Starting phenix.real_space_refine on Tue Aug 26 10:17:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wlz_37636/08_2025/8wlz_37636.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wlz_37636/08_2025/8wlz_37636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wlz_37636/08_2025/8wlz_37636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wlz_37636/08_2025/8wlz_37636.map" model { file = "/net/cci-nas-00/data/ceres_data/8wlz_37636/08_2025/8wlz_37636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wlz_37636/08_2025/8wlz_37636.cif" } resolution = 4.45 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= 0.000 sd= 0.026 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 181 5.16 5 C 22615 2.51 5 N 5822 2.21 5 O 6880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.03s 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: 35498 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8332 Classifications: {'peptide': 1068} Link IDs: {'PTRANS': 60, 'TRANS': 1007} Chain breaks: 2 Chain: "B" Number of atoms: 8319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8319 Classifications: {'peptide': 1067} Link IDs: {'CIS': 1, 'PTRANS': 60, 'TRANS': 1005} Chain breaks: 2 Chain: "C" Number of atoms: 8332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8332 Classifications: {'peptide': 1068} Link IDs: {'PTRANS': 60, 'TRANS': 1007} Chain breaks: 2 Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "G" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "E" 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.69, per 1000 atoms: 0.19 Number of scatterers: 35498 At special positions: 0 Unit cell: (153.26, 184.3, 239.59, 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 181 16.00 O 6880 8.00 N 5822 7.00 C 22615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 160 " distance=2.04 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 349 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 420 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 512 " distance=2.03 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS A 604 " - pdb=" SG CYS A 636 " distance=2.04 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 658 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 743 " distance=2.02 Simple disulfide: pdb=" SG CYS A 726 " - pdb=" SG CYS A 732 " distance=2.02 Simple disulfide: pdb=" SG CYS A1015 " - pdb=" SG CYS A1026 " distance=2.03 Simple disulfide: pdb=" SG CYS A1065 " - pdb=" SG CYS A1109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 134 " distance=2.02 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 160 " distance=2.04 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 420 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 512 " distance=2.04 Simple disulfide: pdb=" SG CYS B 468 " - pdb=" SG CYS B 475 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 604 " - pdb=" SG CYS B 636 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 658 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 743 " distance=2.02 Simple disulfide: pdb=" SG CYS B 726 " - pdb=" SG CYS B 732 " distance=2.02 Simple disulfide: pdb=" SG CYS B1015 " - pdb=" SG CYS B1026 " distance=2.02 Simple disulfide: pdb=" SG CYS B1065 " - pdb=" SG CYS B1109 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 160 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 420 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 512 " distance=2.03 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 525 " - pdb=" SG CYS C 577 " distance=2.03 Simple disulfide: pdb=" SG CYS C 604 " - pdb=" SG CYS C 636 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 658 " distance=2.04 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 743 " distance=2.02 Simple disulfide: pdb=" SG CYS C 726 " - pdb=" SG CYS C 732 " distance=2.03 Simple disulfide: pdb=" SG CYS C1015 " - pdb=" SG CYS C1026 " distance=2.02 Simple disulfide: pdb=" SG CYS C1065 " - pdb=" SG CYS C1109 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS G 133 " - pdb=" SG CYS G 141 " distance=2.03 Simple disulfide: pdb=" SG CYS G 344 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 530 " - pdb=" SG CYS G 542 " distance=2.02 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 603 " " NAG A1302 " - " ASN A 692 " " NAG A1303 " - " ASN A1057 " " NAG A1304 " - " ASN A 319 " " NAG B1301 " - " ASN B 66 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 692 " " NAG B1305 " - " ASN B1057 " " NAG B1306 " - " ASN B1117 " " NAG B1307 " - " ASN B 319 " " NAG C1301 " - " ASN C 66 " " NAG C1302 " - " ASN C 110 " " NAG C1303 " - " ASN C 159 " " NAG C1304 " - " ASN C 228 " " NAG C1305 " - " ASN C 590 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 692 " " NAG C1308 " - " ASN C1057 " " NAG C1309 " - " ASN C 120 " " NAG C1310 " - " ASN C 319 " " NAG E 1 " - " ASN A 700 " " NAG F 1 " - " ASN A1081 " " NAG H 1 " - " ASN A1117 " " NAG I 1 " - " ASN A 784 " " NAG J 1 " - " ASN A 270 " " NAG K 1 " - " ASN B 120 " " NAG L 1 " - " ASN B 590 " " NAG M 1 " - " ASN B 700 " " NAG N 1 " - " ASN B 784 " " NAG O 1 " - " ASN B1081 " " NAG P 1 " - " ASN B 270 " " NAG Q 1 " - " ASN C 270 " " NAG R 1 " - " ASN C 700 " " NAG S 1 " - " ASN C 784 " " NAG T 1 " - " ASN C1081 " " NAG U 1 " - " ASN C1117 " Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 8746 Ramachandran restraints generated. 4373 Oldfield, 0 Emsley, 4373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8270 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 56 sheets defined 34.9% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 392 through 396 Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.455A pdb=" N TYR A 409 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.503A pdb=" N VAL A 607 " --> pdb=" O CYS A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 726 Processing helix chain 'A' and resid 734 through 739 removed outlier: 3.588A pdb=" N TYR A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 766 removed outlier: 4.332A pdb=" N LEU A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 809 removed outlier: 3.859A pdb=" N ASN A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 867 Processing helix chain 'A' and resid 868 through 871 removed outlier: 3.841A pdb=" N PHE A 871 " --> pdb=" O GLY A 868 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 868 through 871' Processing helix chain 'A' and resid 880 through 891 Processing helix chain 'A' and resid 895 through 923 removed outlier: 4.115A pdb=" N LEU A 899 " --> pdb=" O THR A 895 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS A 904 " --> pdb=" O TYR A 900 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 951 removed outlier: 4.384A pdb=" N VAL A 934 " --> pdb=" O LYS A 930 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 936 " --> pdb=" O GLN A 932 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 967 removed outlier: 3.815A pdb=" N ILE A 963 " --> pdb=" O VAL A 959 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 967 " --> pdb=" O ILE A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 1015 Processing helix chain 'B' and resid 282 through 292 Processing helix chain 'B' and resid 325 through 331 Processing helix chain 'B' and resid 352 through 358 removed outlier: 3.551A pdb=" N LEU B 356 " --> pdb=" O ASP B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.768A pdb=" N LEU B 375 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN B 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 396 removed outlier: 4.021A pdb=" N ARG B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 392 through 396' Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 741 through 766 Processing helix chain 'B' and resid 799 through 809 removed outlier: 3.511A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 867 Processing helix chain 'B' and resid 868 through 871 removed outlier: 3.654A pdb=" N PHE B 871 " --> pdb=" O GLY B 868 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 868 through 871' Processing helix chain 'B' and resid 880 through 893 Processing helix chain 'B' and resid 895 through 902 removed outlier: 4.117A pdb=" N LEU B 899 " --> pdb=" O THR B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 923 Processing helix chain 'B' and resid 928 through 951 Processing helix chain 'B' and resid 959 through 967 Processing helix chain 'B' and resid 968 through 996 removed outlier: 3.624A pdb=" N GLU B 973 " --> pdb=" O PRO B 969 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLN B 975 " --> pdb=" O GLU B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1016 Processing helix chain 'C' and resid 282 through 292 Processing helix chain 'C' and resid 325 through 331 removed outlier: 3.537A pdb=" N VAL C 329 " --> pdb=" O PRO C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 360 removed outlier: 3.616A pdb=" N ASN C 358 " --> pdb=" O SER C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 398 removed outlier: 4.239A pdb=" N ARG C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN C 397 " --> pdb=" O ASP C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 720 through 726 removed outlier: 3.728A pdb=" N TYR C 724 " --> pdb=" O ASP C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 741 through 766 removed outlier: 3.566A pdb=" N GLN C 745 " --> pdb=" O SER C 741 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR C 761 " --> pdb=" O GLN C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 811 removed outlier: 4.758A pdb=" N LEU C 811 " --> pdb=" O ASN C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 868 removed outlier: 3.922A pdb=" N GLY C 868 " --> pdb=" O THR C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 871 No H-bonds generated for 'chain 'C' and resid 869 through 871' Processing helix chain 'C' and resid 880 through 893 removed outlier: 3.537A pdb=" N GLN C 884 " --> pdb=" O PRO C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 902 removed outlier: 4.360A pdb=" N LEU C 899 " --> pdb=" O THR C 895 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 900 " --> pdb=" O GLN C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 923 Processing helix chain 'C' and resid 928 through 948 removed outlier: 3.810A pdb=" N VAL C 935 " --> pdb=" O LEU C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 967 removed outlier: 3.578A pdb=" N ILE C 963 " --> pdb=" O VAL C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 1016 removed outlier: 4.590A pdb=" N VAL C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1101 No H-bonds generated for 'chain 'C' and resid 1099 through 1101' Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.370A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.787A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.909A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.912A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 155 Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.645A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 194 Proline residue: D 178 - end of helix removed outlier: 3.663A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 219 through 231 removed outlier: 4.029A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 252 removed outlier: 4.265A pdb=" N LEU D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.501A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.679A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.833A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 386 Processing helix chain 'D' and resid 387 through 388 No H-bonds generated for 'chain 'D' and resid 387 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 397 through 412 removed outlier: 4.473A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.740A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 466 removed outlier: 3.782A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU D 450 " --> pdb=" O ILE D 446 " (cutoff:3.500A) Proline residue: D 451 - end of helix Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.630A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA D 533 " --> pdb=" O LEU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.654A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.823A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.841A pdb=" N GLU D 564 " --> pdb=" O GLY D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 Processing helix chain 'D' and resid 581 through 599 Proline residue: D 590 - end of helix Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing helix chain 'G' and resid 20 through 53 removed outlier: 4.519A pdb=" N ASP G 38 " --> pdb=" O HIS G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 81 removed outlier: 3.754A pdb=" N ASN G 64 " --> pdb=" O GLN G 60 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA G 65 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU G 79 " --> pdb=" O GLU G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 102 removed outlier: 3.770A pdb=" N GLN G 96 " --> pdb=" O THR G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 130 removed outlier: 3.795A pdb=" N LYS G 114 " --> pdb=" O GLU G 110 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 155 removed outlier: 3.911A pdb=" N ILE G 151 " --> pdb=" O GLY G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 172 removed outlier: 3.681A pdb=" N ARG G 169 " --> pdb=" O TRP G 165 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL G 172 " --> pdb=" O TRP G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 194 Proline residue: G 178 - end of helix removed outlier: 3.765A pdb=" N VAL G 185 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 205 Processing helix chain 'G' and resid 219 through 231 removed outlier: 4.016A pdb=" N ILE G 223 " --> pdb=" O ARG G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 252 removed outlier: 4.241A pdb=" N LEU G 236 " --> pdb=" O GLU G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 281 removed outlier: 3.559A pdb=" N LEU G 278 " --> pdb=" O TRP G 275 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER G 280 " --> pdb=" O ASN G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 300 Processing helix chain 'G' and resid 303 through 318 Processing helix chain 'G' and resid 324 through 331 removed outlier: 3.936A pdb=" N TRP G 328 " --> pdb=" O THR G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 385 Processing helix chain 'G' and resid 386 through 388 No H-bonds generated for 'chain 'G' and resid 386 through 388' Processing helix chain 'G' and resid 389 through 393 Processing helix chain 'G' and resid 397 through 414 removed outlier: 4.523A pdb=" N HIS G 401 " --> pdb=" O ASN G 397 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU G 402 " --> pdb=" O GLU G 398 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET G 408 " --> pdb=" O VAL G 404 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER G 409 " --> pdb=" O GLY G 405 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR G 414 " --> pdb=" O LEU G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 422 removed outlier: 4.073A pdb=" N SER G 420 " --> pdb=" O LYS G 416 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY G 422 " --> pdb=" O LEU G 418 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 466 removed outlier: 3.682A pdb=" N GLU G 435 " --> pdb=" O ASP G 431 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR G 445 " --> pdb=" O LYS G 441 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU G 450 " --> pdb=" O ILE G 446 " (cutoff:3.500A) Proline residue: G 451 - end of helix Processing helix chain 'G' and resid 472 through 484 Processing helix chain 'G' and resid 499 through 503 Processing helix chain 'G' and resid 512 through 532 removed outlier: 3.874A pdb=" N TYR G 516 " --> pdb=" O PHE G 512 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE G 523 " --> pdb=" O THR G 519 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA G 532 " --> pdb=" O ALA G 528 " (cutoff:3.500A) Processing helix chain 'G' and resid 538 through 542 removed outlier: 3.508A pdb=" N LYS G 541 " --> pdb=" O PRO G 538 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS G 542 " --> pdb=" O LEU G 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 538 through 542' Processing helix chain 'G' and resid 548 through 559 removed outlier: 4.193A pdb=" N MET G 557 " --> pdb=" O LYS G 553 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG G 559 " --> pdb=" O PHE G 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 564 removed outlier: 3.511A pdb=" N SER G 563 " --> pdb=" O LEU G 560 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU G 564 " --> pdb=" O GLY G 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 560 through 564' Processing helix chain 'G' and resid 565 through 574 Processing helix chain 'G' and resid 581 through 599 Proline residue: G 590 - end of helix Processing helix chain 'G' and resid 600 through 602 No H-bonds generated for 'chain 'G' and resid 600 through 602' Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 4.098A pdb=" N THR A 32 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 9.639A pdb=" N ASN A 66 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR A 257 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR A 68 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N SER A 199 " --> pdb=" O PRO A 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 60 removed outlier: 6.725A pdb=" N LYS A 266 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 83 removed outlier: 7.030A pdb=" N ASN A 231 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE A 104 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ARG A 233 " --> pdb=" O TRP A 102 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TRP A 102 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU A 235 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS A 129 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 156 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 148 through 149 removed outlier: 3.858A pdb=" N VAL A 140 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASN A 231 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE A 104 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ARG A 233 " --> pdb=" O TRP A 102 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TRP A 102 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU A 235 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS A 129 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 305 removed outlier: 4.299A pdb=" N VAL A 582 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 313 removed outlier: 6.158A pdb=" N LYS A 312 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ASN A 529 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP A 561 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 562 " --> pdb=" O GLY A 553 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 342 through 345 removed outlier: 4.068A pdb=" N GLU A 342 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS A 420 " --> pdb=" O LEU A 500 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AB1, first strand: chain 'A' and resid 631 through 632 Processing sheet with id=AB2, first strand: chain 'A' and resid 641 through 642 removed outlier: 6.132A pdb=" N GLU A 641 " --> pdb=" O ALA A 677 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA A 659 " --> pdb=" O PRO A 652 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 684 through 686 Processing sheet with id=AB4, first strand: chain 'A' and resid 694 through 703 removed outlier: 6.800A pdb=" N THR A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR A1059 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLU A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 706 " --> pdb=" O HIS A1047 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 694 through 703 removed outlier: 6.800A pdb=" N THR A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR A1059 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLU A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR A1050 " --> pdb=" O HIS A1031 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N HIS A1031 " --> pdb=" O TYR A1050 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 717 through 719 Processing sheet with id=AB7, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AB8, first strand: chain 'A' and resid 1103 through 1108 removed outlier: 3.680A pdb=" N SER A1106 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA A1070 " --> pdb=" O SER A1106 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A1064 " --> pdb=" O TYR A1071 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1077 through 1080 Processing sheet with id=AC1, first strand: chain 'B' and resid 32 through 35 removed outlier: 5.751A pdb=" N SER B 199 " --> pdb=" O PRO B 219 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N TYR B 201 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 9.943A pdb=" N LEU B 217 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL B 41 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 52 through 60 removed outlier: 5.188A pdb=" N ASP B 275 " --> pdb=" O LYS B 266 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.592A pdb=" N PHE B 162 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 140 through 141 removed outlier: 3.650A pdb=" N VAL B 140 " --> pdb=" O ILE B 149 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 299 through 306 removed outlier: 6.714A pdb=" N VAL B 582 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASN B 305 " --> pdb=" O GLY B 580 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY B 580 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 342 through 346 removed outlier: 3.593A pdb=" N VAL B 383 