Starting phenix.real_space_refine on Mon Aug 25 14:49:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g76_29798/08_2025/8g76_29798.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g76_29798/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8g76_29798/08_2025/8g76_29798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g76_29798/08_2025/8g76_29798.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g76_29798/08_2025/8g76_29798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g76_29798/08_2025/8g76_29798.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.85, per 1000 atoms: 0.27 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: 2.69 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.54 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: 7.92 Time building geometry restraints manager: 3.58 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 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 13 \ 11)) selection = (chain 'D' and (resid 14 through 623 or resid 634 through 676 or resid 690 throu \ gh 827 or resid 855 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: 5.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.280 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.550 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG B 454 TYR 0.018 0.001 TYR A 505 PHE 0.025 0.001 PHE E 29 TRP 0.022 0.001 TRP B 104 HIS 0.006 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00435 (29215) covalent geometry : angle 0.65863 (39754) SS BOND : bond 0.00409 ( 44) SS BOND : angle 0.88804 ( 88) hydrogen bonds : bond 0.23797 ( 1029) hydrogen bonds : angle 8.64212 ( 2820) link_BETA1-4 : bond 0.00257 ( 10) link_BETA1-4 : angle 1.04971 ( 30) link_NAG-ASN : bond 0.01717 ( 43) link_NAG-ASN : angle 4.00107 ( 129) *********************** 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 : 1.072 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: 0.7245 (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: 0.7033 (m-80) REVERT: A 515 PHE cc_start: 0.8168 (m-80) cc_final: 0.7965 (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: 0.6920 (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: 0.6300 (m-10) REVERT: D 204 TYR cc_start: 0.7061 (m-80) cc_final: 0.6810 (m-80) 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: 0.7694 (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: 0.7190 (m-80) REVERT: E 69 ILE cc_start: 0.7362 (tt) cc_final: 0.7138 (tp) REVERT: H 45 ARG cc_start: 0.4396 (ptt180) cc_final: 0.4110 (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: 0.5059 (tt) REVERT: H 89 ASP cc_start: 0.4888 (m-30) cc_final: 0.4550 (m-30) REVERT: H 109 GLN cc_start: 0.7382 (pm20) cc_final: 0.7157 (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: 0.1946 time to fit residues: 167.9004 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 : 1.010 ------------------------------------------------------------------------------- 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 197 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 A 506 GLN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 690 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 690 GLN B1005 GLN ** D 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.152224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.101444 restraints weight = 59206.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.101430 restraints weight = 40741.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.101416 restraints weight = 30021.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.101838 restraints weight = 28411.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.102094 restraints weight = 26438.456| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 29312 Z= 0.212 Angle : 0.762 18.347 40001 Z= 0.378 Chirality : 0.049 0.496 4634 Planarity : 0.005 0.110 5083 Dihedral : 7.135 59.101 4953 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.44 % Favored : 94.42 % Rotamer: Outliers : 3.41 % Allowed : 20.32 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.14), residues: 3528 helix: 1.73 (0.20), residues: 711 sheet: -0.31 (0.17), residues: 869 loop : -1.29 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 357 TYR 0.028 0.002 TYR B 453 PHE 0.025 0.002 PHE A 464 TRP 0.024 0.002 TRP A 104 HIS 0.008 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00495 (29215) covalent geometry : angle 0.71041 (39754) SS BOND : bond 0.00412 ( 44) SS BOND : angle 2.70478 ( 88) hydrogen bonds : bond 0.06408 ( 1029) hydrogen bonds : angle 6.73325 ( 2820) link_BETA1-4 : bond 0.00571 ( 10) link_BETA1-4 : angle 1.09631 ( 30) link_NAG-ASN : bond 0.00622 ( 43) link_NAG-ASN : angle 4.38135 ( 129) *********************** 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 448 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 342 time to evaluate : 1.201 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: 0.9233 (tm-30) cc_final: 0.8838 (tm-30) REVERT: A 140 PHE cc_start: 0.8146 (p90) cc_final: 0.7498 (p90) REVERT: A 321 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7687 (pm20) REVERT: A 347 PHE cc_start: 0.6104 (m-80) cc_final: 0.5491 (m-80) REVERT: A 351 TYR cc_start: 0.8276 (p90) cc_final: 0.7593 (p90) REVERT: A 454 ARG cc_start: 0.5029 (mtt180) cc_final: 0.4318 (tpp80) REVERT: A 515 PHE cc_start: 0.8055 (m-80) cc_final: 0.7765 (m-80) REVERT: A 560 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7981 (mm) REVERT: A 654 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7806 (pt0) REVERT: A 691 SER cc_start: 0.8066 (OUTLIER) cc_final: 0.7696 (p) REVERT: A 855 PHE cc_start: 0.6212 (m-80) cc_final: 0.5774 (m-80) REVERT: A 902 MET cc_start: 0.8689 (tpp) cc_final: 0.8313 (mmt) REVERT: A 957 GLN cc_start: 0.8978 (tm-30) cc_final: 0.8307 (tm-30) REVERT: A 1014 ARG cc_start: 0.8295 (tpp80) cc_final: 0.8007 (mtp85) REVERT: A 1029 MET cc_start: 0.9267 (tpp) cc_final: 0.8934 (tpp) REVERT: A 1094 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8339 (m) REVERT: B 115 GLN cc_start: 0.7413 (pm20) cc_final: 0.6710 (tp40) REVERT: B 321 GLN cc_start: 0.7762 (tp40) cc_final: 0.7455 (tm-30) REVERT: B 351 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7588 (p90) REVERT: B 396 TYR cc_start: 0.7445 (m-10) cc_final: 0.6586 (m-10) REVERT: B 400 PHE cc_start: 0.8310 (p90) cc_final: 0.8049 (p90) REVERT: B 424 LYS cc_start: 0.7908 (tptt) cc_final: 0.7587 (ttmm) REVERT: B 560 LEU cc_start: 0.8377 (mt) cc_final: 0.7749 (mp) REVERT: B 699 LEU cc_start: 0.8774 (mt) cc_final: 0.8553 (mt) REVERT: B 858 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8025 (mt) REVERT: B 1014 ARG cc_start: 0.8287 (tpp80) cc_final: 0.8058 (mtp85) REVERT: D 44 ARG cc_start: 0.6735 (mtt-85) cc_final: 0.6102 (mtt-85) REVERT: D 140 PHE cc_start: 0.8305 (p90) cc_final: 0.7690 (p90) REVERT: D 200 TYR cc_start: 0.6480 (m-80) cc_final: 0.5637 (m-80) REVERT: D 335 LEU cc_start: 0.8177 (mm) cc_final: 0.7806 (tp) REVERT: D 392 PHE cc_start: 0.7912 (m-80) cc_final: 0.7577 (m-80) REVERT: D 400 PHE cc_start: 0.7681 (p90) cc_final: 0.7452 (p90) REVERT: D 424 LYS cc_start: 0.7513 (ttmm) cc_final: 0.7275 (ptmm) REVERT: D 560 LEU cc_start: 0.8476 (mm) cc_final: 0.7963 (mp) REVERT: D 950 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8023 (p0) REVERT: D 955 ASN cc_start: 0.8413 (t0) cc_final: 0.8029 (t0) REVERT: D 957 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8360 (tm-30) REVERT: E 35 GLU cc_start: 0.7565 (tt0) cc_final: 0.6766 (mt-10) REVERT: E 86 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7760 (ptpp) REVERT: H 80 LEU cc_start: 0.5184 (tt) cc_final: 0.4531 (tt) REVERT: I 20 