0.00257 ( 10) link_BETA1-4 : angle 1.04971 ( 30) hydrogen bonds : bond 0.23797 ( 1029) hydrogen bonds : angle 8.64212 ( 2820) SS BOND : bond 0.00409 ( 44) SS BOND : angle 0.88804 ( 88) covalent geometry : bond 0.00435 (29215) covalent geometry : angle 0.65863 (39754) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 545 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8182 (m) cc_final: 0.7701 (m) REVERT: A 290 ASP cc_start: 0.7471 (t0) cc_final: 0.7244 (t0) REVERT: A 320 VAL cc_start: 0.7469 (t) cc_final: 0.7104 (t) REVERT: A 321 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7744 (tm-30) REVERT: A 347 PHE cc_start: 0.5534 (m-80) cc_final: 0.5251 (m-10) REVERT: A 351 TYR cc_start: 0.8391 (p90) cc_final: 0.8138 (p90) REVERT: A 429 PHE cc_start: 0.5604 (t80) cc_final: 0.5289 (t80) REVERT: A 508 TYR cc_start: 0.7461 (m-80) cc_final: 0.7034 (m-80) REVERT: A 515 PHE cc_start: 0.8168 (m-80) cc_final: 0.7931 (m-80) REVERT: A 725 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6812 (mt-10) REVERT: A 855 PHE cc_start: 0.6044 (m-80) cc_final: 0.5275 (m-80) REVERT: A 1014 ARG cc_start: 0.7348 (tpp80) cc_final: 0.6985 (mtp85) REVERT: A 1092 GLU cc_start: 0.8272 (tp30) cc_final: 0.7658 (pm20) REVERT: B 351 TYR cc_start: 0.8531 (p90) cc_final: 0.7994 (p90) REVERT: B 383 SER cc_start: 0.7191 (t) cc_final: 0.6828 (p) REVERT: B 396 TYR cc_start: 0.7441 (m-10) cc_final: 0.6917 (m-10) REVERT: B 424 LYS cc_start: 0.7446 (tptt) cc_final: 0.7234 (ttmm) REVERT: B 560 LEU cc_start: 0.7996 (mt) cc_final: 0.7484 (mp) REVERT: B 605 SER cc_start: 0.8266 (t) cc_final: 0.7848 (m) REVERT: B 663 ASP cc_start: 0.8448 (t0) cc_final: 0.8217 (t0) REVERT: B 699 LEU cc_start: 0.8265 (mt) cc_final: 0.7936 (mt) REVERT: B 725 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6318 (mt-10) REVERT: B 1014 ARG cc_start: 0.7110 (tpp80) cc_final: 0.6839 (mtp85) REVERT: B 1092 GLU cc_start: 0.8206 (tp30) cc_final: 0.7657 (pm20) REVERT: B 1107 ARG cc_start: 0.7863 (mtt180) cc_final: 0.7626 (mtt-85) REVERT: B 1135 ASN cc_start: 0.8187 (t0) cc_final: 0.7909 (t0) REVERT: B 1138 TYR cc_start: 0.6911 (t80) cc_final: 0.6528 (m-80) REVERT: D 44 ARG cc_start: 0.5799 (mtt-85) cc_final: 0.5031 (mtt-85) REVERT: D 200 TYR cc_start: 0.6949 (m-80) cc_final: 0.6302 (m-10) REVERT: D 321 GLN cc_start: 0.8109 (tp40) cc_final: 0.7648 (pm20) REVERT: D 335 LEU cc_start: 0.7960 (mm) cc_final: 0.7689 (tp) REVERT: D 369 TYR cc_start: 0.8786 (t80) cc_final: 0.8481 (t80) REVERT: D 400 PHE cc_start: 0.7257 (p90) cc_final: 0.6960 (p90) REVERT: D 465 GLU cc_start: 0.6943 (tp30) cc_final: 0.6355 (tm-30) REVERT: D 558 LYS cc_start: 0.7806 (mmtp) cc_final: 0.7361 (mmtm) REVERT: D 560 LEU cc_start: 0.8220 (mm) cc_final: 0.7901 (mm) REVERT: D 613 GLN cc_start: 0.7837 (pp30) cc_final: 0.7490 (mt0) REVERT: D 699 LEU cc_start: 0.8466 (mt) cc_final: 0.8148 (mt) REVERT: D 731 MET cc_start: 0.7081 (ttp) cc_final: 0.6315 (ptm) REVERT: D 869 MET cc_start: 0.6932 (mtm) cc_final: 0.6600 (ptm) REVERT: D 955 ASN cc_start: 0.7719 (t0) cc_final: 0.7469 (t0) REVERT: D 957 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7693 (tm-30) REVERT: D 1092 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7853 (pm20) REVERT: E 59 TYR cc_start: 0.7613 (m-80) cc_final: 0.7187 (m-80) REVERT: E 69 ILE cc_start: 0.7362 (tt) cc_final: 0.7130 (tp) REVERT: H 45 ARG cc_start: 0.4396 (ptt180) cc_final: 0.4111 (ptm160) REVERT: H 59 TYR cc_start: 0.7796 (m-80) cc_final: 0.6779 (m-80) REVERT: H 80 LEU cc_start: 0.5420 (tt) cc_final: 0.5048 (tt) REVERT: H 89 ASP cc_start: 0.4888 (m-30) cc_final: 0.4571 (m-30) REVERT: H 109 GLN cc_start: 0.7382 (pm20) cc_final: 0.7153 (tp40) REVERT: I 20 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6188 (mm) REVERT: I 29 PHE cc_start: 0.7516 (m-80) cc_final: 0.7047 (m-80) REVERT: I 39 GLN cc_start: 0.5272 (mt0) cc_final: 0.4898 (mm-40) REVERT: I 51 ILE cc_start: 0.5529 (tp) cc_final: 0.5194 (tp) REVERT: I 106 ARG cc_start: 0.8452 (mmp80) cc_final: 0.7597 (mmp80) outliers start: 13 outliers final: 0 residues processed: 555 average time/residue: 0.4464 time to fit residues: 387.1216 Evaluate side-chains 326 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 325 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 20 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 0.9980 chunk 268 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 277 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 168 optimal weight: 0.0270 chunk 206 optimal weight: 2.9990 chunk 321 optimal weight: 4.9990 overall best weight: 1.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** D 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 39 GLN H 81 GLN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.154293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.103582 restraints weight = 58774.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.103301 restraints weight = 44796.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.103883 restraints weight = 30621.314| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 29312 Z= 0.168 Angle : 0.745 18.440 40001 Z= 0.367 Chirality : 0.048 0.494 4634 Planarity : 0.005 0.119 5083 Dihedral : 7.093 57.807 4953 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.96 % Favored : 94.90 % Rotamer: Outliers : 2.89 % Allowed : 20.38 % Favored : 76.73 % 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: -0.45 (0.14), residues: 3528 helix: 1.98 (0.20), residues: 699 sheet: -0.25 (0.17), residues: 866 loop : -1.20 (0.14), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 104 HIS 0.008 0.001 HIS H 96 PHE 0.026 0.002 PHE A 464 TYR 0.028 0.001 TYR B 453 ARG 0.006 0.001 ARG D 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 43) link_NAG-ASN : angle 4.47068 ( 129) link_BETA1-4 : bond 0.00576 ( 10) link_BETA1-4 : angle 1.09551 ( 30) hydrogen bonds : bond 0.06011 ( 1029) hydrogen bonds : angle 6.68788 ( 2820) SS BOND : bond 0.00392 ( 44) SS BOND : angle 2.51739 ( 88) covalent geometry : bond 0.00385 (29215) covalent geometry : angle 0.69211 (39754) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 348 time to evaluate : 3.