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 349 through 350 removed outlier: 6.396A pdb=" N CYS B 349 " --> pdb=" O CYS B 512 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 440 through 442 Processing sheet with id=AC9, first strand: chain 'B' and resid 525 through 530 removed outlier: 5.076A pdb=" N ASP B 561 " --> pdb=" O ILE B 574 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 651 through 654 removed outlier: 6.491A pdb=" N ILE B 657 " --> pdb=" O ILE B 653 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 684 through 686 Processing sheet with id=AD3, first strand: chain 'B' and resid 694 through 711 removed outlier: 6.284A pdb=" N THR B 694 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR B1059 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET B1033 " --> pdb=" O VAL B1048 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR B1050 " --> pdb=" O HIS B1031 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N HIS B1031 " --> pdb=" O TYR B1050 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 717 through 719 Processing sheet with id=AD5, first strand: chain 'B' and resid 779 through 780 Processing sheet with id=AD6, first strand: chain 'B' and resid 1103 through 1105 Processing sheet with id=AD7, first strand: chain 'B' and resid 1077 through 1080 Processing sheet with id=AD8, first strand: chain 'C' and resid 32 through 35 removed outlier: 4.233A pdb=" N THR C 32 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASN C 66 " --> pdb=" O TYR C 257 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TYR C 257 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C 252 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU C 195 " --> pdb=" O LYS C 222 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS C 222 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL C 197 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR C 201 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ALA C 216 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL C 41 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 53 through 60 removed outlier: 3.849A pdb=" N ASP C 58 " --> pdb=" O THR C 261 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP C 275 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.657A pdb=" N PHE C 139 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL C 140 " --> pdb=" O ILE C 149 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.674A pdb=" N GLY C 101 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER C 114 " --> pdb=" O CYS C 129 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU C 124 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASN C 130 " --> pdb=" O CYS C 160 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N CYS C 160 " --> pdb=" O ASN C 130 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLU C 132 " --> pdb=" O PHE C 158 " (cutoff:3.500A) removed outlier: 9.351A pdb=" N PHE C 158 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 299 through 300 removed outlier: 3.824A pdb=" N GLY C 299 " --> pdb=" O THR C 586 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR C 586 " --> pdb=" O GLY C 299 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 306 through 307 Processing sheet with id=AE5, first strand: chain 'C' and resid 313 through 316 removed outlier: 6.520A pdb=" N VAL C 314 " --> pdb=" O ASN C 529 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 364 through 367 removed outlier: 3.841A pdb=" N THR C 418 " --> pdb=" O PHE C 502 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 380 through 381 Processing sheet with id=AE8, first strand: chain 'C' and resid 440 through 442 Processing sheet with id=AE9, first strand: chain 'C' and resid 641 through 642 removed outlier: 6.674A pdb=" N GLU C 641 " --> pdb=" O ALA C 677 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N THR C 679 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA C 659 " --> pdb=" O PRO C 652 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 694 through 711 removed outlier: 6.382A pdb=" N THR C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR C1059 " --> pdb=" O THR C 694 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLU C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET C1033 " --> pdb=" O VAL C1048 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR C1050 " --> pdb=" O HIS C1031 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N HIS C1031 " --> pdb=" O TYR C1050 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 717 through 719 Processing sheet with id=AF3, first strand: chain 'C' and resid 779 through 780 Processing sheet with id=AF4, first strand: chain 'C' and resid 1103 through 1104 removed outlier: 3.557A pdb=" N PHE C1104 " --> pdb=" O PHE C1072 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C1064 " --> pdb=" O TYR C1071 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1077 through 1080 Processing sheet with id=AF6, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AF7, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.868A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AF9, first strand: chain 'G' and resid 131 through 133 Processing sheet with id=AG1, first strand: chain 'G' and resid 262 through 263 removed outlier: 5.742A pdb=" N LEU G 262 " --> pdb=" O VAL G 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'G' and resid 347 through 350 1458 hydrogen bonds defined for protein. 4146 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: 7.93 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 36115 1.57 - 1.92: 262 1.92 - 2.26: 0 2.26 - 2.61: 0 2.61 - 2.96: 1 Bond restraints: 36378 Sorted by residual: bond pdb=" C ILE B 996 " pdb=" N ALA B 998 " ideal model delta sigma weight residual 1.329 2.963 -1.634 1.40e-02 5.10e+03 1.36e+04 bond pdb=" C PHE C1035 " pdb=" N PRO C1036 " ideal model delta sigma weight residual 1.330 1.299 0.031 1.23e-02 6.61e+03 6.47e+00 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.47e+00 bond pdb=" CB MET D 480 " pdb=" CG MET D 480 " ideal model delta sigma weight residual 1.520 1.453 0.067 3.00e-02 1.11e+03 4.98e+00 bond pdb=" CA ILE B 996 " pdb=" CB ILE B 996 " ideal model delta sigma weight residual 1.540 1.513 0.028 1.36e-02 5.41e+03 4.12e+00 ... (remaining 36373 not shown) Histogram of bond angle deviations from ideal: 0.00 - 16.77: 49502 16.77 - 33.53: 0 33.53 - 50.30: 1 50.30 - 67.06: 0 67.06 - 83.83: 1 Bond angle restraints: 49504 Sorted by residual: angle pdb=" O ILE B 996 " pdb=" C ILE B 996 " pdb=" N ALA B 998 " ideal model delta sigma weight residual 122.57 38.74 83.83 1.25e+00 6.40e-01 4.50e+03 angle pdb=" C ILE B 996 " pdb=" N ALA B 998 " pdb=" CA ALA B 998 " ideal model delta sigma weight residual 121.70 170.29 -48.59 1.80e+00 3.09e-01 7.29e+02 angle pdb=" CA ILE B 996 " pdb=" C ILE B 996 " pdb=" N ALA B 998 " ideal model delta sigma weight residual 116.60 103.01 13.59 1.45e+00 4.76e-01 8.79e+01 angle pdb=" C PHE C 838 " pdb=" CA PHE C 838 " pdb=" CB PHE C 838 " ideal model delta sigma weight residual 116.54 109.69 6.85 1.15e+00 7.56e-01 3.55e+01 angle pdb=" N GLY C 954 " pdb=" CA GLY C 954 " pdb=" C GLY C 954 " ideal model delta sigma weight residual 115.64 107.07 8.57 1.46e+00 4.69e-01 3.45e+01 ... (remaining 49499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.87: 21056 21.87 - 43.74: 1166 43.74 - 65.61: 99 65.61 - 87.49: 56 87.49 - 109.36: 14 Dihedral angle restraints: 22391 sinusoidal: 9550 harmonic: 12841 Sorted by residual: dihedral pdb=" CB CYS A 468 " pdb=" SG CYS A 468 " pdb=" SG CYS A 475 " pdb=" CB CYS A 475 " ideal model delta sinusoidal sigma weight residual 93.00 -176.84 -90.16 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS A 721 " pdb=" SG CYS A 721 " pdb=" SG CYS A 743 " pdb=" CB CYS A 743 " ideal model delta sinusoidal sigma weight residual -86.00 -3.38 -82.62 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS A 604 " pdb=" SG CYS A 604 " pdb=" SG CYS A 636 " pdb=" CB CYS A 636 " ideal model delta sinusoidal sigma weight residual 93.00 173.01 -80.01 1 1.00e+01 1.00e-02 7.93e+01 ... (remaining 22388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 5431 0.104 - 0.209: 182 0.209 - 0.313: 9 0.313 - 0.417: 2 0.417 - 0.521: 1 Chirality restraints: 5625 Sorted by residual: chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 110 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.79e+00 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 3.82e+00 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 159 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.33e+00 ... (remaining 5622 not shown) Planarity restraints: 6407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 996 " 0.109 2.00e-02 2.50e+03 2.09e-01 4.37e+02 pdb=" C ILE B 996 " -0.302 2.00e-02 2.50e+03 pdb=" O ILE B 996 " 0.259 2.00e-02 2.50e+03 pdb=" N ALA B 998 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 546 " 0.027 2.00e-02 2.50e+03 2.96e-02 1.53e+01 pdb=" CG PHE C 546 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE C 546 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE C 546 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 546 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE C 546 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE C 546 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 733 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.19e+00 pdb=" C ALA C 733 " -0.049 2.00e-02 2.50e+03 pdb=" O ALA C 733 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN C 734 " 0.017 2.00e-02 2.50e+03 ... (remaining 6404 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 396 2.54 - 3.13: 30705 3.13 - 3.72: 59025 3.72 - 4.31: 82279 4.31 - 4.90: 129348 Nonbonded interactions: 301753 Sorted by model distance: nonbonded pdb=" O SER A 741 " pdb=" OG1 THR A 744 " model vdw 1.955 3.040 nonbonded pdb=" NH1 ARG B 189 " pdb=" O ASN B 190 " model vdw 2.071 3.120 nonbonded pdb=" O GLN A 918 " pdb=" OG1 THR A 922 " model vdw 2.105 3.040 nonbonded pdb=" O GLN B 918 " pdb=" OG1 THR B 922 " model vdw 2.118 3.040 nonbonded pdb=" OG SER C 562 " pdb=" OD1 ASP C 573 " model vdw 2.126 3.040 ... (remaining 301748 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 19 through 608 or resid 626 through 996 or resid 998 throu \ gh 1304)) selection = (chain 'B' and (resid 19 through 811 or resid 837 through 1304)) selection = (chain 'C' and (resid 19 through 608 or resid 626 through 996 or resid 998 throu \ gh 1304)) } ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'S' } 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: 8.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 29.330 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 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 : 0.010 1.634 36482 Z= 0.663 Angle : 0.962 83.831 49768 Z= 0.567 Chirality : 0.049 0.521 5625 Planarity : 0.006 0.209 6370 Dihedral : 13.322 109.358 13977 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 23.