Starting phenix.real_space_refine on Fri Feb 6 15:26:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9atq_43833/02_2026/9atq_43833.cif Found real_map, /net/cci-nas-00/data/ceres_data/9atq_43833/02_2026/9atq_43833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9atq_43833/02_2026/9atq_43833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9atq_43833/02_2026/9atq_43833.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9atq_43833/02_2026/9atq_43833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9atq_43833/02_2026/9atq_43833.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 117 5.16 5 C 16131 2.51 5 N 4143 2.21 5 O 4911 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25302 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 8196 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 57, 'TRANS': 989} Chain breaks: 7 Chain: "B" Number of atoms: 8196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 8196 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 57, 'TRANS': 989} Chain breaks: 7 Chain: "C" Number of atoms: 8196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 8196 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 57, 'TRANS': 989} Chain breaks: 7 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "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: "V" 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: "W" 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" 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 Time building chain proxies: 5.47, per 1000 atoms: 0.22 Number of scatterers: 25302 At special positions: 0 Unit cell: (142.539, 142.539, 193.888, 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 117 16.00 O 4911 8.00 N 4143 7.00 C 16131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 332 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 375 " - pdb=" SG CYS A 428 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 521 " distance=2.04 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 645 " distance=2.03 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 667 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 332 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 375 " - pdb=" SG CYS B 428 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 667 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.03 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.03 Simple disulfide: pdb=" SG CYS B1078 " - pdb=" SG CYS B1122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 297 " distance=2.03 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 357 " distance=2.03 Simple disulfide: pdb=" SG CYS C 375 " - pdb=" SG CYS C 428 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 521 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 534 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 613 " - pdb=" SG CYS C 645 " distance=2.03 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 667 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 756 " distance=2.03 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " distance=2.03 Simple disulfide: pdb=" SG CYS C1078 " - pdb=" SG CYS C1122 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 58 " " NAG A1302 " - " ASN A 161 " " NAG A1303 " - " ASN A 230 " " NAG A1304 " - " ASN A 278 " " NAG A1305 " - " ASN A 339 " " NAG A1306 " - " ASN A 705 " " NAG B1301 " - " ASN B 58 " " NAG B1302 " - " ASN B 161 " " NAG B1303 " - " ASN B 230 " " NAG B1304 " - " ASN B 278 " " NAG B1305 " - " ASN B 327 " " NAG B1306 " - " ASN B 705 " " NAG C1301 " - " ASN C 58 " " NAG C1302 " - " ASN C 161 " " NAG C1303 " - " ASN C 230 " " NAG C1304 " - " ASN C 278 " " NAG C1305 " - " ASN C 327 " " NAG C1306 " - " ASN C 339 " " NAG C1307 " - " ASN C 705 " " NAG G 1 " - " ASN A 713 " " NAG H 1 " - " ASN A 797 " " NAG I 1 " - " ASN A1070 " " NAG J 1 " - " ASN A1094 " " NAG K 1 " - " ASN A1130 " " NAG M 1 " - " ASN B 713 " " NAG N 1 " - " ASN B 797 " " NAG O 1 " - " ASN B1070 " " NAG P 1 " - " ASN B1094 " " NAG Q 1 " - " ASN B1130 " " NAG R 1 " - " ASN C 119 " " NAG S 1 " - " ASN C 713 " " NAG T 1 " - " ASN C 797 " " NAG U 1 " - " ASN C1070 " " NAG V 1 " - " ASN C1094 " " NAG W 1 " - " ASN C1130 " Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 875.1 milliseconds 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5904 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 45 sheets defined 25.4% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 360 through 366 removed outlier: 4.269A pdb=" N ILE A 364 " --> pdb=" O ASP A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.893A pdb=" N ASN A 384 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 412 through 418 Processing helix chain 'A' and resid 434 through 439 Processing helix chain 'A' and resid 612 through 616 removed outlier: 3.935A pdb=" N VAL A 616 " --> pdb=" O CYS A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 742 through 751 removed outlier: 3.601A pdb=" N SER A 746 " --> pdb=" O SER A 742 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 779 removed outlier: 3.655A pdb=" N ASP A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 845 through 852 removed outlier: 3.671A pdb=" N ASN A 852 " --> pdb=" O ALA A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 880 Processing helix chain 'A' and resid 893 through 905 removed outlier: 3.521A pdb=" N ILE A 905 " --> pdb=" O ARG A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 915 removed outlier: 4.023A pdb=" N LEU A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 937 Processing helix chain 'A' and resid 941 through 961 removed outlier: 3.508A pdb=" N GLN A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 981 through 1029 Processing helix chain 'A' and resid 1136 through 1143 removed outlier: 4.069A pdb=" N GLU A1140 " --> pdb=" O PRO A1136 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 333 through 339 removed outlier: 4.235A pdb=" N VAL B 337 " --> pdb=" O PRO B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 379 through 386 removed outlier: 4.712A pdb=" N ASN B 384 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 386 " --> pdb=" O LEU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 418 Processing helix chain 'B' and resid 434 through 439 removed outlier: 3.595A pdb=" N SER B 439 " --> pdb=" O ASN B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 616 removed outlier: 3.901A pdb=" N VAL B 616 " --> pdb=" O CYS B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 742 through 751 removed outlier: 3.710A pdb=" N SER B 746 " --> pdb=" O SER B 742 