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9224 (tm-30) cc_final: 0.8822 (tm-30) REVERT: A 140 PHE cc_start: 0.8124 (p90) cc_final: 0.7485 (p90) REVERT: A 321 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7891 (tm-30) REVERT: A 347 PHE cc_start: 0.6206 (m-80) cc_final: 0.5598 (m-80) REVERT: A 351 TYR cc_start: 0.8242 (p90) cc_final: 0.7567 (p90) REVERT: A 454 ARG cc_start: 0.4927 (mtt180) cc_final: 0.4313 (tpp80) REVERT: A 515 PHE cc_start: 0.8150 (m-80) cc_final: 0.7917 (m-80) REVERT: A 560 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7945 (mm) REVERT: A 855 PHE cc_start: 0.6174 (m-80) cc_final: 0.5688 (m-80) REVERT: A 902 MET cc_start: 0.8492 (tpp) cc_final: 0.8078 (mmt) REVERT: A 1014 ARG cc_start: 0.8198 (tpp80) cc_final: 0.7924 (mtp85) REVERT: A 1029 MET cc_start: 0.9166 (tpp) cc_final: 0.8910 (tpp) REVERT: B 90 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8598 (m) REVERT: B 115 GLN cc_start: 0.7367 (pm20) cc_final: 0.6661 (tp40) REVERT: B 321 GLN cc_start: 0.7690 (tp40) cc_final: 0.7439 (tm-30) REVERT: B 351 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.7521 (p90) REVERT: B 396 TYR cc_start: 0.7358 (m-10) cc_final: 0.6568 (m-10) REVERT: B 400 PHE cc_start: 0.8278 (p90) cc_final: 0.8031 (p90) REVERT: B 424 LYS cc_start: 0.7920 (tptt) cc_final: 0.7618 (ttmm) REVERT: B 560 LEU cc_start: 0.8384 (mt) cc_final: 0.7763 (mp) REVERT: B 699 LEU cc_start: 0.8742 (mt) cc_final: 0.8516 (mt) REVERT: B 858 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8023 (mt) REVERT: B 957 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8232 (tm-30) REVERT: B 1014 ARG cc_start: 0.8221 (tpp80) cc_final: 0.8005 (mtp85) REVERT: D 140 PHE cc_start: 0.8305 (p90) cc_final: 0.7710 (p90) REVERT: D 200 TYR cc_start: 0.6487 (m-80) cc_final: 0.5659 (m-80) REVERT: D 321 GLN cc_start: 0.8090 (tp40) cc_final: 0.7848 (pm20) REVERT: D 335 LEU cc_start: 0.8211 (mm) cc_final: 0.7801 (tp) REVERT: D 400 PHE cc_start: 0.7651 (p90) cc_final: 0.7395 (p90) REVERT: D 424 LYS cc_start: 0.7583 (ttmm) cc_final: 0.7341 (ptmm) REVERT: D 560 LEU cc_start: 0.8495 (mm) cc_final: 0.8120 (mt) REVERT: D 816 SER cc_start: 0.8777 (t) cc_final: 0.8301 (p) REVERT: D 819 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8364 (mt-10) REVERT: D 950 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7974 (p0) REVERT: D 957 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8325 (tm-30) REVERT: D 1050 MET cc_start: 0.8912 (ptp) cc_final: 0.8430 (ptm) REVERT: E 35 GLU cc_start: 0.7500 (tt0) cc_final: 0.6681 (mt-10) REVERT: I 20 LEU cc_start: 0.6758 (pt) cc_final: 0.6304 (mm) REVERT: I 106 ARG cc_start: 0.8621 (mmp80) cc_final: 0.7926 (mmp80) outliers start: 90 outliers final: 33 residues processed: 407 average time/residue: 0.3767 time to fit residues: 248.0178 Evaluate side-chains 322 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 284 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 675 GLN Chi-restraints excluded: chain D residue 803 SER Chi-restraints excluded: chain D residue 950 ASP Chi-restraints excluded: chain D residue 1134 ASN Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 87 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 183 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 chunk 252 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 192 optimal weight: 0.6980 chunk 342 optimal weight: 0.0870 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 493 GLN B 690 GLN D 49 HIS D 536 ASN D 641 ASN D1011 GLN H 39 GLN H 73 ASN I 73 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.153252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.111109 restraints weight = 58211.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.109924 restraints weight = 48956.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.110738 restraints weight = 52448.180| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29312 Z= 0.167 Angle : 0.687 18.036 40001 Z= 0.341 Chirality : 0.047 0.480 4634 Planarity : 0.004 0.047 5083 Dihedral : 6.502 59.553 4951 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.62 % Favored : 95.24 % Rotamer: Outliers : 4.11 % Allowed : 19.93 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3528 helix: 1.92 (0.20), residues: 705 sheet: -0.37 (0.18), residues: 819 loop : -1.20 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 104 HIS 0.004 0.001 HIS H 38 PHE 0.022 0.002 PHE E 29 TYR 0.020 0.001 TYR B1067 ARG 0.004 0.000 ARG E 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 43) link_NAG-ASN : angle 3.84323 ( 129) link_BETA1-4 : bond 0.00278 ( 10) link_BETA1-4 : angle 1.06825 ( 30) hydrogen bonds : bond 0.05553 ( 1029) hydrogen bonds : angle 6.26626 ( 2820) SS BOND : bond 0.00294 ( 44) SS BOND : angle 2.33875 ( 88) covalent geometry : bond 0.00390 (29215) covalent geometry : angle 0.64325 (39754) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 306 time to evaluate : 3.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9199 (tm-30) cc_final: 0.8775 (tm-30) REVERT: A 140 PHE cc_start: 0.7881 (p90) cc_final: 0.7311 (p90) REVERT: A 321 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7756 (pm20) REVERT: A 335 LEU cc_start: 0.8498 (tt) cc_final: 0.8222 (mp) REVERT: A 347 PHE cc_start: 0.5985 (OUTLIER) cc_final: 0.5536 (m-80) REVERT: A 351 TYR cc_start: 0.7796 (p90) cc_final: 0.7369 (p90) REVERT: A 454 ARG cc_start: 0.5087 (mtt180) cc_final: 0.4524 (tpp80) REVERT: A 515 PHE cc_start: 0.7930 (m-80) cc_final: 0.7699 (m-80) REVERT: A 654 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: A 691 SER cc_start: 0.8184 (OUTLIER) cc_final: 0.7792 (p) REVERT: A 855 PHE cc_start: 0.6330 (m-80) cc_final: 0.5972 (m-80) REVERT: A 902 MET cc_start: 0.8125 (tpp) cc_final: 0.7818 (mmt) REVERT: A 1014 ARG cc_start: 0.8281 (tpp80) cc_final: 0.8048 (mtp85) REVERT: A 1029 MET cc_start: 0.9227 (tpp) cc_final: 0.8563 (tpp) REVERT: A 1092 GLU cc_start: 0.7559 (pm20) cc_final: 0.7322 (pm20) REVERT: B 229 LEU cc_start: 0.8070 (tp) cc_final: 0.7834 (tp) REVERT: B 351 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.7252 (p90) REVERT: B 396 TYR cc_start: 0.7069 (m-10) cc_final: 0.6424 (m-10) REVERT: B 400 PHE cc_start: 0.8143 (p90) cc_final: 0.7906 (p90) REVERT: B 560 LEU cc_start: 0.8268 (mt) cc_final: 0.7662 (mp) REVERT: B 588 THR cc_start: 0.8815 (m) cc_final: 0.8560 (p) REVERT: B 634 ARG cc_start: 0.4468 (OUTLIER) cc_final: 0.3484 (mtp-110) REVERT: B 902 MET cc_start: 0.8263 (tpt) cc_final: 0.7693 (tpt) REVERT: B 957 