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.01 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.45 (0.12), residues: 4373 helix: 0.10 (0.14), residues: 1311 sheet: -1.10 (0.19), residues: 638 loop : -1.54 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 759 TYR 0.027 0.002 TYR D 385 PHE 0.065 0.002 PHE C 546 TRP 0.037 0.002 TRP C 869 HIS 0.011 0.002 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.01003 (36378) covalent geometry : angle 0.93646 (49504) SS BOND : bond 0.00507 ( 48) SS BOND : angle 2.12187 ( 96) hydrogen bonds : bond 0.14555 ( 1446) hydrogen bonds : angle 7.56266 ( 4146) link_BETA1-4 : bond 0.00461 ( 19) link_BETA1-4 : angle 2.03332 ( 57) link_NAG-ASN : bond 0.00631 ( 37) link_NAG-ASN : angle 4.17824 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8746 Ramachandran restraints generated. 4373 Oldfield, 0 Emsley, 4373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8746 Ramachandran restraints generated. 4373 Oldfield, 0 Emsley, 4373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9381 (m-70) cc_final: 0.8937 (m-70) REVERT: A 313 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8344 (mm-30) REVERT: A 533 LEU cc_start: 0.8805 (mp) cc_final: 0.8604 (mp) REVERT: A 555 ASP cc_start: 0.9221 (t70) cc_final: 0.8994 (t70) REVERT: A 709 VAL cc_start: 0.9566 (t) cc_final: 0.9279 (p) REVERT: A 753 ILE cc_start: 0.9401 (mt) cc_final: 0.9145 (mt) REVERT: A 993 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8130 (tm-30) REVERT: B 108 MET cc_start: 0.9014 (mpp) cc_final: 0.8644 (mpp) REVERT: B 313 GLU cc_start: 0.9348 (pm20) cc_final: 0.9130 (pm20) REVERT: B 495 TYR cc_start: 0.9208 (m-80) cc_final: 0.8768 (m-80) REVERT: B 502 PHE cc_start: 0.8307 (m-80) cc_final: 0.7710 (m-10) REVERT: B 841 LEU cc_start: 0.9099 (mt) cc_final: 0.8821 (mt) REVERT: B 883 MET cc_start: 0.8931 (mmt) cc_final: 0.8685 (mmt) REVERT: B 936 ASN cc_start: 0.9296 (m110) cc_final: 0.9077 (m110) REVERT: B 948 GLN cc_start: 0.9443 (mm110) cc_final: 0.9201 (mm110) REVERT: B 953 PHE cc_start: 0.8324 (m-10) cc_final: 0.7731 (m-10) REVERT: B 994 GLN cc_start: 0.9039 (mm110) cc_final: 0.8574 (mm110) REVERT: C 45 ASP cc_start: 0.8898 (p0) cc_final: 0.8420 (p0) REVERT: C 47 ILE cc_start: 0.9247 (mt) cc_final: 0.8787 (mt) REVERT: C 61 LEU cc_start: 0.8391 (tp) cc_final: 0.8093 (tp) REVERT: C 380 PHE cc_start: 0.3696 (m-80) cc_final: 0.3371 (m-80) REVERT: C 408 ASP cc_start: 0.6191 (m-30) cc_final: 0.5981 (m-30) REVERT: C 933 ASP cc_start: 0.9135 (m-30) cc_final: 0.8859 (m-30) REVERT: C 975 GLN cc_start: 0.8989 (tt0) cc_final: 0.8475 (tt0) REVERT: C 1013 SER cc_start: 0.8768 (p) cc_final: 0.8300 (p) REVERT: C 1047 HIS cc_start: 0.8361 (m170) cc_final: 0.8097 (m90) REVERT: D 366 MET cc_start: 0.0301 (ppp) cc_final: 0.0087 (ppp) REVERT: D 455 MET cc_start: 0.6434 (tmm) cc_final: 0.5882 (tmm) REVERT: D 480 MET cc_start: 0.1251 (ptt) cc_final: 0.0902 (ptt) REVERT: G 323 MET cc_start: -0.2065 (mmt) cc_final: -0.3354 (mtt) REVERT: G 332 MET cc_start: 0.1366 (tmm) cc_final: 0.0815 (tmm) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.1994 time to fit residues: 149.4166 Evaluate side-chains 378 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 0.1980 chunk 424 optimal weight: 30.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN A 531 ASN A 878 GLN A 884 GLN A 905 GLN A 932 GLN ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN A1019 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN B 436 ASN B 480 ASN ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 662 HIS ** B 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 940 GLN ** B 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 745 GLN G 33 ASN G 42 GLN G 265 HIS ** G 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.138370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.112623 restraints weight = 216400.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.110120 restraints weight = 162353.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.110729 restraints weight = 133144.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.110825 restraints weight = 104269.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.110945 restraints weight = 98580.282| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 36482 Z= 0.153 Angle : 0.682 16.140 49768 Z= 0.352 Chirality : 0.046 0.508 5625 Planarity : 0.005 0.070 6370 Dihedral : 7.744 66.581 5893 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.01 % Favored : 94.93 % Rotamer: Outliers : 0.10 % Allowed : 4.94 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.12 (0.12), residues: 4375 helix: 0.51 (0.14), residues: 1372 sheet: -0.95 (0.20), residues: 631 loop : -1.47 (0.12), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 316 TYR 0.027 0.002 TYR D 385 PHE 0.034 0.002 PHE C 546 TRP 0.012 0.001 TRP C 869 HIS 0.009 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00330 (36378) covalent geometry : angle 0.65837 (49504) SS BOND : bond 0.00370 ( 48) SS BOND : angle 1.58537 ( 96) hydrogen bonds : bond 0.04849 ( 1446) hydrogen bonds : angle 6.24558 ( 4146) link_BETA1-4 : bond 0.00361 ( 19) link_BETA1-4 : angle 1.95558 ( 57) link_NAG-ASN : bond 0.00505 ( 37) link_NAG-ASN : angle 3.37455 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 474 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9383 (m-70) cc_final: 0.8897 (m-70) REVERT: A 313 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8337 (mm-30) REVERT: A 555 ASP cc_start: 0.9318 (t70) cc_final: 0.9041 (t70) REVERT: A 709 VAL cc_start: 0.9482 (t) cc_final: 0.9243 (p) REVERT: A 745 GLN cc_start: 0.8669 (pm20) cc_final: 0.8446 (pm20) REVERT: A 756 GLU cc_start: 0.8665 (tp30) cc_final: 0.8148 (tp30) REVERT: A 933 ASP cc_start: 0.9339 (p0) cc_final: 0.8932 (p0) REVERT: A 953 PHE cc_start: 0.8567 (m-10) cc_final: 0.8308 (m-10) REVERT: A 993 GLN cc_start: 0.9090 (tm130) cc_final: 0.8611 (tm-30) REVERT: A 997 ARG cc_start: 0.9049 (tpp80) cc_final: 0.8638 (mmm-85) REVERT: A 1002 ARG cc_start: 0.8888 (tpt90) cc_final: 0.8436 (tpp80) REVERT: A 1028 LYS cc_start: 0.8767 (tptp) cc_final: 0.8534 (tptp) REVERT: B 108 MET cc_start: 0.9047 (mpp) cc_final: 0.8653 (mpp) REVERT: B 292 LYS cc_start: 0.9073 (tptp) cc_final: 0.8763 (tptt) REVERT: B 495 TYR cc_start: 0.9129 (m-80) cc_final: 0.8638 (m-80) REVERT: B 502 PHE cc_start: 0.8393 (m-80) cc_final: 0.7798 (m-10) REVERT: B 710 MET cc_start: 0.9073 (mtp) cc_final: 0.8768 (mtp) REVERT: B 759 ARG cc_start: 0.8613 (ttp80) cc_final: 0.8129 (ttp80) REVERT: B 841 LEU cc_start: 0.9131 (mt) cc_final: 0.8848 (mt) REVERT: B 883 MET cc_start: 0.8806 (mmt) cc_final: 0.8513 (mmt) REVERT: B 948 GLN cc_start: 0.9219 (mm110) cc_final: 0.8931 (mm-40) REVERT: B 978 ARG cc_start: 0.9355 (mmm160) cc_final: 0.8960 (mmm-85) REVERT: B 994 GLN cc_start: 0.9133 (mm110) cc_final: 0.8616 (mm110) REVERT: B 1002 ARG cc_start: 0.9048 (ttt-90) cc_final: 0.8760 (ttt-90) REVERT: B 1006 ASN cc_start: 0.9373 (m110) cc_final: 0.8748 (m110) REVERT: B 1014 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8202 (tm-30) REVERT: C 45 ASP cc_start: 0.8874 (p0) cc_final: 0.8419 (p0) REVERT: C 47 ILE cc_start: 0.9250 (mt) cc_final: 0.8750 (mt) REVERT: C 59 HIS cc_start: 0.8026 (m170) cc_final: 0.7758 (m170) REVERT: C 61 LEU cc_start: 0.8182 (tp) cc_final: 0.7876 (tp) REVERT: C 408 ASP cc_start: 0.6444 (m-30) cc_final: 0.6191 (m-30) REVERT: C 724 TYR cc_start: 0.9168 (t80) cc_final: 0.8886 (t80) REVERT: C 945 LEU cc_start: 0.9441 (tp) cc_final: 0.9177 (tp) REVERT: C 975 GLN cc_start: 0.8618 (tt0) cc_final: 0.8351 (tt0) REVERT: D 366 MET cc_start: -0.0154 (ppp) cc_final: -0.0371 (ppp) REVERT: D 455 MET cc_start: 0.6525 (tmm) cc_final: 0.6001 (tmm) REVERT: D 480 MET cc_start: 0.1789 (ptt) cc_final: 0.1079 (ptt) REVERT: G 152 MET cc_start: -0.1660 (ttm) cc_final: -0.2110 (ttm) REVERT: G 323 MET cc_start: -0.2569 (mmt) cc_final: -0.4037 (mtt) REVERT: G 332 MET cc_start: 0.1503 (tmm) cc_final: 0.1008 (tmm) outliers start: 4 outliers final: 0 residues processed: 476 average time/residue: 0.1945 time to fit residues: 152.3996 Evaluate side-chains 387 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 365 optimal weight: 30.0000 chunk 196 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 428 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 379 optimal weight: 8.9990 chunk 360 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN A 884 GLN A 890 ASN A 905 GLN ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1041 HIS ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN ** B 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 GLN ** B 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1066 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 GLN C 884 GLN ** C1066 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 524 GLN ** G 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.133165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.107486 restraints weight = 218890.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.104503 restraints weight = 181692.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.104754 restraints weight = 167585.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.104905 restraints weight = 127484.