LEU cc_start: 0.6736 (pt) cc_final: 0.6312 (mm) REVERT: I 106 ARG cc_start: 0.8620 (mmp80) cc_final: 0.7928 (mmp80) outliers start: 106 outliers final: 46 residues processed: 417 average time/residue: 0.1894 time to fit residues: 128.3241 Evaluate side-chains 340 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 286 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 274 THR 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 654 GLU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 70 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 620 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 803 SER 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 1001 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1097 SER 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 286 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 525 CYS 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 48 VAL Chi-restraints excluded: chain E residue 86 LYS 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 80 LEU 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 289 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 267 optimal weight: 10.0000 chunk 317 optimal weight: 0.7980 chunk 342 optimal weight: 6.9990 chunk 222 optimal weight: 8.9990 chunk 173 optimal weight: 0.6980 chunk 255 optimal weight: 7.9990 chunk 287 optimal weight: 2.9990 chunk 261 optimal weight: 30.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 992 GLN D 536 ASN D 641 ASN D1011 GLN E 3 GLN H 39 GLN H 73 ASN I 3 GLN I 73 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.150120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.099720 restraints weight = 59544.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.099573 restraints weight = 39875.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.099668 restraints weight = 30271.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.100033 restraints weight = 28758.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.100357 restraints weight = 26631.078| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 29312 Z= 0.220 Angle : 0.726 18.101 40001 Z= 0.364 Chirality : 0.049 0.473 4634 Planarity : 0.004 0.044 5083 Dihedral : 6.556 58.297 4951 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.27 % Favored : 94.59 % Rotamer: Outliers : 5.34 % Allowed : 20.09 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.14), residues: 3528 helix: 1.55 (0.20), residues: 711 sheet: -0.55 (0.17), residues: 849 loop : -1.37 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 355 TYR 0.025 0.002 TYR B1067 PHE 0.024 0.002 PHE A 392 TRP 0.024 0.002 TRP A 104 HIS 0.006 0.001 HIS D1058 Details of bonding type rmsd covalent geometry : bond 0.00522 (29215) covalent geometry : angle 0.68425 (39754) SS BOND : bond 0.00474 ( 44) SS BOND : angle 2.29977 ( 88) hydrogen bonds : bond 0.06173 ( 1029) hydrogen bonds : angle 6.32829 ( 2820) link_BETA1-4 : bond 0.00285 ( 10) link_BETA1-4 : angle 1.07238 ( 30) link_NAG-ASN : bond 0.00627 ( 43) link_NAG-ASN : angle 3.90490 ( 129) *********************** 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 485 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 319 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.5897 (OUTLIER) cc_final: 0.5457 (mpt-90) REVERT: A 52 GLN cc_start: 0.9248 (tm-30) cc_final: 0.8741 (tm-30) REVERT: A 140 PHE cc_start: 0.8177 (p90) cc_final: 0.7519 (p90) REVERT: A 321 GLN cc_start: 0.8338 (mm-40) cc_final: 0.8073 (pm20) REVERT: A 346 ARG cc_start: 0.7759 (mpp-170) cc_final: 0.7444 (tpm170) REVERT: A 347 PHE cc_start: 0.6341 (OUTLIER) cc_final: 0.5864 (m-80) REVERT: A 351 TYR cc_start: 0.8337 (p90) cc_final: 0.7677 (p90) REVERT: A 454 ARG cc_start: 0.4983 (mtt180) cc_final: 0.4345 (tpp80) REVERT: A 562 PHE cc_start: 0.8563 (p90) cc_final: 0.8139 (p90) REVERT: A 855 PHE cc_start: 0.6283 (m-80) cc_final: 0.6060 (m-80) REVERT: A 957 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8364 (tm-30) REVERT: A 1092 GLU cc_start: 0.7632 (pm20) cc_final: 0.7402 (pm20) REVERT: B 52 GLN cc_start: 0.9379 (tm-30) cc_final: 0.8944 (tm-30) REVERT: B 115 GLN cc_start: 0.7404 (pm20) cc_final: 0.6846 (tp40) REVERT: B 229 LEU cc_start: 0.8028 (tp) cc_final: 0.7798 (tp) REVERT: B 321 GLN cc_start: 0.7863 (tp40) cc_final: 0.7415 (tm-30) REVERT: B 351 TYR cc_start: 0.8274 (OUTLIER) cc_final: 0.7647 (p90) REVERT: B 396 TYR cc_start: 0.7517 (m-10) cc_final: 0.6996 (m-10) REVERT: B 400 PHE cc_start: 0.8202 (p90) cc_final: 0.7932 (p90) REVERT: B 402 ILE cc_start: 0.7019 (tp) cc_final: 0.6812 (tp) REVERT: B 408 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6885 (tpp-160) REVERT: B 424 LYS cc_start: 0.7931 (tptt) cc_final: 0.7597 (ttmm) REVERT: B 560 LEU cc_start: 0.8354 (mt) cc_final: 0.7775 (mp) REVERT: B 588 THR cc_start: 0.8693 (m) cc_final: 0.8412 (p) REVERT: B 634 ARG cc_start: 0.4655 (OUTLIER) cc_final: 0.3763 (mtm-85) REVERT: B 902 MET cc_start: 0.8827 (tpt) cc_final: 0.8290 (tpt) REVERT: B 957 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8398 (tm-30) REVERT: B 1014 ARG cc_start: 0.8471 (tpp80) cc_final: 0.8160 (mtp85) REVERT: D 44 ARG cc_start: 0.6991 (mtt-85) cc_final: 0.6348 (mtt-85) REVERT: D 140 PHE cc_start: 0.8347 (p90) cc_final: 0.7889 (p90) REVERT: D 335 LEU cc_start: 0.8162 (mm) cc_final: 0.7846 (tp) REVERT: D 392 PHE cc_start: 0.7986 (m-80) cc_final: 0.7683 (m-80) REVERT: D 560 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8006 (mp) REVERT: D 621 PRO cc_start: 0.8480 (Cg_exo) cc_final: 0.8273 (Cg_endo) REVERT: D 904 TYR cc_start: 0.7798 (m-10) cc_final: 0.7524 (m-10) REVERT: D 950 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8156 (p0) REVERT: D 955 ASN cc_start: 0.8498 (t0) cc_final: 0.8154 (t0) REVERT: D 957 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8398 (tm-30) REVERT: D 990 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8290 (mm-30) REVERT: D 1029 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.8876 (tpp) REVERT: I 20 LEU cc_start: 0.6887 (pt) cc_final: 0.6641 (mm) REVERT: I 32 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7414 (pp20) REVERT: I 66 ARG cc_start: 0.7421 (mtp180) cc_final: 0.6975 (ttt-90) outliers start: 166 outliers final: 88 residues processed: 447 average time/residue: 0.1855 time to fit residues: 134.9628 Evaluate side-chains 377 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 281 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS 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 399 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 585 LEU 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 806 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1061 VAL 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 104 TRP 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 167 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 302 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 408 ARG 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 734 THR Chi-restraints excluded: chain B residue 736 VAL 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 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 126 VAL 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 382 VAL Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 803 SER Chi-restraints excluded: chain D residue 816 SER 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 950 ASP Chi-restraints excluded: chain D residue 977 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 111 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 6 optimal weight: 30.0000 chunk 134 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 270 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 144 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 138 optimal weight: 20.