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8262 (tm-30) REVERT: B 1001 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7955 (mm) REVERT: B 1014 ARG cc_start: 0.8409 (tpp80) cc_final: 0.8083 (mtp85) REVERT: D 140 PHE cc_start: 0.8174 (p90) cc_final: 0.7846 (p90) REVERT: D 200 TYR cc_start: 0.6211 (m-80) cc_final: 0.5333 (m-80) REVERT: D 335 LEU cc_start: 0.8303 (mm) cc_final: 0.7901 (tp) REVERT: D 560 LEU cc_start: 0.8562 (mm) cc_final: 0.8150 (mt) REVERT: D 621 PRO cc_start: 0.8480 (Cg_exo) cc_final: 0.8268 (Cg_endo) REVERT: D 816 SER cc_start: 0.8820 (t) cc_final: 0.8379 (p) REVERT: D 819 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8369 (mt-10) REVERT: D 950 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7989 (p0) REVERT: E 35 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: E 80 LEU cc_start: 0.7496 (tp) cc_final: 0.7242 (tt) REVERT: E 82 MET cc_start: 0.8343 (mmm) cc_final: 0.7423 (mmm) REVERT: E 86 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7883 (ptpp) REVERT: I 106 ARG cc_start: 0.8487 (mmp80) cc_final: 0.7947 (mmp80) outliers start: 128 outliers final: 64 residues processed: 398 average time/residue: 0.3779 time to fit residues: 245.6786 Evaluate side-chains 349 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 276 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 803 SER Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 950 ASP Chi-restraints excluded: chain D residue 1134 ASN Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 87 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 33 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 234 optimal weight: 0.5980 chunk 164 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 324 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 350 optimal weight: 9.9990 chunk 182 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 334 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN I 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.151487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.100508 restraints weight = 58809.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.100592 restraints weight = 40645.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.101034 restraints weight = 29030.903| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 29312 Z= 0.196 Angle : 0.712 17.689 40001 Z= 0.351 Chirality : 0.050 0.938 4634 Planarity : 0.004 0.068 5083 Dihedral : 6.274 58.883 4951 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.75 % Favored : 94.10 % Rotamer: Outliers : 4.98 % Allowed : 20.38 % Favored : 74.64 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 3528 helix: 1.79 (0.20), residues: 711 sheet: -0.43 (0.18), residues: 822 loop : -1.30 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 104 HIS 0.005 0.001 HIS D1058 PHE 0.037 0.002 PHE E 29 TYR 0.024 0.001 TYR E 59 ARG 0.013 0.001 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00762 ( 43) link_NAG-ASN : angle 4.33064 ( 129) link_BETA1-4 : bond 0.00236 ( 10) link_BETA1-4 : angle 1.11097 ( 30) hydrogen bonds : bond 0.05634 ( 1029) hydrogen bonds : angle 6.10757 ( 2820) SS BOND : bond 0.00420 ( 44) SS BOND : angle 2.53929 ( 88) covalent geometry : bond 0.00462 (29215) covalent geometry : angle 0.65902 (39754) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 301 time to evaluate : 2.782 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 52 GLN cc_start: 0.9235 (tm-30) cc_final: 0.8772 (tm-30) REVERT: A 71 SER cc_start: 0.5460 (OUTLIER) cc_final: 0.5113 (m) REVERT: A 140 PHE cc_start: 0.8140 (p90) cc_final: 0.7472 (p90) REVERT: A 321 GLN cc_start: 0.8331 (mm-40) cc_final: 0.8073 (pm20) REVERT: A 347 PHE cc_start: 0.6075 (m-80) cc_final: 0.5794 (m-80) REVERT: A 351 TYR cc_start: 0.8262 (p90) cc_final: 0.7571 (p90) REVERT: A 454 ARG cc_start: 0.5122 (mtt180) cc_final: 0.4534 (tpp80) REVERT: A 562 PHE cc_start: 0.8536 (p90) cc_final: 0.8103 (p90) REVERT: A 691 SER cc_start: 0.8226 (OUTLIER) cc_final: 0.7788 (p) REVERT: A 855 PHE cc_start: 0.6229 (m-80) cc_final: 0.5963 (m-80) REVERT: A 957 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8292 (tm-30) REVERT: A 1014 ARG cc_start: 0.8332 (tpp80) cc_final: 0.8078 (tpt90) REVERT: A 1029 MET cc_start: 0.9266 (tpp) cc_final: 0.8913 (tpp) REVERT: A 1092 GLU cc_start: 0.7692 (pm20) cc_final: 0.7322 (pm20) REVERT: A 1094 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8412 (m) REVERT: B 52 GLN cc_start: 0.9360 (tm-30) cc_final: 0.8962 (tm-30) REVERT: B 351 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7573 (p90) REVERT: B 396 TYR cc_start: 0.7467 (m-10) cc_final: 0.7021 (m-10) REVERT: B 408 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6757 (tpp-160) REVERT: B 467 ASP cc_start: 0.4578 (OUTLIER) cc_final: 0.4183 (m-30) REVERT: B 560 LEU cc_start: 0.8386 (mt) cc_final: 0.7818 (mp) REVERT: B 584 ILE cc_start: 0.8603 (mp) cc_final: 0.8301 (mm) REVERT: B 634 ARG cc_start: 0.4603 (OUTLIER) cc_final: 0.3683 (mtm-85) REVERT: B 902 MET cc_start: 0.8704 (tpt) cc_final: 0.8194 (tpt) REVERT: B 957 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8285 (tm-30) REVERT: B 1014 ARG cc_start: 0.8445 (tpp80) cc_final: 0.8117 (mtp85) REVERT: D 140 PHE cc_start: 0.8334 (p90) cc_final: 0.7718 (p90) REVERT: D 335 LEU cc_start: 0.8136 (mm) cc_final: 0.7784 (tp) REVERT: D 378 LYS cc_start: 0.7990 (pttt) cc_final: 0.7583 (pttt) REVERT: D 392 PHE cc_start: 0.7416 (m-80) cc_final: 0.7211 (m-10) REVERT: D 560 LEU cc_start: 0.8590 (mm) cc_final: 0.8212 (mm) REVERT: D 621 PRO cc_start: 0.8420 (Cg_exo) cc_final: 0.8192 (Cg_endo) REVERT: D 904 TYR cc_start: 0.7671 (m-10) cc_final: 0.7436 (m-10) REVERT: D 950 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8128 (p0) REVERT: D 955 ASN cc_start: 0.8451 (t0) cc_final: 0.8104 (t0) REVERT: D 1029 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.8805 (tpp) REVERT: E 35 GLU cc_start: 0.8094 (tt0) cc_final: 0.7596 (tt0) outliers start: 155 outliers final: 93 residues processed: 419 average time/residue: 0.3737 time to fit residues: 252.4004 Evaluate side-chains 381 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 279 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 950 ASP Chi-restraints excluded: chain D residue 1029 MET Chi-restraints excluded: chain D residue 1094 VAL Chi-restraints excluded: chain D residue 1134 ASN Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 83 ASN Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 99 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 201 optimal weight: 1.9990 chunk 313 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 232 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 309 optimal weight: 2.9990 chunk 301 optimal weight: 4.9990 chunk 282 optimal weight: 0.9980 chunk 349 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 437 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN H 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.152171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.110922 restraints weight = 58129.