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.105003 restraints weight = 116117.244| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 36482 Z= 0.349 Angle : 0.863 14.758 49768 Z= 0.443 Chirality : 0.049 0.447 5625 Planarity : 0.006 0.066 6370 Dihedral : 7.509 58.052 5893 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.70 % Favored : 93.21 % Rotamer: Outliers : 0.23 % Allowed : 6.08 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.54 (0.12), residues: 4375 helix: 0.01 (0.13), residues: 1375 sheet: -1.22 (0.20), residues: 624 loop : -1.61 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 69 TYR 0.029 0.002 TYR A 89 PHE 0.037 0.003 PHE B 549 TRP 0.019 0.002 TRP C 869 HIS 0.007 0.002 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00735 (36378) covalent geometry : angle 0.83747 (49504) SS BOND : bond 0.00605 ( 48) SS BOND : angle 2.06578 ( 96) hydrogen bonds : bond 0.05409 ( 1446) hydrogen bonds : angle 6.78404 ( 4146) link_BETA1-4 : bond 0.00719 ( 19) link_BETA1-4 : angle 2.51617 ( 57) link_NAG-ASN : bond 0.01067 ( 37) link_NAG-ASN : angle 3.74625 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 438 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.9058 (tp) cc_final: 0.8749 (tp) REVERT: A 59 HIS cc_start: 0.9481 (m-70) cc_final: 0.9037 (m-70) REVERT: A 108 MET cc_start: 0.2259 (mmt) cc_final: 0.1947 (mmt) REVERT: A 527 ASN cc_start: 0.9473 (t0) cc_final: 0.9262 (t0) REVERT: A 555 ASP cc_start: 0.9279 (t70) cc_final: 0.9021 (t70) REVERT: A 601 ASP cc_start: 0.8130 (m-30) cc_final: 0.7467 (t0) REVERT: A 756 GLU cc_start: 0.8702 (tp30) cc_final: 0.8381 (tp30) REVERT: A 936 ASN cc_start: 0.9249 (m110) cc_final: 0.9022 (m110) REVERT: A 993 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8781 (tm-30) REVERT: A 1002 ARG cc_start: 0.9021 (tpt90) cc_final: 0.8668 (tpp80) REVERT: B 60 PHE cc_start: 0.8350 (m-80) cc_final: 0.8094 (m-80) REVERT: B 108 MET cc_start: 0.8982 (mpp) cc_final: 0.8598 (mpp) REVERT: B 495 TYR cc_start: 0.9150 (m-80) cc_final: 0.8687 (m-80) REVERT: B 500 LEU cc_start: 0.9090 (tp) cc_final: 0.8831 (tp) REVERT: B 502 PHE cc_start: 0.8449 (m-80) cc_final: 0.7822 (m-10) REVERT: B 682 LEU cc_start: 0.8250 (mt) cc_final: 0.8012 (mt) REVERT: B 710 MET cc_start: 0.9053 (mtp) cc_final: 0.8671 (mtp) REVERT: B 759 ARG cc_start: 0.8737 (ttp80) cc_final: 0.8461 (ttp80) REVERT: B 841 LEU cc_start: 0.9156 (mt) cc_final: 0.8917 (mt) REVERT: B 948 GLN cc_start: 0.9152 (mm110) cc_final: 0.8857 (mm-40) REVERT: B 978 ARG cc_start: 0.9408 (mmm160) cc_final: 0.8961 (mmm-85) REVERT: B 987 LEU cc_start: 0.9660 (mt) cc_final: 0.9367 (mt) REVERT: B 994 GLN cc_start: 0.9166 (mm110) cc_final: 0.8676 (mm110) REVERT: B 1006 ASN cc_start: 0.9463 (m110) cc_final: 0.9043 (m110) REVERT: B 1014 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8477 (tm-30) REVERT: C 59 HIS cc_start: 0.8280 (m170) cc_final: 0.8020 (m170) REVERT: C 61 LEU cc_start: 0.8345 (tp) cc_final: 0.8032 (tp) REVERT: C 594 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8272 (tp30) REVERT: C 748 ARG cc_start: 0.9219 (ttm110) cc_final: 0.8954 (ttp80) REVERT: C 757 GLN cc_start: 0.8974 (tp-100) cc_final: 0.8441 (tm-30) REVERT: C 933 ASP cc_start: 0.9078 (m-30) cc_final: 0.8783 (m-30) REVERT: C 948 GLN cc_start: 0.9068 (pt0) cc_final: 0.8438 (pt0) REVERT: C 975 GLN cc_start: 0.8863 (tt0) cc_final: 0.8427 (tt0) REVERT: C 985 GLN cc_start: 0.9028 (pp30) cc_final: 0.8827 (pp30) REVERT: D 366 MET cc_start: -0.0126 (ppp) cc_final: -0.0393 (ppp) REVERT: D 455 MET cc_start: 0.6514 (tmm) cc_final: 0.6120 (tmm) REVERT: D 480 MET cc_start: 0.1910 (ptt) cc_final: 0.1306 (ptt) REVERT: G 152 MET cc_start: -0.0963 (ttm) cc_final: -0.1989 (ttm) REVERT: G 323 MET cc_start: -0.2076 (mmt) cc_final: -0.3484 (mtt) REVERT: G 332 MET cc_start: 0.2129 (tmm) cc_final: 0.1366 (tmm) outliers start: 9 outliers final: 3 residues processed: 446 average time/residue: 0.1949 time to fit residues: 143.0978 Evaluate side-chains 361 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 358 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 304 optimal weight: 0.6980 chunk 330 optimal weight: 8.9990 chunk 333 optimal weight: 20.0000 chunk 291 optimal weight: 0.9990 chunk 233 optimal weight: 0.8980 chunk 387 optimal weight: 50.0000 chunk 113 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 381 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 113 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN A 905 GLN ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN B 529 ASN B 734 ASN ** B 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 GLN B 940 GLN ** B 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 GLN C 136 ASN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 488 ASN C 745 GLN ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 GLN C1019 GLN G 149 ASN ** G 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.137610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.110647 restraints weight = 215535.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.107725 restraints weight = 170929.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.108245 restraints weight = 135669.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.108358 restraints weight = 107391.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.108482 restraints weight = 99276.224| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36482 Z= 0.144 Angle : 0.686 13.564 49768 Z= 0.350 Chirality : 0.046 0.456 5625 Planarity : 0.005 0.064 6370 Dihedral : 6.699 58.300 5893 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.14 % Favored : 94.77 % Rotamer: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.14 (0.12), residues: 4375 helix: 0.54 (0.14), residues: 1385 sheet: -1.15 (0.20), residues: 632 loop : -1.46 (0.12), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 997 TYR 0.020 0.002 TYR B 368 PHE 0.034 0.002 PHE C 546 TRP 0.016 0.001 TRP C 869 HIS 0.008 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00314 (36378) covalent geometry : angle 0.66089 (49504) SS BOND : bond 0.00511 ( 48) SS BOND : angle 1.98253 ( 96) hydrogen bonds : bond 0.04550 ( 1446) hydrogen bonds : angle 6.12173 ( 4146) link_BETA1-4 : bond 0.00420 ( 19) link_BETA1-4 : angle 1.80939 ( 57) link_NAG-ASN : bond 0.00464 ( 37) link_NAG-ASN : angle 3.29402 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 476 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9513 (m-70) cc_final: 0.8965 (m-70) REVERT: A 108 MET cc_start: 0.2596 (mmt) cc_final: 0.2319 (mmt) REVERT: A 262 THR cc_start: 0.8284 (t) cc_final: 0.8046 (t) REVERT: A 264 MET cc_start: 0.8156 (ttt) cc_final: 0.7908 (ptm) REVERT: A 278 ASP cc_start: 0.8948 (m-30) cc_final: 0.8112 (t0) REVERT: A 527 ASN cc_start: 0.9473 (t0) cc_final: 0.9253 (t0) REVERT: A 555 ASP cc_start: 0.9296 (t70) cc_final: 0.9047 (t70) REVERT: A 680 MET cc_start: 0.8733 (pmm) cc_final: 0.8096 (pmm) REVERT: A 745 GLN cc_start: 0.8937 (pm20) cc_final: 0.8701 (pm20) REVERT: A 756 GLU cc_start: 0.8829 (tp30) cc_final: 0.8057 (tp30) REVERT: A 759 ARG cc_start: 0.9257 (tmm-80) cc_final: 0.8986 (tmm-80) REVERT: A 933 ASP cc_start: 0.9303 (p0) cc_final: 0.9051 (p0) REVERT: A 936 ASN cc_start: 0.9368 (m110) cc_final: 0.9054 (m110) REVERT: A 948 GLN cc_start: 0.9359 (mm110) cc_final: 0.8949 (mm-40) REVERT: A 953 PHE cc_start: 0.8557 (m-10) cc_final: 0.7168 (m-10) REVERT: A 978 ARG cc_start: 0.9190 (mtm180) cc_final: 0.8921 (mtm180) REVERT: A 993 GLN cc_start: 0.9067 (tm130) cc_final: 0.8780 (tm-30) REVERT: A 1002 ARG cc_start: 0.8941 (tpt90) cc_final: 0.8461 (tpp80) REVERT: B 60 PHE cc_start: 0.8324 (m-80) cc_final: 0.8072 (m-80) REVERT: B 108 MET cc_start: 0.9004 (mpp) cc_final: 0.8581 (mpp) REVERT: B 495 TYR cc_start: 0.9245 (m-80) cc_final: 0.8727 (m-80) REVERT: B 500 LEU cc_start: 0.9194 (tp) cc_final: 0.8983 (pp) REVERT: B 502 PHE cc_start: 0.8533 (m-80) cc_final: 0.7515 (m-10) REVERT: B 579 PHE cc_start: 0.7993 (t80) cc_final: 0.7787 (t80) REVERT: B 682 LEU cc_start: 0.8216 (mt) cc_final: 0.7960 (mt) REVERT: B 710 MET cc_start: 0.8962 (mtp) cc_final: 0.8562 (mtp) REVERT: B 759 ARG cc_start: 0.8758 (ttp80) cc_final: 0.8328 (ttp80) REVERT: B 839 ASN cc_start: 0.9032 (m-40) cc_final: 0.8776 (m-40) REVERT: B 936 ASN cc_start: 0.9057 (m110) cc_final: 0.8834 (m110) REVERT: B 948 GLN cc_start: 0.9168 (mm110) cc_final: 0.8741 (mm-40) REVERT: B 959 VAL cc_start: 0.8952 (t) cc_final: 0.8599 (p) REVERT: B 987 LEU cc_start: 0.9610 (mt) cc_final: 0.9385 (mt) REVERT: B 994 GLN cc_start: 0.9227 (mm110) cc_final: 0.8502 (mm110) REVERT: B 1014 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8316 (tm-30) REVERT: C 59 HIS cc_start: 0.8388 (m170) cc_final: 0.7874 (m170) REVERT: C 61 LEU cc_start: 0.8309 (tp) cc_final: 0.8009 (tp) REVERT: C 745 GLN cc_start: 0.9287 (pt0) cc_final: 0.8996 (pt0) REVERT: C 757 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8673 (tp40) REVERT: C 936 ASN cc_start: 0.8993 (m110) cc_final: 0.8772 (m110) REVERT: D 455 MET cc_start: 0.6755 (tmm) cc_final: 0.6283 (tmm) REVERT: D 480 MET cc_start: 0.2149 (ptt) cc_final: 0.1835 (ptt) REVERT: G 152 MET cc_start: -0.1247 (ttm) cc_final: -0.2180 (ttm) REVERT: G 323 MET cc_start: -0.1816 (mmt) cc_final: -0.3098 (mtt) REVERT: G 332 MET cc_start: 0.1686 (tmm) cc_final: 0.0948 (tmm) REVERT: G 480 MET cc_start: -0.3197 (mtt) cc_final: -0.3508 (mtt) REVERT: G 579 MET cc_start: -0.1283 (ttt) cc_final: -0.1558 (ttt) outliers start: 4 outliers final: 0 residues processed: 477 average time/residue: 0.1914 time to fit residues: 149.8587 Evaluate side-chains 386 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 94 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 316 optimal weight: 2.9990 chunk 294 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 396 optimal weight: 40.0000 chunk 159 optimal weight: 6.9990 chunk 57 optimal weight: 0.0000 overall best weight: 1.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A 878 GLN A 905 GLN ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 GLN B 734 ASN ** B 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 GLN ** B 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN C 136 ASN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 722 ASN C 985 GLN ** G 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.137036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.109953 restraints weight = 217065.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.107275 restraints weight = 161614.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.107511 restraints weight = 139772.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.107694 restraints weight = 112133.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.107819 restraints weight = 101455.944| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 36482 Z= 0.165 Angle : 0.693 16.326 49768 Z= 0.353 Chirality : 0.046 0.435 5625 Planarity : 0.005 0.075 6370 Dihedral : 6.562 62.464 5893 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.58 % Favored : 94.33 % Rotamer: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.06 (0.12), residues: 4375 helix: 0.67 (0.14), residues: 1374 sheet: -1.10 (0.20), residues: 631 loop : -1.44 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 316 TYR 0.021 0.002 TYR A 441 PHE 0.030 0.002 PHE C 546 TRP 0.018 0.001 TRP C 869 HIS 0.007 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00359 (36378) covalent geometry : angle 0.66669 (49504) SS BOND : bond 0.00400 ( 48) SS BOND : angle 1.85776 ( 96) hydrogen bonds : bond 0.04419 ( 1446) hydrogen bonds : angle 6.05874 ( 4146) link_BETA1-4 : bond 0.00384 ( 19) link_BETA1-4 : angle 1.85461 ( 57) link_NAG-ASN : bond 0.00537 ( 37) link_NAG-ASN : angle 3.47985 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 466 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 59 HIS cc_start: 0.9506 (m-70) cc_final: 0.8960 (m-70) REVERT: A 108 MET cc_start: 0.2587 (mmt) cc_final: 0.2334 (mmt) REVERT: A 262 THR cc_start: 0.8404 (t) cc_final: 0.8176 (t) REVERT: A 278 ASP cc_start: 0.8965 (m-30) cc_final: 0.7657 (t0) REVERT: A 527 ASN cc_start: 0.9488 (t0) cc_final: 0.9242 (t0) REVERT: A 555 ASP cc_start: 0.9333 (t70) cc_final: 0.9068 (t70) REVERT: A 680 MET cc_start: 0.8764 (pmm) cc_final: 0.8180 (pmm) REVERT: A 709 VAL cc_start: 0.9346 (t) cc_final: 0.8934 (p) REVERT: A 710 MET cc_start: 0.8906 (mtm) cc_final: 0.8646 (mtm) REVERT: A 756 