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 GLN E 3 GLN H 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.151924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.110873 restraints weight = 58527.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.106980 restraints weight = 53244.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.109336 restraints weight = 54704.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.109364 restraints weight = 33267.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.109649 restraints weight = 30441.765| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29312 Z= 0.161 Angle : 0.688 17.646 40001 Z= 0.337 Chirality : 0.047 0.473 4634 Planarity : 0.004 0.064 5083 Dihedral : 6.202 55.448 4951 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.44 % Favored : 94.42 % Rotamer: Outliers : 4.24 % Allowed : 21.92 % Favored : 73.83 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.14), residues: 3528 helix: 1.82 (0.20), residues: 705 sheet: -0.47 (0.17), residues: 835 loop : -1.37 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 346 TYR 0.020 0.001 TYR B1067 PHE 0.032 0.001 PHE E 29 TRP 0.019 0.001 TRP A 104 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00373 (29215) covalent geometry : angle 0.63682 (39754) SS BOND : bond 0.00526 ( 44) SS BOND : angle 2.39542 ( 88) hydrogen bonds : bond 0.05449 ( 1029) hydrogen bonds : angle 6.03769 ( 2820) link_BETA1-4 : bond 0.00276 ( 10) link_BETA1-4 : angle 1.11627 ( 30) link_NAG-ASN : bond 0.00590 ( 43) link_NAG-ASN : angle 4.20855 ( 129) *********************** 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 448 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 316 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9213 (tm-30) cc_final: 0.8708 (tm-30) REVERT: A 71 SER cc_start: 0.4827 (OUTLIER) cc_final: 0.4393 (m) REVERT: A 140 PHE cc_start: 0.7969 (p90) cc_final: 0.7596 (p90) REVERT: A 335 LEU cc_start: 0.8607 (tt) cc_final: 0.8296 (mp) REVERT: A 347 PHE cc_start: 0.6273 (m-80) cc_final: 0.5631 (m-10) REVERT: A 351 TYR cc_start: 0.8133 (p90) cc_final: 0.7606 (p90) REVERT: A 454 ARG cc_start: 0.5109 (mtt180) cc_final: 0.4549 (tpp80) REVERT: A 691 SER cc_start: 0.8353 (m) cc_final: 0.7901 (p) REVERT: A 957 GLN cc_start: 0.8990 (tm-30) cc_final: 0.8406 (tm-30) REVERT: A 1014 ARG cc_start: 0.8443 (tpp80) cc_final: 0.8161 (mtp85) REVERT: A 1092 GLU cc_start: 0.7714 (pm20) cc_final: 0.7513 (pm20) REVERT: B 52 GLN cc_start: 0.9335 (tm-30) cc_final: 0.8836 (tm-30) REVERT: B 351 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.7432 (p90) REVERT: B 396 TYR cc_start: 0.7262 (m-10) cc_final: 0.6852 (m-10) REVERT: B 400 PHE cc_start: 0.8062 (p90) cc_final: 0.7852 (p90) REVERT: B 424 LYS cc_start: 0.7872 (tptt) cc_final: 0.7636 (ttmm) REVERT: B 467 ASP cc_start: 0.4375 (OUTLIER) cc_final: 0.4054 (m-30) REVERT: B 516 GLU cc_start: 0.6936 (tt0) cc_final: 0.6453 (tt0) REVERT: B 560 LEU cc_start: 0.8370 (mt) cc_final: 0.7807 (mp) REVERT: B 634 ARG cc_start: 0.4768 (OUTLIER) cc_final: 0.3940 (mtm-85) REVERT: B 902 MET cc_start: 0.8111 (tpt) cc_final: 0.7643 (tpt) REVERT: B 957 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8205 (tm-30) REVERT: B 995 ARG cc_start: 0.8005 (mmm-85) cc_final: 0.7768 (mtm-85) REVERT: B 1014 ARG cc_start: 0.8442 (tpp80) cc_final: 0.8119 (mtp85) REVERT: D 140 PHE cc_start: 0.8341 (p90) cc_final: 0.7711 (p90) REVERT: D 200 TYR cc_start: 0.6358 (m-80) cc_final: 0.5766 (m-80) REVERT: D 335 LEU cc_start: 0.8190 (mm) cc_final: 0.7805 (tp) REVERT: D 390 LEU cc_start: 0.8866 (mt) cc_final: 0.8660 (mt) REVERT: D 392 PHE cc_start: 0.7860 (m-80) cc_final: 0.7479 (m-80) REVERT: D 560 LEU cc_start: 0.8681 (mm) cc_final: 0.8292 (mm) REVERT: D 621 PRO cc_start: 0.8431 (Cg_exo) cc_final: 0.8212 (Cg_endo) REVERT: D 904 TYR cc_start: 0.7623 (m-10) cc_final: 0.7359 (m-10) REVERT: D 955 ASN cc_start: 0.8528 (t0) cc_final: 0.8153 (t0) REVERT: D 957 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8346 (tm-30) REVERT: E 35 GLU cc_start: 0.7962 (tt0) cc_final: 0.7156 (tt0) REVERT: E 37 TYR cc_start: 0.7061 (m-80) cc_final: 0.6091 (m-80) REVERT: E 86 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7835 (ptpp) REVERT: H 82 MET cc_start: 0.8005 (mmm) cc_final: 0.7638 (mmp) REVERT: I 80 LEU cc_start: 0.5998 (pt) cc_final: 0.5783 (pt) outliers start: 132 outliers final: 74 residues processed: 421 average time/residue: 0.1907 time to fit residues: 129.5393 Evaluate side-chains 359 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 280 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 216 LEU 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 511 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 585 LEU 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 981 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1061 VAL 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 152 TRP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 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 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 634 ARG 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 934 ILE Chi-restraints excluded: chain B residue 1004 LEU 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 362 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 714 ILE Chi-restraints excluded: chain D residue 791 THR 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 977 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 68 ILE Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 99 THR 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 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 103 optimal weight: 0.8980 chunk 138 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 321 optimal weight: 2.9990 chunk 210 optimal weight: 0.6980 chunk 256 optimal weight: 8.9990 chunk 263 optimal weight: 8.9990 chunk 348 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 317 ASN D 49 HIS D 69 HIS D 388 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 992 GLN E 73 ASN H 73 ASN ** H 109 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 = 0.4051 r_free = 0.4051 target = 0.153060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.111897 restraints weight = 57863.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.109715 restraints weight = 51050.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111207 restraints weight = 54397.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.111605 restraints weight = 32707.