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.108521 restraints weight = 53959.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.109586 restraints weight = 60191.623| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29312 Z= 0.164 Angle : 0.681 17.431 40001 Z= 0.334 Chirality : 0.048 0.568 4634 Planarity : 0.004 0.038 5083 Dihedral : 5.983 57.627 4951 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.05 % Favored : 94.81 % Rotamer: Outliers : 4.47 % Allowed : 21.44 % Favored : 74.09 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3528 helix: 1.88 (0.20), residues: 712 sheet: -0.45 (0.18), residues: 828 loop : -1.30 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 104 HIS 0.004 0.001 HIS H 38 PHE 0.033 0.001 PHE A 541 TYR 0.021 0.001 TYR I 79 ARG 0.004 0.000 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00649 ( 43) link_NAG-ASN : angle 4.25613 ( 129) link_BETA1-4 : bond 0.00276 ( 10) link_BETA1-4 : angle 1.06444 ( 30) hydrogen bonds : bond 0.05318 ( 1029) hydrogen bonds : angle 5.94525 ( 2820) SS BOND : bond 0.00447 ( 44) SS BOND : angle 2.31170 ( 88) covalent geometry : bond 0.00385 (29215) covalent geometry : angle 0.62812 (39754) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 303 time to evaluate : 3.563 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 52 GLN cc_start: 0.9204 (tm-30) cc_final: 0.8878 (tm-30) REVERT: A 71 SER cc_start: 0.4641 (OUTLIER) cc_final: 0.4148 (m) REVERT: A 140 PHE cc_start: 0.7904 (p90) cc_final: 0.7266 (p90) REVERT: A 190 ARG cc_start: 0.7630 (mtt180) cc_final: 0.6458 (mtp180) REVERT: A 235 ILE cc_start: 0.6699 (tt) cc_final: 0.6495 (tp) REVERT: A 335 LEU cc_start: 0.8609 (tt) cc_final: 0.8265 (mp) REVERT: A 347 PHE cc_start: 0.5887 (m-80) cc_final: 0.5527 (m-10) REVERT: A 351 TYR cc_start: 0.7997 (p90) cc_final: 0.7557 (p90) REVERT: A 454 ARG cc_start: 0.5169 (mtt180) cc_final: 0.4580 (tpp80) REVERT: A 642 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8515 (t) REVERT: A 691 SER cc_start: 0.8381 (OUTLIER) cc_final: 0.7913 (p) REVERT: A 855 PHE cc_start: 0.6429 (m-80) cc_final: 0.6212 (m-80) REVERT: A 957 GLN cc_start: 0.8995 (tm-30) cc_final: 0.8370 (tm-30) REVERT: A 1014 ARG cc_start: 0.8343 (tpp80) cc_final: 0.8110 (tpt90) REVERT: A 1092 GLU cc_start: 0.7761 (pm20) cc_final: 0.7333 (pm20) REVERT: B 52 GLN cc_start: 0.9297 (tm-30) cc_final: 0.8877 (tm-30) REVERT: B 351 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.7332 (p90) REVERT: B 396 TYR cc_start: 0.7088 (m-10) cc_final: 0.6761 (m-10) REVERT: B 402 ILE cc_start: 0.7163 (tp) cc_final: 0.6921 (tp) REVERT: B 467 ASP cc_start: 0.4216 (OUTLIER) cc_final: 0.3967 (m-30) REVERT: B 516 GLU cc_start: 0.6783 (tt0) cc_final: 0.6386 (tt0) REVERT: B 560 LEU cc_start: 0.8315 (mt) cc_final: 0.7755 (mp) REVERT: B 584 ILE cc_start: 0.8700 (mp) cc_final: 0.8421 (mm) REVERT: B 634 ARG cc_start: 0.4772 (OUTLIER) cc_final: 0.3934 (mtm-85) REVERT: B 661 GLU cc_start: 0.7678 (pm20) cc_final: 0.7344 (pt0) REVERT: B 902 MET cc_start: 0.8172 (tpt) cc_final: 0.7696 (tpt) REVERT: B 957 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8338 (tm-30) REVERT: B 995 ARG cc_start: 0.7988 (mmm-85) cc_final: 0.7772 (mtm-85) REVERT: B 1001 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7833 (mm) REVERT: B 1014 ARG cc_start: 0.8410 (tpp80) cc_final: 0.8086 (mtp85) REVERT: D 140 PHE cc_start: 0.8279 (p90) cc_final: 0.7670 (p90) REVERT: D 200 TYR cc_start: 0.6282 (m-80) cc_final: 0.5626 (m-80) REVERT: D 335 LEU cc_start: 0.8187 (mm) cc_final: 0.7795 (tp) REVERT: D 541 PHE cc_start: 0.8229 (p90) cc_final: 0.7980 (p90) REVERT: D 621 PRO cc_start: 0.8443 (Cg_exo) cc_final: 0.8229 (Cg_endo) REVERT: D 904 TYR cc_start: 0.7578 (m-10) cc_final: 0.7305 (m-10) REVERT: D 955 ASN cc_start: 0.8533 (t0) cc_final: 0.8182 (t0) REVERT: D 957 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8477 (tm-30) REVERT: D 1029 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8668 (tpp) REVERT: E 37 TYR cc_start: 0.7052 (m-80) cc_final: 0.6663 (m-10) REVERT: I 106 ARG cc_start: 0.7862 (mmp80) cc_final: 0.7500 (mmp80) outliers start: 139 outliers final: 88 residues processed: 409 average time/residue: 0.4781 time to fit residues: 317.3404 Evaluate side-chains 373 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 277 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 1029 MET Chi-restraints excluded: chain D residue 1094 VAL Chi-restraints excluded: chain D residue 1134 ASN Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 99 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 155 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 151 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 307 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 271 optimal weight: 0.5980 chunk 141 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN B 30 ASN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B1125 ASN D 69 HIS D 388 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 GLN H 73 ASN H 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.150279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.109273 restraints weight = 59124.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.105981 restraints weight = 54928.