GLU cc_start: 0.8745 (tp30) cc_final: 0.7862 (tp30) REVERT: A 933 ASP cc_start: 0.9393 (p0) cc_final: 0.9065 (p0) REVERT: A 936 ASN cc_start: 0.9358 (m110) cc_final: 0.9009 (m110) REVERT: A 948 GLN cc_start: 0.9385 (mm110) cc_final: 0.9045 (mm-40) REVERT: A 953 PHE cc_start: 0.8643 (m-10) cc_final: 0.7895 (m-10) REVERT: A 1002 ARG cc_start: 0.8933 (tpt90) cc_final: 0.8490 (tpp80) REVERT: B 60 PHE cc_start: 0.8376 (m-80) cc_final: 0.8040 (m-10) REVERT: B 108 MET cc_start: 0.8999 (mpp) cc_final: 0.8556 (mpp) REVERT: B 292 LYS cc_start: 0.9059 (tptp) cc_final: 0.8824 (tptt) REVERT: B 306 PHE cc_start: 0.8697 (t80) cc_final: 0.8294 (t80) REVERT: B 374 LYS cc_start: 0.8571 (pttt) cc_final: 0.8285 (pttm) REVERT: B 495 TYR cc_start: 0.9253 (m-80) cc_final: 0.8741 (m-80) REVERT: B 502 PHE cc_start: 0.8616 (m-80) cc_final: 0.8177 (m-10) REVERT: B 682 LEU cc_start: 0.8189 (mt) cc_final: 0.7546 (mt) REVERT: B 710 MET cc_start: 0.9043 (mtp) cc_final: 0.8591 (mtp) REVERT: B 759 ARG cc_start: 0.9118 (ttp80) cc_final: 0.8589 (ttp80) REVERT: B 839 ASN cc_start: 0.9023 (m-40) cc_final: 0.8671 (m-40) REVERT: B 936 ASN cc_start: 0.9006 (m110) cc_final: 0.8794 (m110) REVERT: B 948 GLN cc_start: 0.9214 (mm110) cc_final: 0.8871 (mm-40) REVERT: B 987 LEU cc_start: 0.9628 (mt) cc_final: 0.9368 (mt) REVERT: B 1002 ARG cc_start: 0.9123 (ttt-90) cc_final: 0.8923 (ttt-90) REVERT: B 1014 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8493 (tm-30) REVERT: C 59 HIS cc_start: 0.8316 (m170) cc_final: 0.7876 (m170) REVERT: C 61 LEU cc_start: 0.8300 (tp) cc_final: 0.8027 (tp) REVERT: C 265 LEU cc_start: 0.9501 (mp) cc_final: 0.9258 (mp) REVERT: C 307 ARG cc_start: 0.7742 (mmm-85) cc_final: 0.7461 (mtp85) REVERT: C 530 PHE cc_start: 0.8571 (m-10) cc_final: 0.7998 (m-80) REVERT: C 940 GLN cc_start: 0.9524 (mp10) cc_final: 0.9177 (mp10) REVERT: C 945 LEU cc_start: 0.9206 (tt) cc_final: 0.9001 (tt) REVERT: D 366 MET cc_start: -0.0190 (ppp) cc_final: -0.0416 (ppp) REVERT: D 455 MET cc_start: 0.6748 (tmm) cc_final: 0.6312 (tmm) REVERT: D 480 MET cc_start: 0.2117 (ptt) cc_final: 0.1706 (ptt) REVERT: D 536 GLU cc_start: 0.4836 (mm-30) cc_final: 0.4374 (mt-10) REVERT: G 123 MET cc_start: 0.1506 (mpp) cc_final: 0.1269 (mpp) REVERT: G 323 MET cc_start: -0.2343 (mmt) cc_final: -0.3650 (mtt) REVERT: G 332 MET cc_start: 0.1953 (tmm) cc_final: 0.1246 (tmm) REVERT: G 471 ASP cc_start: 0.5651 (p0) cc_final: 0.5270 (m-30) outliers start: 4 outliers final: 0 residues processed: 469 average time/residue: 0.1910 time to fit residues: 146.4723 Evaluate side-chains 379 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 88 optimal weight: 0.0970 chunk 351 optimal weight: 40.0000 chunk 354 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 247 optimal weight: 30.0000 chunk 61 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 305 optimal weight: 0.7980 chunk 223 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN A 884 GLN A 905 GLN ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 HIS ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 GLN ** B 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1006 ASN C 136 ASN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 GLN ** C 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 GLN C1037 GLN ** G 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.138233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.110625 restraints weight = 216069.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.107894 restraints weight = 158995.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.108203 restraints weight = 129076.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.108261 restraints weight = 105330.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.108439 restraints weight = 96704.781| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36482 Z= 0.132 Angle : 0.666 14.783 49768 Z= 0.337 Chirality : 0.045 0.438 5625 Planarity : 0.005 0.072 6370 Dihedral : 6.194 56.327 5893 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.98 % Favored : 94.97 % Rotamer: Outliers : 0.08 % Allowed : 2.42 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.91 (0.12), residues: 4375 helix: 0.81 (0.14), residues: 1378 sheet: -0.98 (0.20), residues: 609 loop : -1.38 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 978 TYR 0.025 0.001 TYR C 439 PHE 0.024 0.001 PHE B 889 TRP 0.020 0.001 TRP C 869 HIS 0.007 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00286 (36378) covalent geometry : angle 0.64043 (49504) SS BOND : bond 0.00634 ( 48) SS BOND : angle 1.89477 ( 96) hydrogen bonds : bond 0.04188 ( 1446) hydrogen bonds : angle 5.81376 ( 4146) link_BETA1-4 : bond 0.00450 ( 19) link_BETA1-4 : angle 1.68678 ( 57) link_NAG-ASN : bond 0.00627 ( 37) link_NAG-ASN : angle 3.35416 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 477 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9485 (m-70) cc_final: 0.8935 (m-70) REVERT: A 108 MET cc_start: 0.3035 (mmt) cc_final: 0.2693 (mmt) REVERT: A 262 THR cc_start: 0.8442 (t) cc_final: 0.8186 (t) REVERT: A 264 MET cc_start: 0.8000 (ptm) cc_final: 0.7799 (ptm) REVERT: A 278 ASP cc_start: 0.9042 (m-30) cc_final: 0.7992 (t0) REVERT: A 555 ASP cc_start: 0.9324 (t70) cc_final: 0.9062 (t70) REVERT: A 709 VAL cc_start: 0.9284 (t) cc_final: 0.8819 (p) REVERT: A 746 LEU cc_start: 0.9596 (mt) cc_final: 0.9339 (mt) REVERT: A 756 GLU cc_start: 0.8847 (tp30) cc_final: 0.7942 (tp30) REVERT: A 759 ARG cc_start: 0.9286 (tmm-80) cc_final: 0.8958 (tmm-80) REVERT: A 841 LEU cc_start: 0.9270 (mm) cc_final: 0.9066 (mm) REVERT: A 936 ASN cc_start: 0.9369 (m110) cc_final: 0.9013 (m110) REVERT: A 948 GLN cc_start: 0.9366 (mm110) cc_final: 0.8992 (mm-40) REVERT: A 953 PHE cc_start: 0.8590 (m-10) cc_final: 0.7761 (m-10) REVERT: A 978 ARG cc_start: 0.9186 (mtm180) cc_final: 0.8905 (mtm180) REVERT: A 1000 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8434 (tm-30) REVERT: A 1002 ARG cc_start: 0.8945 (tpt90) cc_final: 0.8407 (tpp80) REVERT: A 1028 LYS cc_start: 0.8550 (tptp) cc_final: 0.8325 (tptp) REVERT: B 60 PHE cc_start: 0.8369 (m-80) cc_final: 0.8106 (m-80) REVERT: B 108 MET cc_start: 0.8970 (mpp) cc_final: 0.8510 (mpp) REVERT: B 306 PHE cc_start: 0.8744 (t80) cc_final: 0.8304 (t80) REVERT: B 326 PHE cc_start: 0.8675 (m-80) cc_final: 0.8443 (m-10) REVERT: B 495 TYR cc_start: 0.9295 (m-80) cc_final: 0.9027 (m-80) REVERT: B 502 PHE cc_start: 0.8705 (m-80) cc_final: 0.8181 (m-10) REVERT: B 682 LEU cc_start: 0.8135 (mt) cc_final: 0.7551 (mt) REVERT: B 710 MET cc_start: 0.8967 (mtp) cc_final: 0.8506 (mtp) REVERT: B 722 ASN cc_start: 0.8512 (t0) cc_final: 0.8288 (t0) REVERT: B 757 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8742 (mm-40) REVERT: B 759 ARG cc_start: 0.9003 (ttp80) cc_final: 0.8583 (ttp80) REVERT: B 839 ASN cc_start: 0.9114 (m-40) cc_final: 0.8744 (m-40) REVERT: B 932 GLN cc_start: 0.9039 (tp40) cc_final: 0.8774 (mm110) REVERT: B 987 LEU cc_start: 0.9578 (mt) cc_final: 0.9308 (mt) REVERT: B 1002 ARG cc_start: 0.9238 (ttt-90) cc_final: 0.9019 (ttt-90) REVERT: B 1014 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8545 (tm-30) REVERT: C 59 HIS cc_start: 0.8376 (m170) cc_final: 0.7898 (m170) REVERT: C 61 LEU cc_start: 0.8315 (tp) cc_final: 0.8028 (tp) REVERT: C 530 PHE cc_start: 0.8559 (m-10) cc_final: 0.8012 (m-80) REVERT: C 723 MET cc_start: 0.8820 (tpp) cc_final: 0.8522 (mmm) REVERT: C 745 GLN cc_start: 0.9284 (pt0) cc_final: 0.8915 (pt0) REVERT: C 757 GLN cc_start: 0.9111 (tp-100) cc_final: 0.8794 (tp40) REVERT: C 936 ASN cc_start: 0.9148 (m110) cc_final: 0.8870 (m110) REVERT: C 952 ASN cc_start: 0.9021 (p0) cc_final: 0.8784 (p0) REVERT: C 975 GLN cc_start: 0.8420 (mm-40) cc_final: 0.7927 (tt0) REVERT: D 366 MET cc_start: -0.0204 (ppp) cc_final: -0.0435 (ppp) REVERT: D 455 MET cc_start: 0.6739 (tmm) cc_final: 0.6303 (tmm) REVERT: D 480 MET cc_start: 0.2175 (ptt) cc_final: 0.1812 (ptt) REVERT: D 536 GLU cc_start: 0.4845 (mm-30) cc_final: 0.4416 (mt-10) REVERT: G 323 MET cc_start: -0.1721 (mmt) cc_final: -0.2758 (mtt) REVERT: G 332 MET cc_start: 0.1502 (tmm) cc_final: 0.0891 (tmm) REVERT: G 471 ASP cc_start: 0.5804 (p0) cc_final: 0.5550 (m-30) REVERT: G 579 MET cc_start: -0.1367 (ttt) cc_final: -0.1609 (ttt) outliers start: 3 outliers final: 0 residues processed: 479 average time/residue: 0.1985 time to fit residues: 157.7233 Evaluate side-chains 395 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 235 optimal weight: 5.9990 chunk 385 optimal weight: 30.0000 chunk 217 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 335 optimal weight: 40.0000 chunk 203 optimal weight: 4.9990 chunk 293 optimal weight: 0.7980 chunk 413 optimal weight: 20.0000 chunk 289 optimal weight: 6.9990 chunk 292 optimal weight: 0.7980 chunk 180 optimal weight: 8.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN A 884 GLN A 905 GLN ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN A1041 HIS ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 GLN B 993 GLN ** B1066 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 GLN ** C1066 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 599 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.135157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.108409 restraints weight = 217769.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.105295 restraints weight = 164373.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.105518 restraints weight = 153850.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.105459 restraints weight = 121364.