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.112093 restraints weight = 29210.482| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29312 Z= 0.130 Angle : 0.660 17.363 40001 Z= 0.321 Chirality : 0.047 0.471 4634 Planarity : 0.004 0.038 5083 Dihedral : 5.936 58.992 4951 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.73 % Favored : 95.12 % Rotamer: Outliers : 4.66 % Allowed : 21.86 % Favored : 73.48 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.14), residues: 3528 helix: 2.01 (0.20), residues: 705 sheet: -0.51 (0.18), residues: 844 loop : -1.27 (0.13), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 346 TYR 0.017 0.001 TYR B1067 PHE 0.032 0.001 PHE A 541 TRP 0.019 0.001 TRP D 104 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00294 (29215) covalent geometry : angle 0.60891 (39754) SS BOND : bond 0.00354 ( 44) SS BOND : angle 2.13186 ( 88) hydrogen bonds : bond 0.05003 ( 1029) hydrogen bonds : angle 5.81256 ( 2820) link_BETA1-4 : bond 0.00269 ( 10) link_BETA1-4 : angle 1.05564 ( 30) link_NAG-ASN : bond 0.00627 ( 43) link_NAG-ASN : angle 4.16576 ( 129) *********************** 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 467 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 322 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6074 (OUTLIER) cc_final: 0.5838 (mpt-90) REVERT: A 52 GLN cc_start: 0.9167 (tm-30) cc_final: 0.8668 (tm-30) REVERT: A 71 SER cc_start: 0.4840 (OUTLIER) cc_final: 0.4424 (m) REVERT: A 140 PHE cc_start: 0.7955 (p90) cc_final: 0.7556 (p90) REVERT: A 190 ARG cc_start: 0.7575 (mtt180) cc_final: 0.6423 (mtp180) REVERT: A 213 VAL cc_start: 0.6421 (OUTLIER) cc_final: 0.6089 (m) REVERT: A 335 LEU cc_start: 0.8680 (tt) cc_final: 0.8281 (mp) REVERT: A 347 PHE cc_start: 0.6669 (m-80) cc_final: 0.6126 (m-10) REVERT: A 351 TYR cc_start: 0.8083 (p90) cc_final: 0.7560 (p90) REVERT: A 454 ARG cc_start: 0.5223 (mtt180) cc_final: 0.4627 (tpp80) REVERT: A 515 PHE cc_start: 0.7468 (m-80) cc_final: 0.7155 (m-80) REVERT: A 642 VAL cc_start: 0.8804 (OUTLIER) cc_final: 0.8539 (t) REVERT: A 691 SER cc_start: 0.8361 (m) cc_final: 0.7903 (p) REVERT: A 957 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8377 (tm-30) REVERT: A 1014 ARG cc_start: 0.8426 (tpp80) cc_final: 0.8134 (mtp85) REVERT: A 1092 GLU cc_start: 0.7727 (pm20) cc_final: 0.7478 (pm20) REVERT: B 52 GLN cc_start: 0.9306 (tm-30) cc_final: 0.8816 (tm-30) REVERT: B 351 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7352 (p90) REVERT: B 396 TYR cc_start: 0.7165 (m-10) cc_final: 0.6778 (m-10) REVERT: B 408 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6742 (tpp-160) REVERT: B 424 LYS cc_start: 0.7886 (tptt) cc_final: 0.7669 (ttmm) REVERT: B 467 ASP cc_start: 0.4214 (OUTLIER) cc_final: 0.3969 (m-30) REVERT: B 508 TYR cc_start: 0.8143 (m-10) cc_final: 0.7660 (m-80) REVERT: B 516 GLU cc_start: 0.6880 (tt0) cc_final: 0.6429 (tt0) REVERT: B 560 LEU cc_start: 0.8384 (mt) cc_final: 0.7816 (mp) REVERT: B 584 ILE cc_start: 0.8660 (mp) cc_final: 0.8374 (mm) REVERT: B 634 ARG cc_start: 0.4544 (OUTLIER) cc_final: 0.3935 (mtm-85) REVERT: B 661 GLU cc_start: 0.7699 (pm20) cc_final: 0.7395 (pt0) REVERT: B 902 MET cc_start: 0.8217 (tpt) cc_final: 0.7691 (tpt) REVERT: B 957 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8216 (tm-30) REVERT: B 1014 ARG cc_start: 0.8444 (tpp80) cc_final: 0.8078 (mtp85) REVERT: D 140 PHE cc_start: 0.8307 (p90) cc_final: 0.7704 (p90) REVERT: D 200 TYR cc_start: 0.6265 (m-80) cc_final: 0.5625 (m-80) REVERT: D 335 LEU cc_start: 0.8177 (mm) cc_final: 0.7780 (tp) REVERT: D 378 LYS cc_start: 0.8236 (pttt) cc_final: 0.7553 (pptt) REVERT: D 392 PHE cc_start: 0.7813 (m-80) cc_final: 0.7475 (m-80) REVERT: D 541 PHE cc_start: 0.8093 (p90) cc_final: 0.7847 (p90) REVERT: D 621 PRO cc_start: 0.8388 (Cg_exo) cc_final: 0.8187 (Cg_endo) REVERT: D 819 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8431 (mt-10) REVERT: D 955 ASN cc_start: 0.8459 (t0) cc_final: 0.8096 (t0) REVERT: D 957 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8365 (tm-30) REVERT: D 1014 ARG cc_start: 0.8461 (tpp80) cc_final: 0.8096 (tpt90) REVERT: D 1029 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.7809 (tpp) REVERT: E 29 PHE cc_start: 0.8053 (t80) cc_final: 0.7598 (t80) REVERT: E 35 GLU cc_start: 0.7832 (tt0) cc_final: 0.7157 (tt0) REVERT: E 82 MET cc_start: 0.8472 (mmm) cc_final: 0.8183 (mmm) REVERT: H 35 GLU cc_start: 0.6949 (mp0) cc_final: 0.6259 (mp0) REVERT: I 32 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7694 (pp20) REVERT: I 101 THR cc_start: 0.8692 (m) cc_final: 0.8359 (p) outliers start: 145 outliers final: 90 residues processed: 434 average time/residue: 0.1896 time to fit residues: 133.8792 Evaluate side-chains 374 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 275 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 44 ARG 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 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 274 THR 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 417 LYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 585 LEU 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 981 LEU Chi-restraints excluded: chain B residue 19 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 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 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 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 664 ILE Chi-restraints excluded: chain B residue 736 VAL 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 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 128 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 362 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 525 CYS Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 816 SER 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 963 VAL Chi-restraints excluded: chain D residue 977 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 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 78 VAL 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 204 optimal weight: 0.5980 chunk 216 optimal weight: 6.9990 chunk 209 optimal weight: 0.6980 chunk 188 optimal weight: 3.9990 chunk 340 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 321 optimal weight: 3.9990 chunk 41 optimal weight: 0.0870 chunk 323 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 198 optimal weight: 0.7980 overall best weight: 0.8360 ------------------------------------------------------------------------------- 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 388 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.153811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.112601 restraints weight = 58128.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.110213 restraints weight = 52320.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.111480 restraints weight = 58306.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.112386 restraints weight = 35877.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.113423 restraints weight = 30884.069| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29312 Z= 0.123 Angle : 0.667 17.146 40001 Z= 0.320 Chirality : 0.046 0.469 4634 Planarity : 0.004 0.055 5083 Dihedral : 5.752 54.829 4951 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.68 % Favored : 95.18 % Rotamer: Outliers : 4.24 % Allowed : 22.40 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.14), residues: 3528 helix: 2.11 (0.20), residues: 699 sheet: -0.44 (0.18), residues: 830 loop : -1.24 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 66 TYR 0.019 0.001 TYR I 59 PHE 0.023 0.001 PHE A 541 TRP 0.017 0.001 TRP D 104 HIS 0.002 0.001 HIS D 69 Details of bonding type rmsd covalent geometry : bond 0.00276 (29215) covalent geometry : angle 0.61945 (39754) SS BOND : bond 0.00373 ( 44) SS BOND : angle 2.04115 ( 88) hydrogen bonds : bond 0.04722 ( 1029) hydrogen bonds : angle 5.67037 ( 2820) link_BETA1-4 : bond 0.00274 ( 10) link_BETA1-4 : angle 1.05990 ( 30) link_NAG-ASN : bond 0.00621 ( 43) link_NAG-ASN : angle 4.07282 ( 129) *********************** 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 439 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 307 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6063 (OUTLIER) cc_final: 0.5777 (mpt-90) REVERT: A 52 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8827 (tm-30) REVERT: A 71 SER cc_start: 0.4957 (OUTLIER) cc_final: 0.4599 (m) REVERT: A 115 GLN cc_start: 0.7289 (tp-100) cc_final: 0.7059 (tp40) REVERT: A 140 PHE cc_start: 0.7885 (p90) cc_final: 0.7516 (p90) REVERT: A 190 ARG cc_start: 0.7443 (mtt180) cc_final: 0.6297 (mtp180) REVERT: A 335 LEU cc_start: 0.8690 (tt) cc_final: 0.8275 (mp) REVERT: A 347 PHE cc_start: 0.6560 (m-80) cc_final: 0.6007 (m-10) REVERT: A 351 TYR cc_start: 0.8030 (p90) cc_final: 0.7531 (p90) REVERT: A 454 ARG cc_start: 0.5114 (mtt180) cc_final: 0.4654 (tpp80) REVERT: A 515 PHE cc_start: 0.7381 (m-80) cc_final: 0.7051 (m-80) REVERT: A 642 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8647 (t) REVERT: A 691 SER cc_start: 0.8332 (OUTLIER) cc_final: 0.7862 (p) REVERT: A 957 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8352 (tm-30) REVERT: A 1014 ARG cc_start: 0.8407 (tpp80) cc_final: 0.8126 (mtp85) REVERT: A 1092 GLU cc_start: 0.7794 (pm20) cc_final: 0.7522 (pm20) REVERT: B 52 GLN cc_start: 0.9304 (tm-30) cc_final: 0.8837 (tm-30) REVERT: B 351 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.7330 (p90) REVERT: B 467 ASP cc_start: 0.4215 (OUTLIER) cc_final: 0.3958 (m-30) REVERT: B 508 TYR cc_start: 0.8122 (m-10) cc_final: 0.7578 (m-80) REVERT: B 516 GLU cc_start: 0.6829 (tt0) cc_final: 0.6610 (tt0) REVERT: B 560 LEU cc_start: 0.8415 (mt) cc_final: 0.7830 (mp) REVERT: B 634 ARG cc_start: 0.4284 (OUTLIER) cc_final: 0.3896 (mtm-85) REVERT: B 902 MET cc_start: 0.8147 (tpt) cc_final: 0.7622 (tpt) REVERT: B 957 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8216 (tm-30) REVERT: B 1001 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7704 (mm) REVERT: B 1014 ARG cc_start: 0.8394 (tpp80) cc_final: 0.8072 (mtp85) REVERT: D 140 PHE cc_start: 0.8317 (p90) cc_final: 0.7708 (p90) REVERT: D 210 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7773 (tt) REVERT: D 335 LEU cc_start: 0.8165 (mm) cc_final: 0.7730 (tp) REVERT: D 541 PHE cc_start: 0.8119 (p90) cc_final: 0.7792 (p90) REVERT: D 552 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6810 (pp) REVERT: D 819 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8300 (mt-10) REVERT: D 955 ASN cc_start: 0.8446 (t0) cc_final: 0.8096 (t0) REVERT: D 1014 ARG cc_start: 0.8434 (tpp80) cc_final: 0.8054 (tpt90) REVERT: D 1029 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.7738 (tpp) REVERT: E 5 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7820 (tm-30) REVERT: E 29 PHE cc_start: 0.7657 (t80) cc_final: 0.7312 (t80) REVERT: E 35 GLU cc_start: 0.7740 (tt0) cc_final: 0.7457 (tt0) REVERT: E 37 TYR cc_start: 0.6862 (m-80) cc_final: 0.5946 (m-80) REVERT: H 86 LYS cc_start: 0.8428 (ptpt) cc_final: 0.8221 (ptpp) REVERT: I 31 MET cc_start: 0.8285 (tpp) cc_final: 0.8026 (ttm) REVERT: I 32 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7717 (pp20) REVERT: I 81 GLN cc_start: 0.8232 (mm110) cc_final: 0.7680 (mp10) outliers start: 132 outliers final: 89 residues processed: 408 average time/residue: 0.1900 time to fit residues: 125.7338 Evaluate side-chains 378 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 278 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 44 ARG 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 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 128 ILE 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 425 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR 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 752 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1118 ASP 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 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 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 390 LEU 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 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 923 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 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 513 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 977 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 86 LYS Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain H residue 22 CYS 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 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 302 optimal weight: 3.9990 chunk 312 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 245 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 350 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 177 optimal weight: 7.9990 chunk 269 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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** D 388 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.151084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.110343 restraints weight = 58088.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.107498 restraints weight = 54693.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.109296 restraints weight = 57267.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.109592 restraints weight = 34096.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.109862 restraints weight = 30615.000| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29312 Z= 0.181 Angle : 0.707 23.338 40001 Z= 0.339 Chirality : 0.054 1.718 4634 Planarity : 0.004 0.069 5083 Dihedral : 5.915 58.205 4951 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.39 % Favored : 94.50 % Rotamer: Outliers : 4.44 % Allowed : 22.79 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.14), residues: 3528 helix: 2.00 (0.20), residues: 706 sheet: -0.53 (0.18), residues: 844 loop : -1.28 (0.13), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 66 TYR 0.023 0.001 TYR B 396 PHE 0.032 0.001 PHE A 541 TRP 0.014 0.001 TRP A 104 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00429 (29215) covalent geometry : angle 0.65060 (39754) SS BOND : bond 0.00389 ( 44) SS BOND : angle 2.17312 ( 88) hydrogen bonds : bond 0.05179 ( 1029) hydrogen bonds : angle 5.73995 ( 2820) link_BETA1-4 : bond 0.00276 ( 10) link_BETA1-4 : angle 1.09362 ( 30) link_NAG-ASN : bond 0.00888 ( 43) link_NAG-ASN : angle 4.58398 ( 129) *********************** 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 428 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 290 time to evaluate : 1.083 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 44 ARG cc_start: 0.6244 (OUTLIER) cc_final: 0.5951 (mpt-90) REVERT: A 52 GLN cc_start: 0.9202 (tm-30) cc_final: 0.8931 (tm-30) REVERT: A 115 GLN cc_start: 0.7433 (tp-100) cc_final: 0.6956 (tp-100) REVERT: A 213 VAL cc_start: 0.6248 (OUTLIER) cc_final: 0.5888 (m) REVERT: A 347 PHE cc_start: 0.6680 (m-80) cc_final: 0.6129 (m-10) REVERT: A 351 TYR cc_start: 0.8116 (p90) cc_final: 0.7622 (p90) REVERT: A 454 ARG cc_start: 0.5125 (mtt180) cc_final: 0.4650 (tpp80) REVERT: A 642 VAL cc_start: 0.8840 (OUTLIER) cc_final: 0.8574 (t) REVERT: A 691 SER cc_start: 0.8433 (OUTLIER) cc_final: 0.7962 (p) REVERT: A 957 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8371 (tm-30) REVERT: A 1014 ARG cc_start: 0.8476 (tpp80) cc_final: 0.8145 (mtp85) REVERT: B 52 GLN cc_start: 0.9323 (tm-30) cc_final: 0.8893 (tm-30) REVERT: B 204 TYR cc_start: 0.8294 (m-80) cc_final: 0.7957 (m-80) REVERT: B 351 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7433 (p90) REVERT: B 467 ASP cc_start: 0.4452 (OUTLIER) cc_final: 0.4109 (m-30) REVERT: B 560 LEU cc_start: 0.8410 (mt) cc_final: 0.7798 (mp) REVERT: B 634 ARG cc_start: 0.4601 (OUTLIER) cc_final: 0.4182 (mtm-85) REVERT: B 957 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8266 (tm-30) REVERT: B 1001 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7702 (mm) REVERT: B 1014 ARG cc_start: 0.8491 (tpp80) cc_final: 0.8123 (mtp85) REVERT: D 140 PHE cc_start: 0.8357 (p90) cc_final: 0.7759 (p90) REVERT: D 210 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7809 (tt) REVERT: D 335 LEU cc_start: 0.8176 (mm) cc_final: 0.7753 (tp) REVERT: D 541 PHE cc_start: 0.8163 (p90) cc_final: 0.7865 (p90) REVERT: D 955 ASN cc_start: 0.8528 (t0) cc_final: 0.8170 (t0) REVERT: D 1014 ARG cc_start: 0.8533 (tpp80) cc_final: 0.8182 (mtp85) REVERT: D 1029 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8581 (tpp) REVERT: E 29 PHE cc_start: 0.7809 (t80) cc_final: 0.7500 (t80) REVERT: E 35 GLU cc_start: 0.7797 (tt0) cc_final: 0.7585 (tt0) REVERT: E 37 TYR cc_start: 0.6877 (m-80) cc_final: 0.6424 (m-80) REVERT: E 75 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7482 (tttt) REVERT: H 76 ASN cc_start: 0.6855 (OUTLIER) cc_final: 0.6574 (m-40) REVERT: I 32 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7885 (pp20) REVERT: I 81 GLN cc_start: 0.8333 (mm110) cc_final: 0.7739 (mp10) REVERT: I 101 THR cc_start: 0.8774 (m) cc_final: 0.8475 (p) outliers start: 138 outliers final: 99 residues processed: 394 average time/residue: 0.1783 time to fit residues: 114.5448 Evaluate side-chains 390 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 279 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 44 ARG 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 197 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 425 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 585 LEU 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 654 GLU Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 691 SER 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 1061 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 19 THR 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 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 390 LEU 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 571 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 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 923 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 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 513 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 816 SER 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 977 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 75 LYS Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain H residue 22 CYS 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 76 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 3 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 159 optimal weight: 0.0980 chunk 320 optimal weight: 7.9990 chunk 255 optimal weight: 20.0000 chunk 285 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 87 optimal weight: 0.4980 chunk 186 optimal weight: 0.0470 chunk 298 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1036 GLN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS D 388 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.152898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.111970 restraints weight = 58653.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.109205 restraints weight = 53448.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.110471 restraints weight = 59149.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.111328 restraints weight = 36375.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.112731 restraints weight = 31256.366| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4011 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= 0.126 Angle : 0.679 21.353 40001 Z= 0.323 Chirality : 0.049 1.032 4634 Planarity : 0.004 0.051 5083 Dihedral : 5.586 56.991 4951 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.56 % Favored : 95.32 % Rotamer: Outliers : 4.02 % Allowed : 23.21 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.14), residues: 3528 helix: 2.12 (0.20), residues: 700 sheet: -0.43 (0.18), residues: 840 loop : -1.23 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 66 TYR 0.017 0.001 TYR A1067 PHE 0.029 0.001 PHE A 541 TRP 0.018 0.001 TRP D 104 HIS 0.003 0.001 HIS I 96 Details of bonding type rmsd covalent geometry : bond 0.00286 (29215) covalent geometry : angle 0.62848 (39754) SS BOND : bond 0.00343 ( 44) SS BOND : angle 1.85211 ( 88) hydrogen bonds : bond 0.04759 ( 1029) hydrogen bonds : angle 5.61791 ( 2820) link_BETA1-4 : bond 0.00286 ( 10) link_BETA1-4 : angle 1.03775 ( 30) link_NAG-ASN : bond 0.00742 ( 43) link_NAG-ASN : angle 4.34013 ( 129) *********************** 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 416 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 291 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6182 (OUTLIER) cc_final: 0.5864 (mpt-90) REVERT: A 52 GLN cc_start: 0.9305 (tm-30) cc_final: 0.8922 (tm-30) REVERT: A 115 GLN cc_start: 0.7476 (tp-100) cc_final: 0.6962 (tp-100) REVERT: A 140 PHE cc_start: 0.7948 (p90) cc_final: 0.7307 (p90) REVERT: A 213 VAL cc_start: 0.6218 (OUTLIER) cc_final: 0.5894 (m) REVERT: A 335 LEU cc_start: 0.8603 (tt) cc_final: 0.8291 (mp) REVERT: A 347 PHE cc_start: 0.6540 (m-80) cc_final: 0.6045 (m-10) REVERT: A 351 TYR cc_start: 0.8051 (p90) cc_final: 0.7645 (p90) REVERT: A 454 ARG cc_start: 0.5117 (mtt180) cc_final: 0.4652 (tpp80) REVERT: A 642 VAL cc_start: 0.8891 (OUTLIER) cc_final: 0.8656 (t) REVERT: A 691 SER cc_start: 0.8338 (OUTLIER) cc_final: 0.7875 (p) REVERT: A 957 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8314 (tm-30) REVERT: A 993 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8197 (mm) REVERT: A 1014 ARG cc_start: 0.8435 (tpp80) cc_final: 0.8116 (mtp85) REVERT: B 52 GLN cc_start: 0.9320 (tm-30) cc_final: 0.8902 (tm-30) REVERT: B 204 TYR cc_start: 0.8359 (m-80) cc_final: 0.7960 (m-80) REVERT: B 351 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.7416 (p90) REVERT: B 467 ASP cc_start: 0.4248 (OUTLIER) cc_final: 0.3956 (m-30) REVERT: B 560 LEU cc_start: 0.8453 (mt) cc_final: 0.7870 (mp) REVERT: B 634 ARG cc_start: 0.4397 (OUTLIER) cc_final: 0.4120 (mtm-85) REVERT: B 957 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8210 (tm-30) REVERT: B 1014 ARG cc_start: 0.8370 (tpp80) cc_final: 0.8045 (mtp85) REVERT: D 140 PHE cc_start: 0.8354 (p90) cc_final: 0.7730 (p90) REVERT: D 200 TYR cc_start: 0.6320 (m-80) cc_final: 0.5847 (m-80) REVERT: D 335 LEU cc_start: 0.8166 (mm) cc_final: 0.7717 (tp) REVERT: D 541 PHE cc_start: 0.8189 (p90) cc_final: 0.7889 (p90) REVERT: D 819 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8317 (mt-10) REVERT: D 955 ASN cc_start: 0.8477 (t0) cc_final: 0.8126 (t0) REVERT: D 1001 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7868 (mm) REVERT: D 1014 ARG cc_start: 0.8421 (tpp80) cc_final: 0.8078 (tpt90) REVERT: D 1029 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.7734 (tpp) REVERT: E 37 TYR cc_start: 0.6995 (m-80) cc_final: 0.6516 (m-80) REVERT: E 75 LYS cc_start: 0.8327 (pttp) cc_final: 0.7416 (tttt) REVERT: I 32 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7704 (pp20) REVERT: I 45 ARG cc_start: 0.6225 (ptt-90) cc_final: 0.5206 (ptm160) REVERT: I 81 GLN cc_start: 0.8306 (mm110) cc_final: 0.7771 (mp10) REVERT: I 101 THR cc_start: 0.8775 (m) cc_final: 0.8411 (p) outliers start: 125 outliers final: 90 residues processed: 384 average time/residue: 0.1809 time to fit residues: 113.4506 Evaluate side-chains 378 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 278 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 44 ARG Chi-restraints excluded: chain A residue 47 VAL 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 197 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 453 TYR Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 585 LEU 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 666 ILE Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 