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.107976 restraints weight = 57417.268| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 29312 Z= 0.190 Angle : 0.693 17.187 40001 Z= 0.342 Chirality : 0.048 0.543 4634 Planarity : 0.004 0.041 5083 Dihedral : 5.923 58.732 4951 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.75 % Favored : 94.10 % Rotamer: Outliers : 4.73 % Allowed : 21.89 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3528 helix: 1.77 (0.20), residues: 712 sheet: -0.48 (0.18), residues: 815 loop : -1.34 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 104 HIS 0.004 0.001 HIS H 38 PHE 0.046 0.002 PHE D 392 TYR 0.023 0.001 TYR B1067 ARG 0.005 0.000 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 43) link_NAG-ASN : angle 4.17335 ( 129) link_BETA1-4 : bond 0.00245 ( 10) link_BETA1-4 : angle 1.10448 ( 30) hydrogen bonds : bond 0.05598 ( 1029) hydrogen bonds : angle 5.92744 ( 2820) SS BOND : bond 0.00662 ( 44) SS BOND : angle 2.18115 ( 88) covalent geometry : bond 0.00450 (29215) covalent geometry : angle 0.64446 (39754) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 308 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8644 (tm-30) REVERT: A 71 SER cc_start: 0.4927 (OUTLIER) cc_final: 0.4506 (m) REVERT: A 140 PHE cc_start: 0.7962 (p90) cc_final: 0.7272 (p90) REVERT: A 190 ARG cc_start: 0.7563 (mtt180) cc_final: 0.6403 (mtp180) REVERT: A 213 VAL cc_start: 0.6306 (OUTLIER) cc_final: 0.5977 (m) REVERT: A 347 PHE cc_start: 0.5894 (m-80) cc_final: 0.5509 (m-10) REVERT: A 351 TYR cc_start: 0.8120 (p90) cc_final: 0.7629 (p90) REVERT: A 454 ARG cc_start: 0.5194 (mtt180) cc_final: 0.4678 (tpp80) REVERT: A 515 PHE cc_start: 0.7683 (m-80) cc_final: 0.7429 (m-10) REVERT: A 541 PHE cc_start: 0.7980 (p90) cc_final: 0.7653 (p90) REVERT: A 642 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8616 (t) REVERT: A 691 SER cc_start: 0.8419 (OUTLIER) cc_final: 0.7945 (p) REVERT: A 957 GLN cc_start: 0.9022 (tm-30) cc_final: 0.8446 (tm-30) REVERT: A 1094 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8347 (m) REVERT: B 52 GLN cc_start: 0.9300 (tm-30) cc_final: 0.8928 (tm-30) REVERT: B 351 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.7440 (p90) REVERT: B 396 TYR cc_start: 0.7254 (m-10) cc_final: 0.6959 (m-10) REVERT: B 408 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6738 (tpp-160) REVERT: B 467 ASP cc_start: 0.4426 (OUTLIER) cc_final: 0.4071 (m-30) REVERT: B 516 GLU cc_start: 0.6784 (tt0) cc_final: 0.6205 (tt0) REVERT: B 560 LEU cc_start: 0.8384 (mt) cc_final: 0.7784 (mp) REVERT: B 634 ARG cc_start: 0.4864 (OUTLIER) cc_final: 0.4172 (mtm-85) REVERT: B 957 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8362 (tm-30) REVERT: B 1001 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7843 (mm) REVERT: B 1014 ARG cc_start: 0.8480 (tpp80) cc_final: 0.8137 (mtp85) REVERT: D 140 PHE cc_start: 0.8325 (p90) cc_final: 0.7698 (p90) REVERT: D 204 TYR cc_start: 0.8156 (m-80) cc_final: 0.7510 (m-80) REVERT: D 210 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7817 (tt) REVERT: D 335 LEU cc_start: 0.8168 (mm) cc_final: 0.7762 (tp) REVERT: D 541 PHE cc_start: 0.8224 (p90) cc_final: 0.7940 (p90) REVERT: D 560 LEU cc_start: 0.8477 (mm) cc_final: 0.8008 (mt) REVERT: D 621 PRO cc_start: 0.8426 (Cg_exo) cc_final: 0.8223 (Cg_endo) REVERT: D 955 ASN cc_start: 0.8500 (t0) cc_final: 0.8152 (t0) REVERT: D 957 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8437 (tm-30) REVERT: D 990 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8214 (mm-30) REVERT: D 1029 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8672 (tpp) REVERT: E 37 TYR cc_start: 0.7143 (m-80) cc_final: 0.6686 (m-10) REVERT: E 46 GLU cc_start: 0.8235 (tp30) cc_final: 0.7841 (tp30) REVERT: H 86 LYS cc_start: 0.8482 (ptpt) cc_final: 0.8246 (ptpp) REVERT: I 106 ARG cc_start: 0.7999 (mmp80) cc_final: 0.7550 (mmp80) outliers start: 147 outliers final: 101 residues processed: 418 average time/residue: 0.3797 time to fit residues: 255.7660 Evaluate side-chains 394 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 281 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1029 MET Chi-restraints excluded: chain D residue 1094 VAL Chi-restraints excluded: chain D residue 1134 ASN Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 83 ASN Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 99 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 115 optimal weight: 9.9990 chunk 337 optimal weight: 6.9990 chunk 138 optimal weight: 0.0070 chunk 184 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 327 optimal weight: 0.8980 chunk 221 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 295 optimal weight: 5.9990 chunk 297 optimal weight: 0.2980 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 334 ASN A 762 GLN B 30 ASN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.151770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.110816 restraints weight = 58716.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.107929 restraints weight = 52301.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.109398 restraints weight = 56730.479| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29312 Z= 0.132 Angle : 0.666 16.965 40001 Z= 0.322 Chirality : 0.047 0.472 4634 Planarity : 0.004 0.038 5083 Dihedral : 5.657 56.213 4951 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.76 % Favored : 95.10 % Rotamer: Outliers : 3.86 % Allowed : 22.98 % Favored : 73.16 % 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: -0.57 (0.14), residues: 3528 helix: 2.02 (0.20), residues: 706 sheet: -0.42 (0.18), residues: 824 loop : -1.29 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 104 HIS 0.003 0.001 HIS D 69 PHE 0.029 0.001 PHE D 392 TYR 0.017 0.001 TYR B1067 ARG 0.014 0.000 ARG H 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00634 ( 43) link_NAG-ASN : angle 4.01531 ( 129) link_BETA1-4 : bond 0.00272 ( 10) link_BETA1-4 : angle 1.06394 ( 30) hydrogen bonds : bond 0.04999 ( 1029) hydrogen bonds : angle 5.77831 ( 2820) SS BOND : bond 0.00372 ( 44) SS BOND : angle 1.99667 ( 88) covalent geometry : bond 0.00297 (29215) covalent geometry : angle 0.62039 (39754) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 313 time to evaluate : 3.