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.105566 restraints weight = 114004.871| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 36482 Z= 0.243 Angle : 0.745 13.988 49768 Z= 0.382 Chirality : 0.046 0.436 5625 Planarity : 0.005 0.080 6370 Dihedral : 6.447 59.261 5893 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.99 % Favored : 93.94 % Rotamer: Outliers : 0.08 % Allowed : 2.10 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.17 (0.12), residues: 4375 helix: 0.48 (0.14), residues: 1393 sheet: -1.11 (0.20), residues: 616 loop : -1.47 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 316 TYR 0.024 0.002 TYR B 253 PHE 0.037 0.002 PHE C 546 TRP 0.028 0.002 TRP C 869 HIS 0.007 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00518 (36378) covalent geometry : angle 0.72128 (49504) SS BOND : bond 0.00510 ( 48) SS BOND : angle 2.07039 ( 96) hydrogen bonds : bond 0.04540 ( 1446) hydrogen bonds : angle 6.13066 ( 4146) link_BETA1-4 : bond 0.00487 ( 19) link_BETA1-4 : angle 1.92828 ( 57) link_NAG-ASN : bond 0.00678 ( 37) link_NAG-ASN : angle 3.35219 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 449 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9497 (m-70) cc_final: 0.8996 (m-70) REVERT: A 70 PHE cc_start: 0.9386 (m-80) cc_final: 0.9160 (m-80) REVERT: A 108 MET cc_start: 0.2512 (mmt) cc_final: 0.2225 (mmt) REVERT: A 262 THR cc_start: 0.8418 (t) cc_final: 0.8193 (t) REVERT: A 278 ASP cc_start: 0.9102 (m-30) cc_final: 0.8053 (t0) REVERT: A 555 ASP cc_start: 0.9309 (t70) cc_final: 0.9057 (t70) REVERT: A 680 MET cc_start: 0.8753 (pmm) cc_final: 0.8460 (pmm) REVERT: A 756 GLU cc_start: 0.8779 (tp30) cc_final: 0.8036 (tp30) REVERT: A 841 LEU cc_start: 0.9314 (mm) cc_final: 0.9096 (mm) REVERT: A 936 ASN cc_start: 0.9340 (m110) cc_final: 0.8904 (m110) REVERT: A 948 GLN cc_start: 0.9446 (mm110) cc_final: 0.8881 (mm-40) REVERT: A 953 PHE cc_start: 0.8924 (m-10) cc_final: 0.7291 (m-10) REVERT: A 975 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8424 (mm110) REVERT: A 1002 ARG cc_start: 0.9004 (tpt90) cc_final: 0.8631 (tpp80) REVERT: B 60 PHE cc_start: 0.8380 (m-80) cc_final: 0.8173 (m-80) REVERT: B 108 MET cc_start: 0.8920 (mpp) cc_final: 0.8467 (mpp) REVERT: B 264 MET cc_start: 0.8484 (tpt) cc_final: 0.8163 (tpt) REVERT: B 306 PHE cc_start: 0.8669 (t80) cc_final: 0.8309 (t80) REVERT: B 495 TYR cc_start: 0.9265 (m-80) cc_final: 0.9019 (m-80) REVERT: B 502 PHE cc_start: 0.8615 (m-80) cc_final: 0.7982 (m-10) REVERT: B 579 PHE cc_start: 0.8181 (t80) cc_final: 0.7906 (t80) REVERT: B 680 MET cc_start: 0.8823 (tmm) cc_final: 0.8519 (tmm) REVERT: B 682 LEU cc_start: 0.8210 (mt) cc_final: 0.7861 (mt) REVERT: B 710 MET cc_start: 0.8943 (mtp) cc_final: 0.8409 (mtp) REVERT: B 722 ASN cc_start: 0.8600 (t0) cc_final: 0.8375 (t0) REVERT: B 723 MET cc_start: 0.8038 (tpt) cc_final: 0.7627 (tpp) REVERT: B 759 ARG cc_start: 0.9050 (ttp80) cc_final: 0.8600 (ttp80) REVERT: B 839 ASN cc_start: 0.9095 (m-40) cc_final: 0.8601 (m-40) REVERT: B 936 ASN cc_start: 0.9035 (m110) cc_final: 0.8821 (m110) REVERT: B 948 GLN cc_start: 0.9230 (mm110) cc_final: 0.8861 (mm-40) REVERT: B 959 VAL cc_start: 0.8849 (t) cc_final: 0.8631 (t) REVERT: B 987 LEU cc_start: 0.9635 (mt) cc_final: 0.9297 (mt) REVERT: B 990 TYR cc_start: 0.9018 (t80) cc_final: 0.8808 (t80) REVERT: B 1006 ASN cc_start: 0.9394 (m-40) cc_final: 0.9006 (m110) REVERT: B 1014 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8524 (tm-30) REVERT: C 61 LEU cc_start: 0.8346 (tp) cc_final: 0.8035 (tp) REVERT: C 307 ARG cc_start: 0.7677 (mmm-85) cc_final: 0.7425 (mtp85) REVERT: C 530 PHE cc_start: 0.8580 (m-10) cc_final: 0.8055 (m-80) REVERT: C 852 MET cc_start: 0.8390 (mmm) cc_final: 0.7991 (mmp) REVERT: C 936 ASN cc_start: 0.9013 (m110) cc_final: 0.8755 (m110) REVERT: C 975 GLN cc_start: 0.8466 (mm-40) cc_final: 0.7896 (tt0) REVERT: D 366 MET cc_start: -0.0302 (ppp) cc_final: -0.0527 (ppp) REVERT: D 455 MET cc_start: 0.6726 (tmm) cc_final: 0.6229 (tmm) REVERT: D 480 MET cc_start: 0.2029 (ptt) cc_final: 0.0614 (ttt) REVERT: G 323 MET cc_start: -0.2041 (mmt) cc_final: -0.3148 (mtt) REVERT: G 332 MET cc_start: 0.1792 (tmm) cc_final: 0.1125 (tmm) REVERT: G 471 ASP cc_start: 0.5929 (p0) cc_final: 0.5723 (m-30) outliers start: 3 outliers final: 1 residues processed: 451 average time/residue: 0.1934 time to fit residues: 142.3806 Evaluate side-chains 373 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 148 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 chunk 255 optimal weight: 7.9990 chunk 331 optimal weight: 30.0000 chunk 129 optimal weight: 6.9990 chunk 322 optimal weight: 30.0000 chunk 236 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 375 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 GLN A 932 GLN ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1066 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 547 GLN C 722 ASN C 916 GLN ** C 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1066 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS D 442 GLN ** G 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 522 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.131013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.103626 restraints weight = 219041.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.099373 restraints weight = 178496.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.099274 restraints weight = 187433.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.099398 restraints weight = 149564.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.099488 restraints weight = 132297.002| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.108 36482 Z= 0.399 Angle : 0.949 18.586 49768 Z= 0.490 Chirality : 0.052 0.409 5625 Planarity : 0.007 0.103 6370 Dihedral : 7.521 58.316 5893 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 27.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.73 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.91 (0.12), residues: 4375 helix: -0.25 (0.13), residues: 1389 sheet: -1.57 (0.20), residues: 577 loop : -1.84 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 888 TYR 0.039 0.003 TYR C 856 PHE 0.050 0.003 PHE B 889 TRP 0.046 0.002 TRP B 869 HIS 0.009 0.002 HIS B 662 Details of bonding type rmsd covalent geometry : bond 0.00846 (36378) covalent geometry : angle 0.92551 (49504) SS BOND : bond 0.00771 ( 48) SS BOND : angle 2.37295 ( 96) hydrogen bonds : bond 0.05552 ( 1446) hydrogen bonds : angle 6.92742 ( 4146) link_BETA1-4 : bond 0.00767 ( 19) link_BETA1-4 : angle 2.37885 ( 57) link_NAG-ASN : bond 0.01043 ( 37) link_NAG-ASN : angle 3.76207 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9308 (m-70) cc_final: 0.8872 (m-70) REVERT: A 70 PHE cc_start: 0.9324 (m-80) cc_final: 0.9102 (m-80) REVERT: A 108 MET cc_start: 0.2711 (mmt) cc_final: 0.2479 (mmt) REVERT: A 278 ASP cc_start: 0.9000 (m-30) cc_final: 0.8257 (t0) REVERT: A 527 ASN cc_start: 0.9505 (t0) cc_final: 0.9239 (t0) REVERT: A 680 MET cc_start: 0.8947 (pmm) cc_final: 0.8746 (pmm) REVERT: A 756 GLU cc_start: 0.8274 (tp30) cc_final: 0.7543 (tp30) REVERT: A 933 ASP cc_start: 0.9452 (p0) cc_final: 0.8980 (p0) REVERT: A 936 ASN cc_start: 0.9141 (m110) cc_final: 0.8671 (m110) REVERT: A 948 GLN cc_start: 0.9232 (mm110) cc_final: 0.8991 (mm-40) REVERT: A 953 PHE cc_start: 0.9185 (m-10) cc_final: 0.8978 (m-10) REVERT: A 975 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8282 (mm110) REVERT: A 1025 PHE cc_start: 0.9016 (t80) cc_final: 0.8807 (t80) REVERT: B 108 MET cc_start: 0.8769 (mpp) cc_final: 0.8370 (mpp) REVERT: B 288 LYS cc_start: 0.9538 (mttt) cc_final: 0.9267 (mtpt) REVERT: B 292 LYS cc_start: 0.9304 (tptt) cc_final: 0.9088 (tptt) REVERT: B 495 TYR cc_start: 0.9186 (m-80) cc_final: 0.8906 (m-80) REVERT: B 500 LEU cc_start: 0.9088 (mp) cc_final: 0.8822 (mt) REVERT: B 502 PHE cc_start: 0.8592 (m-80) cc_final: 0.7968 (m-10) REVERT: B 680 MET cc_start: 0.8870 (tmm) cc_final: 0.8567 (tmm) REVERT: B 682 LEU cc_start: 0.8275 (mt) cc_final: 0.7985 (mt) REVERT: B 710 MET cc_start: 0.8568 (mtp) cc_final: 0.8148 (mtp) REVERT: B 759 ARG cc_start: 0.8749 (ttp80) cc_final: 0.8348 (ttp80) REVERT: B 839 ASN cc_start: 0.8856 (m-40) cc_final: 0.8454 (m110) REVERT: B 936 ASN cc_start: 0.8933 (m110) cc_final: 0.8712 (m110) REVERT: B 948 GLN cc_start: 0.8951 (mm110) cc_final: 0.8579 (mm-40) REVERT: B 953 PHE cc_start: 0.8407 (m-10) cc_final: 0.8100 (m-10) REVERT: C 61 LEU cc_start: 0.8101 (tp) cc_final: 0.7744 (tp) REVERT: C 530 PHE cc_start: 0.8596 (m-10) cc_final: 0.7956 (m-80) REVERT: C 869 TRP cc_start: 0.8598 (p90) cc_final: 0.8288 (p90) REVERT: C 936 ASN cc_start: 0.8788 (m110) cc_final: 0.8585 (m110) REVERT: C 948 GLN cc_start: 0.8520 (pt0) cc_final: 0.8177 (pt0) REVERT: D 366 MET cc_start: -0.0378 (ppp) cc_final: -0.0616 (ppp) REVERT: D 455 MET cc_start: 0.6640 (tmm) cc_final: 0.6133 (tmm) REVERT: D 480 MET cc_start: 0.1935 (ptt) cc_final: 0.0900 (ttt) REVERT: D 579 MET cc_start: 0.1007 (mpp) cc_final: 0.0664 (mmm) REVERT: G 86 GLN cc_start: 0.6481 (tt0) cc_final: 0.6114 (mp10) REVERT: G 332 MET cc_start: 0.1442 (tmm) cc_final: 0.0945 (tmm) REVERT: G 408 MET cc_start: 0.4203 (mmt) cc_final: 0.3835 (mmt) REVERT: G 534 LYS cc_start: 0.2131 (pptt) cc_final: 0.1581 (tptt) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.2336 time to fit residues: 158.4111 Evaluate side-chains 348 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 277 optimal weight: 2.9990 chunk 385 optimal weight: 40.0000 chunk 208 optimal weight: 4.9990 chunk 313 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 294 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 222 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN A 884 GLN A 905 GLN A 932 GLN ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 GLN B1006 ASN C 136 ASN C 170 ASN C 722 ASN C 745 GLN ** C1066 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 522 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.135508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.109380 restraints weight = 216353.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.106925 restraints weight = 164814.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.107361 restraints weight = 133604.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.107429 restraints weight = 105520.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.107569 restraints weight = 99503.129| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 36482 Z= 0.165 Angle : 0.727 13.581 49768 Z= 0.370 Chirality : 0.047 0.380 5625 Planarity : 0.005 0.065 6370 Dihedral : 6.627 56.865 5893 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.81 % Favored : 94.13 % Rotamer: Outliers : 0.03 % Allowed : 0.86 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.42 (0.12), residues: 4375 helix: 0.33 (0.14), residues: 1388 sheet: -1.35 (0.20), residues: 616 loop : -1.64 (0.12), residues: 2371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 316 TYR 0.031 0.002 TYR G 381 PHE 0.031 0.002 PHE B 889 TRP 0.020 0.001 TRP G 271 HIS 0.008 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00357 (36378) covalent geometry : angle 0.70317 (49504) SS BOND : bond 0.00534 ( 48) SS BOND : angle 1.88230 ( 96) hydrogen bonds : bond 0.04553 ( 1446) hydrogen bonds : angle 6.15940 ( 4146) link_BETA1-4 : bond 0.00296 ( 19) link_BETA1-4 : angle 1.78856 ( 57) link_NAG-ASN : bond 0.00480 ( 37) link_NAG-ASN : angle 3.45282 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 456 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9430 (m-70) cc_final: 0.8744 (m-70) REVERT: A 70 PHE cc_start: 0.9342 (m-80) cc_final: 0.9139 (m-80) REVERT: A 86 ASP cc_start: 0.8270 (p0) cc_final: 0.7151 (p0) REVERT: A 108 MET cc_start: 0.1901 (mmt) cc_final: 0.1597 (mmt) REVERT: A 263 PHE cc_start: 0.8100 (m-80) cc_final: 0.7776 (m-10) REVERT: A 278 ASP cc_start: 0.9001 (m-30) cc_final: 0.8229 (t0) REVERT: A 527 ASN cc_start: 0.9508 (t0) cc_final: 0.9245 (t0) REVERT: A 601 ASP cc_start: 0.8066 (m-30) cc_final: 0.7043 (t0) REVERT: A 680 MET cc_start: 0.8789 (pmm) cc_final: 0.8385 (pmm) REVERT: A 883 MET cc_start: 0.9162 (mmm) cc_final: 0.8934 (mmp) REVERT: A 933 ASP cc_start: 0.9500 (p0) cc_final: 0.9136 (p0) REVERT: A 936 ASN cc_start: 0.9358 (m110) cc_final: 0.8793 (m110) REVERT: A 948 GLN cc_start: 0.9400 (mm110) cc_final: 0.9192 (mm-40) REVERT: A 953 PHE cc_start: 0.8970 (m-10) cc_final: 0.8510 (m-10) REVERT: A 975 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8339 (mm110) REVERT: B 108 MET cc_start: 0.8937 (mpp) cc_final: 0.8493 (mpp) REVERT: B 292 LYS cc_start: 0.9186 (tptt) cc_final: 0.8895 (tptt) REVERT: B 495 TYR cc_start: 0.9118 (m-80) cc_final: 0.8882 (m-80) REVERT: B 500 LEU cc_start: 0.9153 (mp) cc_final: 0.8945 (mp) REVERT: B 502 PHE cc_start: 0.8559 (m-80) cc_final: 0.8012 (m-10) REVERT: B 710 MET cc_start: 0.8922 (mtp) cc_final: 0.8434 (mtp) REVERT: B 723 MET cc_start: 0.8357 (tpt) cc_final: 0.7663 (tpp) REVERT: B 757 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8734 (mm-40) REVERT: B 759 ARG cc_start: 0.9125 (ttp80) cc_final: 0.8704 (ttp80) REVERT: B 839 ASN cc_start: 0.9005 (m-40) cc_final: 0.8406 (m-40) REVERT: B 932 GLN cc_start: 0.9025 (tp40) cc_final: 0.8644 (mm-40) REVERT: B 936 ASN cc_start: 0.8965 (m110) cc_final: 0.8744 (m110) REVERT: B 948 GLN cc_start: 0.9221 (mm110) cc_final: 0.8904 (mm-40) REVERT: B 1014 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8654 (tm-30) REVERT: B 1022 ARG cc_start: 0.8442 (ptm160) cc_final: 0.8220 (ptm160) REVERT: C 61 LEU cc_start: 0.8289 (tp) cc_final: 0.7964 (tp) REVERT: C 302 GLN cc_start: 0.8886 (tp40) cc_final: 0.8500 (tm-30) REVERT: C 530 PHE cc_start: 0.8469 (m-10) cc_final: 0.7848 (m-80) REVERT: C 714 MET cc_start: 0.9287 (ptm) cc_final: 0.9062 (ptm) REVERT: C 723 MET cc_start: 0.8936 (tpp) cc_final: 0.8668 (mmm) REVERT: C 757 GLN cc_start: 0.9178 (tp-100) cc_final: 0.8781 (tp40) REVERT: C 869 TRP cc_start: 0.8578 (p90) cc_final: 0.8364 (p90) REVERT: C 930 LYS cc_start: 0.8651 (ptpp) cc_final: 0.8448 (ptpp) REVERT: C 936 ASN cc_start: 0.8992 (m110) cc_final: 0.8705 (m110) REVERT: C 945 LEU cc_start: 0.9254 (tt) cc_final: 0.9008 (tt) REVERT: C 966 ARG cc_start: 0.9052 (ttm110) cc_final: 0.8836 (ptm160) REVERT: C 975 GLN cc_start: 0.8800 (mt0) cc_final: 0.7863 (tt0) REVERT: D 455 MET cc_start: 0.6405 (tmm) cc_final: 0.6036 (tmm) REVERT: D 480 MET cc_start: 0.1579 (ptt) cc_final: 0.0558 (ttt) REVERT: D 579 MET cc_start: 0.0943 (mpp) cc_final: 0.0639 (mmm) REVERT: G 86 GLN cc_start: 0.6420 (tt0) cc_final: 0.6057 (mp10) REVERT: G 323 MET cc_start: -0.0612 (mmt) cc_final: -0.1613 (mmt) REVERT: G 332 MET cc_start: 0.2424 (tmm) cc_final: 0.1565 (tmm) REVERT: G 462 MET cc_start: 0.2575 (mmt) cc_final: 0.2368 (mmp) REVERT: G 534 LYS cc_start: 0.2160 (pptt) cc_final: 0.1407 (tptt) outliers start: 1 outliers final: 0 residues processed: 457 average time/residue: 0.2268 time to fit residues: 168.8548 Evaluate side-chains 368 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 191 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 411 optimal weight: 4.9990 chunk 244 optimal weight: 20.0000 chunk 112 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 383 optimal weight: 6.9990 chunk 158 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 369 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN A 905 GLN A 932 GLN ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1066 HIS C 136 ASN C 722 ASN C 745 GLN C 985 GLN ** C1066 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.136039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.109531 restraints weight = 218499.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.106767 restraints weight = 160058.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.107180 restraints weight = 135724.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.107290 restraints weight = 106187.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.107388 restraints weight = 100349.131| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 36482 Z= 0.155 Angle : 0.712 13.207 49768 Z= 0.361 Chirality : 0.046 0.394 5625 Planarity : 0.005 0.063 6370 Dihedral : 6.266 56.963 5893 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.17 % Favored : 93.76 % Rotamer: Outliers : 0.03 % Allowed : 0.34 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.24 (0.12), residues: 4375 helix: 0.51 (0.14), residues: 1387 sheet: -1.28 (0.20), residues: 599 loop : -1.53 (0.12), residues: 2389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 966 TYR 0.032 0.002 TYR A 441 PHE 0.057 0.002 PHE B 317 TRP 0.023 0.001 TRP G 271 HIS 0.007 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00341 (36378) covalent geometry : angle 0.69041 (49504) SS BOND : bond 0.00436 ( 48) SS BOND : angle 1.85421 ( 96) hydrogen bonds : bond 0.04434 ( 1446) hydrogen bonds : angle 6.04443 ( 4146) link_BETA1-4 : bond 0.00401 ( 19) link_BETA1-4 : angle 1.79783 ( 57) link_NAG-ASN : bond 0.00485 ( 37) link_NAG-ASN : angle 3.16978 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 453 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.9440 (m-70) cc_final: 0.8758 (m-70) REVERT: A 86 ASP cc_start: 0.8237 (p0) cc_final: 0.7236 (p0) REVERT: A 108 MET cc_start: 0.1946 (mmt) cc_final: 0.1667 (mmt) REVERT: A 278 ASP cc_start: 0.8981 (m-30) cc_final: 0.8404 (t0) REVERT: A 527 ASN cc_start: 0.9500 (t0) cc_final: 0.9218 (t0) REVERT: A 601 ASP cc_start: 0.8055 (m-30) cc_final: 0.7572 (t0) REVERT: A 680 MET cc_start: 0.8702 (pmm) cc_final: 0.8346 (pmm) REVERT: A 709 VAL cc_start: 0.9353 (t) cc_final: 0.8880 (p) REVERT: A 756 GLU cc_start: 0.8792 (tp30) cc_final: 0.8166 (tp30) REVERT: A 883 MET cc_start: 0.9114 (mmm) cc_final: 0.8845 (mmt) REVERT: A 933 ASP cc_start: 0.9496 (p0) cc_final: 0.9076 (p0) REVERT: A 936 ASN cc_start: 0.9374 (m110) cc_final: 0.8837 (m110) REVERT: A 948 GLN cc_start: 0.9418 (mm110) cc_final: 0.9215 (mm-40) REVERT: A 953 PHE cc_start: 0.8839 (m-10) cc_final: 0.8448 (m-10) REVERT: A 975 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8272 (mm110) REVERT: A 984 LEU cc_start: 0.9017 (tp) cc_final: 0.8762 (tp) REVERT: A 1002 ARG cc_start: 0.8725 (tpt90) cc_final: 0.8316 (tpp80) REVERT: B 108 MET cc_start: 0.8973 (mpp) cc_final: 0.8533 (mpp) REVERT: B 288 LYS cc_start: 0.9319 (mttt) cc_final: 0.9047 (mttp) REVERT: B 495 TYR cc_start: 0.9167 (m-80) cc_final: 0.8935 (m-80) REVERT: B 500 LEU cc_start: 0.9172 (mp) cc_final: 0.8939 (mp) REVERT: B 502 PHE cc_start: 0.8585 (m-80) cc_final: 0.8071 (m-10) REVERT: B 559 PHE cc_start: 0.9458 (m-80) cc_final: 0.9253 (m-80) REVERT: B 579 PHE cc_start: 0.7779 (t80) cc_final: 0.7576 (t80) REVERT: B 710 MET cc_start: 0.8982 (mtp) cc_final: 0.8455 (mtp) REVERT: B 723 MET cc_start: 0.8293 (tpt) cc_final: 0.8048 (tpp) REVERT: B 759 ARG cc_start: 0.9124 (ttp80) cc_final: 0.8707 (ttp80) REVERT: B 847 LEU cc_start: 0.9292 (tp) cc_final: 0.9009 (tp) REVERT: B 932 GLN cc_start: 0.8949 (tp40) cc_final: 0.8592 (mm-40) REVERT: B 936 ASN cc_start: 0.8932 (m110) cc_final: 0.8731 (m110) REVERT: B 948 GLN cc_start: 0.9215 (mm110) cc_final: 0.8806 (mm-40) REVERT: B 1014 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8661 (tm-30) REVERT: C 290 SER cc_start: 0.9222 (t) cc_final: 0.8828 (p) REVERT: C 302 GLN cc_start: 0.8779 (tp40) cc_final: 0.8474 (tm-30) REVERT: C 530 PHE cc_start: 0.8478 (m-10) cc_final: 0.7847 (m-80) REVERT: C 710 MET cc_start: 0.8044 (mtm) cc_final: 0.7685 (ptm) REVERT: C 723 MET cc_start: 0.8896 (tpp) cc_final: 0.8537 (mmm) REVERT: C 745 GLN cc_start: 0.9196 (pt0) cc_final: 0.8980 (pt0) REVERT: C 748 ARG cc_start: 0.9175 (ttm110) cc_final: 0.8947 (ttp80) REVERT: C 757 GLN cc_start: 0.9213 (tp-100) cc_final: 0.8842 (tp40) REVERT: C 797 LYS cc_start: 0.9218 (mptt) cc_final: 0.9009 (mmtm) REVERT: C 936 ASN cc_start: 0.8986 (m110) cc_final: 0.8712 (m110) REVERT: C 945 LEU cc_start: 0.9179 (tt) cc_final: 0.8905 (tt) REVERT: C 966 ARG cc_start: 0.9056 (ttm110) cc_final: 0.8760 (ptm160) REVERT: C 975 GLN cc_start: 0.8740 (mt0) cc_final: 0.7905 (tt0) REVERT: D 366 MET cc_start: -0.0082 (ppp) cc_final: -0.0290 (ppp) REVERT: D 455 MET cc_start: 0.6409 (tmm) cc_final: 0.5994 (tmm) REVERT: D 480 MET cc_start: 0.1581 (ptt) cc_final: 0.0614 (ttt) REVERT: D 579 MET cc_start: 0.0930 (mpp) cc_final: 0.0676 (mmm) REVERT: G 86 GLN cc_start: 0.6469 (tt0) cc_final: 0.6105 (mp10) REVERT: G 323 MET cc_start: -0.0240 (mmt) cc_final: -0.1308 (mmt) REVERT: G 332 MET cc_start: 0.1975 (tmm) cc_final: 0.1468 (tmm) REVERT: G 534 LYS cc_start: 0.1997 (pptt) cc_final: 0.1327 (tptt) outliers start: 1 outliers final: 0 residues processed: 453 average time/residue: 0.2285 time to fit residues: 170.1277 Evaluate side-chains 370 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 69 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 336 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 174 optimal weight: 0.8980 chunk 401 optimal weight: 30.0000 chunk 237 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN A 905 GLN A 932 GLN ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 662 HIS ** B 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN B 839 ASN ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 985 GLN ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1066 HIS C 136 ASN ** C 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 GLN ** G 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.136274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.109773 restraints weight = 216549.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.107159 restraints weight = 162032.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.107593 restraints weight = 135577.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.107652 restraints weight = 109163.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.107842 restraints weight = 100673.264| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 36482 Z= 0.149 Angle : 0.699 13.109 49768 Z= 0.354 Chirality : 0.046 0.385 5625 Planarity : 0.005 0.062 6370 Dihedral : 6.062 56.885 5893 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.67 % Favored : 94.29 % Rotamer: Outliers : 0.05 % Allowed : 0.34 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.15 (0.12), residues: 4375 helix: 0.58 (0.14), residues: 1386 sheet: -1.17 (0.21), residues: 583 loop : -1.49 (0.12), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 762 TYR 0.024 0.002 TYR C 856 PHE 0.037 0.002 PHE B 317 TRP 0.030 0.001 TRP C 869 HIS 0.014 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00328 (36378) covalent geometry : angle 0.67868 (49504) SS BOND : bond 0.00385 ( 48) SS BOND : angle 1.73406 ( 96) hydrogen bonds : bond 0.04306 ( 1446) hydrogen bonds : angle 5.92084 ( 4146) link_BETA1-4 : bond 0.00369 ( 19) link_BETA1-4 : angle 1.73299 ( 57) link_NAG-ASN : bond 0.00450 ( 37) link_NAG-ASN : angle 3.03742 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6139.04 seconds wall clock time: 107 minutes 32.62 seconds (6452.62 seconds total)