806 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 993 ILE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 19 THR 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 350 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 390 LEU 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 551 VAL Chi-restraints excluded: chain B residue 571 ASP 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 803 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 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 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 432 CYS Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 977 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 27 SER 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 H residue 22 CYS 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 78 VAL Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 28 ILE 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 296 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 214 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 60 optimal weight: 0.0060 chunk 82 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 320 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 266 optimal weight: 9.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1036 GLN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 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 = 0.4046 r_free = 0.4046 target = 0.152540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.111353 restraints weight = 58881.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.108739 restraints weight = 53105.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.110092 restraints weight = 57546.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.110768 restraints weight = 35980.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.111943 restraints weight = 31417.022| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29312 Z= 0.133 Angle : 0.684 21.993 40001 Z= 0.327 Chirality : 0.047 0.517 4634 Planarity : 0.004 0.053 5083 Dihedral : 5.414 55.483 4951 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 3.66 % Allowed : 23.40 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.14), residues: 3528 helix: 2.12 (0.20), residues: 701 sheet: -0.46 (0.18), residues: 840 loop : -1.24 (0.14), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1107 TYR 0.018 0.001 TYR B1067 PHE 0.027 0.001 PHE A 541 TRP 0.018 0.001 TRP D 104 HIS 0.003 0.001 HIS D 69 Details of bonding type rmsd covalent geometry : bond 0.00304 (29215) covalent geometry : angle 0.63271 (39754) SS BOND : bond 0.00332 ( 44) SS BOND : angle 1.74477 ( 88) hydrogen bonds : bond 0.04754 ( 1029) hydrogen bonds : angle 5.58374 ( 2820) link_BETA1-4 : bond 0.00297 ( 10) link_BETA1-4 : angle 1.01560 ( 30) link_NAG-ASN : bond 0.00665 ( 43) link_NAG-ASN : angle 4.41068 ( 129) *********************** 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 400 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 286 time to evaluate : 1.061 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 44 ARG cc_start: 0.6137 (OUTLIER) cc_final: 0.5824 (mpt-90) REVERT: A 52 GLN cc_start: 0.9305 (tm-30) cc_final: 0.8934 (tm-30) REVERT: A 115 GLN cc_start: 0.7546 (tp-100) cc_final: 0.7054 (tp-100) REVERT: A 140 PHE cc_start: 0.7914 (p90) cc_final: 0.7280 (p90) REVERT: A 213 VAL cc_start: 0.6192 (OUTLIER) cc_final: 0.5854 (m) REVERT: A 335 LEU cc_start: 0.8655 (tt) cc_final: 0.8342 (mp) REVERT: A 347 PHE cc_start: 0.6551 (m-80) cc_final: 0.6061 (m-10) REVERT: A 351 TYR cc_start: 0.8023 (p90) cc_final: 0.7627 (p90) REVERT: A 454 ARG cc_start: 0.5213 (mtt180) cc_final: 0.4739 (tpp80) REVERT: A 515 PHE cc_start: 0.7529 (m-80) cc_final: 0.7293 (m-10) REVERT: A 642 VAL cc_start: 0.8823 (OUTLIER) cc_final: 0.8569 (t) REVERT: A 691 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.7895 (p) REVERT: A 957 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8319 (tm-30) REVERT: A 993 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8148 (mm) REVERT: A 1014 ARG cc_start: 0.8422 (tpp80) cc_final: 0.8105 (mtp85) REVERT: B 52 GLN cc_start: 0.9323 (tm-30) cc_final: 0.8913 (tm-30) REVERT: B 204 TYR cc_start: 0.8377 (m-80) cc_final: 0.7987 (m-80) REVERT: B 351 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.7389 (p90) REVERT: B 467 ASP cc_start: 0.4278 (OUTLIER) cc_final: 0.3977 (m-30) REVERT: B 560 LEU cc_start: 0.8481 (mt) cc_final: 0.7895 (mp) REVERT: B 634 ARG cc_start: 0.4440 (OUTLIER) cc_final: 0.4117 (mtm-85) REVERT: B 957 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8232 (tm-30) REVERT: B 1014 ARG cc_start: 0.8388 (tpp80) cc_final: 0.8068 (mtp85) REVERT: D 140 PHE cc_start: 0.8358 (p90) cc_final: 0.7732 (p90) REVERT: D 204 TYR cc_start: 0.7993 (m-80) cc_final: 0.7208 (m-80) REVERT: D 335 LEU cc_start: 0.8131 (mm) cc_final: 0.7676 (tp) REVERT: D 541 PHE cc_start: 0.8063 (p90) cc_final: 0.7747 (p90) REVERT: D 819 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8329 (mt-10) REVERT: D 955 ASN cc_start: 0.8488 (t0) cc_final: 0.8125 (t0) REVERT: D 957 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8435 (tm-30) REVERT: D 1001 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7862 (mm) REVERT: D 1014 ARG cc_start: 0.8418 (tpp80) cc_final: 0.8076 (tpt90) REVERT: D 1029 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.7758 (tpp) REVERT: E 35 GLU cc_start: 0.7620 (tt0) cc_final: 0.6586 (tt0) REVERT: E 37 TYR cc_start: 0.7031 (m-80) cc_final: 0.6279 (m-80) REVERT: E 75 LYS cc_start: 0.8316 (pttp) cc_final: 0.7359 (tttt) REVERT: E 82 MET cc_start: 0.7849 (mmm) cc_final: 0.7427 (mmt) REVERT: H 29 PHE cc_start: 0.7635 (m-80) cc_final: 0.7416 (m-80) REVERT: H 51 ILE cc_start: 0.5819 (OUTLIER) cc_final: 0.5229 (pt) REVERT: I 32 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7817 (pp20) REVERT: I 45 ARG cc_start: 0.6359 (ptt-90) cc_final: 0.5308 (ptm160) REVERT: I 81 GLN cc_start: 0.8301 (mm110) cc_final: 0.7694 (pm20) REVERT: I 101 THR cc_start: 0.8792 (m) cc_final: 0.8440 (p) outliers start: 114 outliers final: 94 residues processed: 370 average time/residue: 0.1712 time to fit residues: 103.1294 Evaluate side-chains 382 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 277 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 44 ARG 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 197 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 453 TYR Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 THR 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 666 ILE Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 806 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 934 ILE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 19 THR 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 299 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 TYR 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 551 VAL Chi-restraints excluded: chain B residue 571 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 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 1008 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 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 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 513 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 977 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 68 ILE Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain H residue 22 CYS 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 72 ASP Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 61 ASP 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 108 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 204 optimal weight: 0.8980 chunk 348 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 236 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 266 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.151281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.109795 restraints weight = 57896.