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9185 (tm-30) cc_final: 0.8818 (tm-30) REVERT: A 71 SER cc_start: 0.4980 (OUTLIER) cc_final: 0.4572 (m) REVERT: A 140 PHE cc_start: 0.7953 (p90) cc_final: 0.7279 (p90) REVERT: A 190 ARG cc_start: 0.7511 (mtt180) cc_final: 0.6290 (mtp180) REVERT: A 213 VAL cc_start: 0.6220 (OUTLIER) cc_final: 0.5859 (m) REVERT: A 335 LEU cc_start: 0.8676 (tt) cc_final: 0.8312 (mp) REVERT: A 347 PHE cc_start: 0.5825 (m-80) cc_final: 0.5460 (m-10) REVERT: A 351 TYR cc_start: 0.8118 (p90) cc_final: 0.7665 (p90) REVERT: A 454 ARG cc_start: 0.5061 (mtt180) cc_final: 0.4570 (tpp80) REVERT: A 541 PHE cc_start: 0.7934 (p90) cc_final: 0.7640 (p90) REVERT: A 642 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8606 (t) REVERT: A 691 SER cc_start: 0.8392 (m) cc_final: 0.7914 (p) REVERT: A 758 SER cc_start: 0.8812 (OUTLIER) cc_final: 0.8558 (p) REVERT: A 957 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8344 (tm-30) REVERT: B 30 ASN cc_start: 0.7388 (OUTLIER) cc_final: 0.6980 (m-40) REVERT: B 52 GLN cc_start: 0.9327 (tm-30) cc_final: 0.8929 (tm-30) REVERT: B 351 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7464 (p90) REVERT: B 396 TYR cc_start: 0.7246 (m-10) cc_final: 0.6938 (m-10) REVERT: B 467 ASP cc_start: 0.4347 (OUTLIER) cc_final: 0.3995 (m-30) REVERT: B 516 GLU cc_start: 0.6862 (tt0) cc_final: 0.6327 (tt0) REVERT: B 560 LEU cc_start: 0.8368 (mt) cc_final: 0.7764 (mp) REVERT: B 634 ARG cc_start: 0.4617 (OUTLIER) cc_final: 0.4155 (mtm-85) REVERT: B 957 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8266 (tm-30) REVERT: B 1001 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7750 (mm) REVERT: B 1014 ARG cc_start: 0.8525 (tpp80) cc_final: 0.8127 (mtp85) REVERT: D 140 PHE cc_start: 0.8349 (p90) cc_final: 0.7740 (p90) REVERT: D 210 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7830 (tt) REVERT: D 335 LEU cc_start: 0.8164 (mm) cc_final: 0.7749 (tp) REVERT: D 434 ILE cc_start: 0.8019 (mm) cc_final: 0.7796 (mm) REVERT: D 541 PHE cc_start: 0.8118 (p90) cc_final: 0.7870 (p90) REVERT: D 955 ASN cc_start: 0.8497 (t0) cc_final: 0.8140 (t0) REVERT: D 957 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8444 (tm-30) REVERT: D 1014 ARG cc_start: 0.8450 (tpp80) cc_final: 0.8026 (tpt90) REVERT: E 35 GLU cc_start: 0.7699 (tt0) cc_final: 0.7242 (tt0) REVERT: E 37 TYR cc_start: 0.7222 (m-80) cc_final: 0.6822 (m-10) REVERT: E 46 GLU cc_start: 0.8251 (tp30) cc_final: 0.7830 (tp30) REVERT: E 82 MET cc_start: 0.8325 (mmm) cc_final: 0.7910 (mmm) REVERT: H 35 GLU cc_start: 0.6632 (mp0) cc_final: 0.5928 (mp0) REVERT: I 32 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7837 (pp20) REVERT: I 101 THR cc_start: 0.8768 (m) cc_final: 0.8461 (p) REVERT: I 106 ARG cc_start: 0.7969 (mmp80) cc_final: 0.7552 (mmp80) outliers start: 120 outliers final: 82 residues processed: 406 average time/residue: 0.3599 time to fit residues: 237.8056 Evaluate side-chains 380 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 288 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 538 CYS Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1134 ASN Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 99 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 58 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 313 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 0.0970 chunk 225 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 341 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 30 ASN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 115 GLN D 388 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 655 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.148924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108355 restraints weight = 59168.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.104528 restraints weight = 54880.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.106628 restraints weight = 58347.427| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 29312 Z= 0.215 Angle : 0.730 16.903 40001 Z= 0.358 Chirality : 0.049 0.533 4634 Planarity : 0.004 0.071 5083 Dihedral : 5.821 57.946 4951 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.04 % Favored : 93.85 % Rotamer: Outliers : 4.05 % Allowed : 22.95 % Favored : 73.00 % 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: -0.81 (0.14), residues: 3528 helix: 1.69 (0.20), residues: 712 sheet: -0.58 (0.18), residues: 791 loop : -1.38 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 104 HIS 0.005 0.001 HIS B1048 PHE 0.041 0.002 PHE E 29 TYR 0.024 0.002 TYR B1067 ARG 0.011 0.001 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00626 ( 43) link_NAG-ASN : angle 4.09977 ( 129) link_BETA1-4 : bond 0.00316 ( 10) link_BETA1-4 : angle 1.10209 ( 30) hydrogen bonds : bond 0.05815 ( 1029) hydrogen bonds : angle 5.99495 ( 2820) SS BOND : bond 0.00794 ( 44) SS BOND : angle 2.09804 ( 88) covalent geometry : bond 0.00512 (29215) covalent geometry : angle 0.68604 (39754) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 301 time to evaluate : 3.264 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 52 GLN cc_start: 0.9190 (tm-30) cc_final: 0.8595 (tm-30) REVERT: A 140 PHE cc_start: 0.8056 (p90) cc_final: 0.7336 (p90) REVERT: A 213 VAL cc_start: 0.6265 (OUTLIER) cc_final: 0.5909 (m) REVERT: A 335 LEU cc_start: 0.8699 (tt) cc_final: 0.8317 (mp) REVERT: A 347 PHE cc_start: 0.5956 (m-80) cc_final: 0.5603 (m-10) REVERT: A 541 PHE cc_start: 0.8035 (p90) cc_final: 0.7725 (p90) REVERT: A 642 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8629 (t) REVERT: A 691 SER cc_start: 0.8496 (m) cc_final: 0.8003 (p) REVERT: A 957 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8410 (tm-30) REVERT: B 30 ASN cc_start: 0.7395 (OUTLIER) cc_final: 0.7072 (m110) REVERT: B 52 GLN cc_start: 0.9322 (tm-30) cc_final: 0.8964 (tm-30) REVERT: B 351 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7525 (p90) REVERT: B 408 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6732 (tpp-160) REVERT: B 467 ASP cc_start: 0.4551 (OUTLIER) cc_final: 0.4112 (m-30) REVERT: B 516 GLU cc_start: 0.6698 (tt0) cc_final: 0.6418 (tt0) REVERT: B 560 LEU cc_start: 0.8407 (mt) cc_final: 0.7795 (mp) REVERT: B 634 ARG cc_start: 0.5076 (OUTLIER) cc_final: 0.4764 (mtm-85) REVERT: B 957 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8372 (tm-30) REVERT: B 1014 ARG cc_start: 0.8569 (tpp80) cc_final: 0.8187 (mtp85) REVERT: D 140 PHE cc_start: 0.8363 (p90) cc_final: 0.7755 (p90) REVERT: D 204 TYR cc_start: 0.8280 (m-80) cc_final: 0.7606 (m-80) REVERT: D 210 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7881 (tt) REVERT: D 237 ARG cc_start: 0.8240 (mtp85) cc_final: 0.8021 (mtm-85) REVERT: D 335 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7682 (tp) REVERT: D 541 PHE cc_start: 0.8147 (p90) cc_final: 0.7897 (p90) REVERT: D 955 ASN cc_start: 0.8572 (t0) cc_final: 0.8220 (t0) REVERT: D 957 GLN cc_start: 0.9081 (tm-30) cc_final: 0.8472 (tm-30) REVERT: D 990 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8253 (mm-30) REVERT: D 1029 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8660 (tpp) REVERT: E 37 TYR cc_start: 0.7113 (m-80) cc_final: 0.6540 (m-10) REVERT: E 46 GLU cc_start: 0.8383 (tp30) cc_final: 0.7973 (tp30) REVERT: E 47 LEU cc_start: 0.7824 (mp) cc_final: 0.7449 (tt) REVERT: H 35 GLU cc_start: 0.6991 (mp0) cc_final: 0.6404 (mp0) REVERT: I 106 ARG cc_start: 0.7995 (mmp80) cc_final: 0.7608 (mmp80) outliers start: 126 outliers final: 92 residues processed: 395 average time/residue: 0.3932 time to fit residues: 250.4612 Evaluate side-chains 386 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 284 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 538 CYS Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 714 ILE Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1029 MET Chi-restraints excluded: chain D residue 1134 ASN Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 99 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 77 optimal weight: 0.9980 chunk 204 optimal weight: 0.8980 chunk 344 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 349 optimal weight: 0.0040 chunk 35 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 324 optimal weight: 5.9990 chunk 346 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.151193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.110135 restraints weight = 58867.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.107896 restraints weight = 52751.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.109343 restraints weight = 55439.085| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29312 Z= 0.137 Angle : 0.685 17.931 40001 Z= 0.330 Chirality : 0.047 0.473 4634 Planarity : 0.004 0.065 5083 Dihedral : 5.571 56.240 4951 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.21 % Rotamer: Outliers : 3.44 % Allowed : 23.79 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3528 helix: 1.96 (0.20), residues: 700 sheet: -0.43 (0.18), residues: 788 loop : -1.34 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 104 HIS 0.003 0.001 HIS D 69 PHE 0.030 0.001 PHE E 29 TYR 0.018 0.001 TYR A1067 ARG 0.011 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00645 ( 43) link_NAG-ASN : angle 3.97421 ( 129) link_BETA1-4 : bond 0.00311 ( 10) link_BETA1-4 : angle 1.06410 ( 30) hydrogen bonds : bond 0.05108 ( 1029) hydrogen bonds : angle 5.78811 ( 2820) SS BOND : bond 0.00380 ( 44) SS BOND : angle 1.86268 ( 88) covalent geometry : bond 0.00315 (29215) covalent geometry : angle 0.64239 (39754) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 316 time to evaluate : 2.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8602 (tm-30) REVERT: A 140 PHE cc_start: 0.7993 (p90) cc_final: 0.7344 (p90) REVERT: A 213 VAL cc_start: 0.6208 (OUTLIER) cc_final: 0.5878 (m) REVERT: A 237 ARG cc_start: 0.8314 (mtm110) cc_final: 0.7841 (mtm-85) REVERT: A 335 LEU cc_start: 0.8706 (tt) cc_final: 0.8315 (mp) REVERT: A 347 PHE cc_start: 0.5854 (m-80) cc_final: 0.5606 (m-10) REVERT: A 351 TYR cc_start: 0.7599 (p90) cc_final: 0.7172 (p90) REVERT: A 378 LYS cc_start: 0.8278 (pptt) cc_final: 0.7693 (pptt) REVERT: A 433 VAL cc_start: 0.8801 (p) cc_final: 0.8583 (p) REVERT: A 451 TYR cc_start: 0.6292 (m-80) cc_final: 0.6024 (m-10) REVERT: A 541 PHE cc_start: 0.7994 (p90) cc_final: 0.7626 (p90) REVERT: A 642 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8617 (t) REVERT: A 691 SER cc_start: 0.8437 (m) cc_final: 0.7952 (p) REVERT: A 957 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8377 (tm-30) REVERT: B 52 GLN cc_start: 0.9324 (tm-30) cc_final: 0.8962 (tm-30) REVERT: B 351 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.7488 (p90) REVERT: B 408 ARG cc_start: 0.7246 (ptm-80) cc_final: 0.6719 (tpp-160) REVERT: B 467 ASP cc_start: 0.4507 (OUTLIER) cc_final: 0.4071 (m-30) REVERT: B 560 LEU cc_start: 0.8444 (mt) cc_final: 0.7880 (mp) REVERT: B 634 ARG cc_start: 0.4739 (OUTLIER) cc_final: 0.4379 (mtm-85) REVERT: B 661 GLU cc_start: 0.7769 (pm20) cc_final: 0.7471 (pt0) REVERT: B 957 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8309 (tm-30) REVERT: B 1001 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7770 (mm) REVERT: B 1014 ARG cc_start: 0.8412 (tpp80) cc_final: 0.8080 (mtp85) REVERT: D 140 PHE cc_start: 0.8395 (p90) cc_final: 0.7742 (p90) REVERT: D 204 TYR cc_start: 0.8243 (m-80) cc_final: 0.7516 (m-80) REVERT: D 237 ARG cc_start: 0.8215 (mtp85) cc_final: 0.8003 (mtm-85) REVERT: D 335 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7722 (tp) REVERT: D 434 ILE cc_start: 0.8092 (mm) cc_final: 0.7872 (mm) REVERT: D 541 PHE cc_start: 0.8133 (p90) cc_final: 0.7889 (p90) REVERT: D 955 ASN cc_start: 0.8548 (t0) cc_final: 0.8174 (t0) REVERT: D 957 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8430 (tm-30) REVERT: D 990 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8176 (mm-30) REVERT: E 37 TYR cc_start: 0.7138 (m-80) cc_final: 0.6766 (m-10) REVERT: E 46 GLU cc_start: 0.8363 (tp30) cc_final: 0.7862 (tp30) REVERT: E 47 LEU cc_start: 0.7816 (mp) cc_final: 0.7333 (tt) REVERT: E 59 TYR cc_start: 0.7127 (m-80) cc_final: 0.6895 (m-80) REVERT: H 35 GLU cc_start: 0.6784 (mp0) cc_final: 0.6207 (mp0) REVERT: H 58 ASN cc_start: 0.7492 (m110) cc_final: 0.7255 (m-40) REVERT: H 59 TYR cc_start: 0.7707 (m-80) cc_final: 0.6865 (m-80) REVERT: I 32 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8031 (pp20) REVERT: I 45 ARG cc_start: 0.6288 (ptt-90) cc_final: 0.5126 (ptm160) REVERT: I 101 THR cc_start: 0.8812 (m) cc_final: 0.8496 (p) outliers start: 107 outliers final: 87 residues processed: 389 average time/residue: 0.3872 time to fit residues: 244.3877 Evaluate side-chains 391 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 297 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 538 CYS Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 714 ILE Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1134 ASN Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 99 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 303 optimal weight: 0.9990 chunk 318 optimal weight: 4.9990 chunk 299 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 251 optimal weight: 6.9990 chunk 333 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.149022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108462 restraints weight = 58095.