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107343 restraints weight = 51556.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108762 restraints weight = 56188.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.109287 restraints weight = 35283.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.110502 restraints weight = 31060.328| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29312 Z= 0.157 Angle : 0.697 19.198 40001 Z= 0.335 Chirality : 0.047 0.471 4634 Planarity : 0.004 0.060 5083 Dihedral : 5.360 56.127 4951 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.44 % Favored : 94.47 % Rotamer: Outliers : 3.47 % Allowed : 24.01 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.14), residues: 3528 helix: 2.05 (0.20), residues: 707 sheet: -0.47 (0.18), residues: 842 loop : -1.27 (0.14), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 66 TYR 0.020 0.001 TYR B1067 PHE 0.025 0.001 PHE A 541 TRP 0.021 0.001 TRP D 104 HIS 0.003 0.001 HIS D 69 Details of bonding type rmsd covalent geometry : bond 0.00369 (29215) covalent geometry : angle 0.64465 (39754) SS BOND : bond 0.00456 ( 44) SS BOND : angle 1.99856 ( 88) hydrogen bonds : bond 0.05039 ( 1029) hydrogen bonds : angle 5.63515 ( 2820) link_BETA1-4 : bond 0.00325 ( 10) link_BETA1-4 : angle 1.07018 ( 30) link_NAG-ASN : bond 0.00685 ( 43) link_NAG-ASN : angle 4.41033 ( 129) ********************** 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 400 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 292 time to evaluate : 1.103 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 44 ARG cc_start: 0.6256 (OUTLIER) cc_final: 0.5929 (mpt-90) REVERT: A 52 GLN cc_start: 0.9291 (tm-30) cc_final: 0.8917 (tm-30) REVERT: A 115 GLN cc_start: 0.7593 (tp-100) cc_final: 0.7098 (tp-100) REVERT: A 140 PHE cc_start: 0.7870 (p90) cc_final: 0.7219 (p90) REVERT: A 213 VAL cc_start: 0.6357 (OUTLIER) cc_final: 0.6039 (m) REVERT: A 335 LEU cc_start: 0.8630 (tt) cc_final: 0.8352 (mp) REVERT: A 347 PHE cc_start: 0.6508 (m-80) cc_final: 0.5963 (m-10) REVERT: A 351 TYR cc_start: 0.8101 (p90) cc_final: 0.7704 (p90) REVERT: A 378 LYS cc_start: 0.8082 (pptt) cc_final: 0.7612 (pptt) REVERT: A 454 ARG cc_start: 0.5099 (mtt180) cc_final: 0.4623 (tpp80) REVERT: A 642 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8674 (t) REVERT: A 691 SER cc_start: 0.8414 (OUTLIER) cc_final: 0.7936 (p) REVERT: A 957 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8333 (tm-30) REVERT: A 1014 ARG cc_start: 0.8467 (tpp80) cc_final: 0.8142 (mtp85) REVERT: B 52 GLN cc_start: 0.9328 (tm-30) cc_final: 0.8927 (tm-30) REVERT: B 351 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7465 (p90) REVERT: B 408 ARG cc_start: 0.7298 (ptm-80) cc_final: 0.6814 (tpp-160) REVERT: B 467 ASP cc_start: 0.4300 (OUTLIER) cc_final: 0.3865 (m-30) REVERT: B 560 LEU cc_start: 0.8495 (mt) cc_final: 0.7942 (mp) REVERT: B 634 ARG cc_start: 0.4432 (OUTLIER) cc_final: 0.4176 (mtm-85) REVERT: B 957 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8237 (tm-30) REVERT: B 1014 ARG cc_start: 0.8469 (tpp80) cc_final: 0.8106 (mtp85) REVERT: D 140 PHE cc_start: 0.8355 (p90) cc_final: 0.7712 (p90) REVERT: D 237 ARG cc_start: 0.8220 (mtp85) cc_final: 0.8011 (mtm-85) REVERT: D 335 LEU cc_start: 0.8139 (mm) cc_final: 0.7682 (tp) REVERT: D 541 PHE cc_start: 0.8074 (p90) cc_final: 0.7767 (p90) REVERT: D 955 ASN cc_start: 0.8531 (t0) cc_final: 0.8157 (t0) REVERT: D 957 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8461 (tm-30) REVERT: D 1014 ARG cc_start: 0.8497 (tpp80) cc_final: 0.8122 (tpt90) REVERT: D 1029 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.7808 (tpp) REVERT: E 35 GLU cc_start: 0.7563 (tt0) cc_final: 0.6471 (tt0) REVERT: E 37 TYR cc_start: 0.6981 (m-80) cc_final: 0.6216 (m-80) REVERT: E 75 LYS cc_start: 0.8318 (pttp) cc_final: 0.7366 (tttt) REVERT: H 51 ILE cc_start: 0.5997 (OUTLIER) cc_final: 0.5414 (pt) REVERT: I 32 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7951 (pp20) REVERT: I 45 ARG cc_start: 0.6403 (ptt-90) cc_final: 0.5280 (ptm160) REVERT: I 101 THR cc_start: 0.8794 (m) cc_final: 0.8566 (t) outliers start: 108 outliers final: 91 residues processed: 371 average time/residue: 0.1838 time to fit residues: 110.0685 Evaluate side-chains 382 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 282 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 44 ARG 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 197 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 248 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 THR 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 666 ILE Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 19 THR 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 350 VAL Chi-restraints excluded: chain B residue 351 TYR 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 551 VAL Chi-restraints excluded: chain B residue 571 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 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 950 ASP Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 90 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 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 513 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 977 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 68 ILE 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 51 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 28 ILE 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 273 optimal weight: 3.9990 chunk 212 optimal weight: 0.6980 chunk 162 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 340 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 272 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.152009 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 = 58838.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.108616 restraints weight = 54129.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.110187 restraints weight = 57381.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.110493 restraints weight = 34610.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.111009 restraints weight = 31204.721| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 29312 Z= 0.140 Angle : 0.682 16.710 40001 Z= 0.328 Chirality : 0.046 0.471 4634 Planarity : 0.004 0.068 5083 Dihedral : 5.272 55.912 4951 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.76 % Rotamer: Outliers : 3.60 % Allowed : 23.95 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.14), residues: 3528 helix: 2.07 (0.20), residues: 707 sheet: -0.43 (0.18), residues: 842 loop : -1.26 (0.14), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1107 TYR 0.032 0.001 TYR B 473 PHE 0.024 0.001 PHE D 515 TRP 0.021 0.001 TRP D 104 HIS 0.003 0.001 HIS D 69 Details of bonding type rmsd covalent geometry : bond 0.00326 (29215) covalent geometry : angle 0.63371 (39754) SS BOND : bond 0.00434 ( 44) SS BOND : angle 1.94244 ( 88) hydrogen bonds : bond 0.04862 ( 1029) hydrogen bonds : angle 5.57343 ( 2820) link_BETA1-4 : bond 0.00311 ( 10) link_BETA1-4 : angle 1.06286 ( 30) link_NAG-ASN : bond 0.00676 ( 43) link_NAG-ASN : angle 4.20539 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5094.08 seconds wall clock time: 89 minutes 9.19 seconds (5349.19 seconds total)