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.105628 restraints weight = 55375.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.106999 restraints weight = 60123.700| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 29312 Z= 0.196 Angle : 0.724 16.664 40001 Z= 0.353 Chirality : 0.049 0.510 4634 Planarity : 0.004 0.086 5083 Dihedral : 5.678 57.411 4951 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.24 % Favored : 93.68 % Rotamer: Outliers : 3.44 % Allowed : 23.98 % Favored : 72.58 % 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: -0.80 (0.14), residues: 3528 helix: 1.71 (0.20), residues: 713 sheet: -0.59 (0.18), residues: 780 loop : -1.38 (0.13), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 104 HIS 0.004 0.001 HIS H 38 PHE 0.020 0.002 PHE E 29 TYR 0.034 0.001 TYR B 473 ARG 0.011 0.001 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00637 ( 43) link_NAG-ASN : angle 4.04934 ( 129) link_BETA1-4 : bond 0.00246 ( 10) link_BETA1-4 : angle 1.08676 ( 30) hydrogen bonds : bond 0.05609 ( 1029) hydrogen bonds : angle 5.88894 ( 2820) SS BOND : bond 0.00367 ( 44) SS BOND : angle 1.98251 ( 88) covalent geometry : bond 0.00468 (29215) covalent geometry : angle 0.68141 (39754) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 299 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8615 (tm-30) REVERT: A 190 ARG cc_start: 0.7655 (mtt180) cc_final: 0.6326 (mtp180) REVERT: A 213 VAL cc_start: 0.6248 (OUTLIER) cc_final: 0.5898 (m) REVERT: A 347 PHE cc_start: 0.5738 (m-80) cc_final: 0.5432 (m-10) REVERT: A 351 TYR cc_start: 0.7640 (p90) cc_final: 0.7185 (p90) REVERT: A 378 LYS cc_start: 0.8258 (pptt) cc_final: 0.7703 (pptt) REVERT: A 451 TYR cc_start: 0.6247 (m-80) cc_final: 0.6010 (m-10) REVERT: A 515 PHE cc_start: 0.7787 (m-80) cc_final: 0.7559 (m-10) REVERT: A 541 PHE cc_start: 0.8031 (p90) cc_final: 0.7638 (p90) REVERT: A 642 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8663 (t) REVERT: A 691 SER cc_start: 0.8594 (m) cc_final: 0.8113 (p) REVERT: A 957 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8384 (tm-30) REVERT: B 52 GLN cc_start: 0.9308 (tm-30) cc_final: 0.8965 (tm-30) REVERT: B 351 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.7497 (p90) REVERT: B 408 ARG cc_start: 0.7348 (ptm-80) cc_final: 0.6861 (tpp-160) REVERT: B 467 ASP cc_start: 0.4515 (OUTLIER) cc_final: 0.3982 (m-30) REVERT: B 560 LEU cc_start: 0.8427 (mt) cc_final: 0.7870 (mp) REVERT: B 634 ARG cc_start: 0.5017 (OUTLIER) cc_final: 0.4752 (mtm-85) REVERT: B 957 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8381 (tm-30) REVERT: B 1001 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7865 (mm) REVERT: B 1014 ARG cc_start: 0.8419 (tpp80) cc_final: 0.8086 (mtp85) REVERT: D 140 PHE cc_start: 0.8331 (p90) cc_final: 0.7697 (p90) REVERT: D 204 TYR cc_start: 0.8345 (m-80) cc_final: 0.7587 (m-80) REVERT: D 335 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7684 (tp) REVERT: D 541 PHE cc_start: 0.8095 (p90) cc_final: 0.7849 (p90) REVERT: D 955 ASN cc_start: 0.8621 (t0) cc_final: 0.8267 (t0) REVERT: D 957 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8472 (tm-30) REVERT: D 990 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8260 (mm-30) REVERT: E 35 GLU cc_start: 0.7549 (tt0) cc_final: 0.7089 (tt0) REVERT: E 37 TYR cc_start: 0.7116 (m-80) cc_final: 0.6675 (m-10) REVERT: E 46 GLU cc_start: 0.8431 (tp30) cc_final: 0.7933 (tp30) REVERT: E 47 LEU cc_start: 0.7957 (mp) cc_final: 0.7548 (tt) REVERT: H 35 GLU cc_start: 0.7021 (mp0) cc_final: 0.6389 (mp0) REVERT: H 58 ASN cc_start: 0.7497 (m110) cc_final: 0.7252 (m-40) REVERT: H 59 TYR cc_start: 0.7555 (m-80) cc_final: 0.6852 (m-80) REVERT: H 86 LYS cc_start: 0.8649 (ptpp) cc_final: 0.8399 (ptpp) REVERT: I 45 ARG cc_start: 0.6443 (ptt-90) cc_final: 0.5202 (ptm160) outliers start: 107 outliers final: 93 residues processed: 377 average time/residue: 0.3731 time to fit residues: 227.1730 Evaluate side-chains 390 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 290 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 538 CYS Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 714 ILE Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1134 ASN Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 83 ASN Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 99 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 71 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 338 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 175 optimal weight: 0.0980 chunk 158 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.151697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.110780 restraints weight = 58661.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.108334 restraints weight = 54274.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.109629 restraints weight = 59618.269| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29312 Z= 0.127 Angle : 0.697 16.727 40001 Z= 0.334 Chirality : 0.047 0.475 4634 Planarity : 0.004 0.062 5083 Dihedral : 5.592 55.802 4951 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.90 % Favored : 95.01 % Rotamer: Outliers : 2.93 % Allowed : 24.46 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3528 helix: 1.99 (0.20), residues: 701 sheet: -0.43 (0.18), residues: 795 loop : -1.31 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 104 HIS 0.003 0.001 HIS D 69 PHE 0.017 0.001 PHE I 67 TYR 0.020 0.001 TYR B 473 ARG 0.011 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00671 ( 43) link_NAG-ASN : angle 4.17446 ( 129) link_BETA1-4 : bond 0.00366 ( 10) link_BETA1-4 : angle 1.05865 ( 30) hydrogen bonds : bond 0.04916 ( 1029) hydrogen bonds : angle 5.68738 ( 2820) SS BOND : bond 0.00354 ( 44) SS BOND : angle 1.78511 ( 88) covalent geometry : bond 0.00282 (29215) covalent geometry : angle 0.65164 (39754) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9396.80 seconds wall clock time: 165 minutes 23.97 seconds (9923.97 seconds total)