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 779 removed outlier: 3.684A pdb=" N ASP B 771 " --> pdb=" O ALA B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 822 removed outlier: 3.506A pdb=" N VAL B 822 " --> pdb=" O LEU B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 851 Processing helix chain 'B' and resid 862 through 881 removed outlier: 3.628A pdb=" N GLY B 881 " --> pdb=" O THR B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 905 removed outlier: 3.560A pdb=" N ILE B 905 " --> pdb=" O ARG B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 915 removed outlier: 4.049A pdb=" N LEU B 912 " --> pdb=" O THR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 937 Processing helix chain 'B' and resid 941 through 961 removed outlier: 3.531A pdb=" N GLN B 945 " --> pdb=" O LEU B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 972 through 980 Processing helix chain 'B' and resid 981 through 1029 removed outlier: 3.666A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1136 through 1143 removed outlier: 4.137A pdb=" N GLU B1140 " --> pdb=" O PRO B1136 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 334 through 339 Processing helix chain 'C' and resid 360 through 366 removed outlier: 4.269A pdb=" N ILE C 364 " --> pdb=" O ASP C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 removed outlier: 3.790A pdb=" N ASN C 384 " --> pdb=" O THR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 403 No H-bonds generated for 'chain 'C' and resid 401 through 403' Processing helix chain 'C' and resid 412 through 418 Processing helix chain 'C' and resid 434 through 439 Processing helix chain 'C' and resid 612 through 616 removed outlier: 3.998A pdb=" N VAL C 616 " --> pdb=" O CYS C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 742 through 750 removed outlier: 3.868A pdb=" N SER C 746 " --> pdb=" O SER C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 753 No H-bonds generated for 'chain 'C' and resid 751 through 753' Processing helix chain 'C' and resid 754 through 779 removed outlier: 3.734A pdb=" N ASP C 771 " --> pdb=" O ALA C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 822 Processing helix chain 'C' and resid 845 through 851 Processing helix chain 'C' and resid 862 through 880 Processing helix chain 'C' and resid 893 through 905 removed outlier: 3.603A pdb=" N ILE C 905 " --> pdb=" O ARG C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 915 removed outlier: 4.157A pdb=" N LEU C 912 " --> pdb=" O THR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 937 Processing helix chain 'C' and resid 941 through 961 Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 972 through 980 Processing helix chain 'C' and resid 981 through 1029 removed outlier: 4.000A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1136 through 1143 removed outlier: 4.143A pdb=" N GLU C1140 " --> pdb=" O PRO C1136 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 27 removed outlier: 7.733A pdb=" N ASN A 58 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TYR A 265 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 87 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 189 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 200 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER A 201 " --> pdb=" O PRO A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.582A pdb=" N ALA C 571 " --> pdb=" O GLY C 562 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASP C 570 " --> pdb=" O ILE C 583 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 52 removed outlier: 3.895A pdb=" N ASP A 283 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.467A pdb=" N ALA A 239 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 98 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLU A 129 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N CYS A 162 " --> pdb=" O GLU A 129 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLN A 131 " --> pdb=" O ASN A 160 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ASN A 160 " --> pdb=" O GLN A 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 307 through 315 removed outlier: 5.187A pdb=" N ILE A 308 " --> pdb=" O THR A 595 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THR A 595 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN A 310 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A 593 " --> pdb=" O GLN A 310 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 312 " --> pdb=" O VAL A 591 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY A 590 " --> pdb=" O GLN A 609 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 324 removed outlier: 3.659A pdb=" N VAL A 535 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ASP A 570 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 571 " --> pdb=" O GLY A 562 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N PHE A 561 " --> pdb=" O PHE B 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 354 removed outlier: 3.659A pdb=" N ALA A 372 " --> pdb=" O ALA A 431 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 358 removed outlier: 6.929A pdb=" N CYS A 357 " --> pdb=" O CYS A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 450 Processing sheet with id=AB2, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.531A pdb=" N TYR A 485 " --> pdb=" O TYR A 469 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 650 through 651 removed outlier: 6.088A pdb=" N GLU A 650 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N THR A 692 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 666 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 697 through 698 removed outlier: 6.995A pdb=" N ALA A 697 " --> pdb=" O ILE B 784 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 707 through 724 removed outlier: 6.455A pdb=" N SER A 707 " --> pdb=" O THR A1072 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR A1072 " --> pdb=" O SER A 707 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA A 709 " --> pdb=" O ASN A1070 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASN A1070 " --> pdb=" O ALA A 709 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLU A1068 " --> pdb=" O PRO A 711 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N TYR A1063 " --> pdb=" O HIS A1044 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N HIS A1044 " --> pdb=" O TYR A1063 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 707 through 724 removed outlier: 6.455A pdb=" N SER A 707 " --> pdb=" O THR A1072 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR A1072 " --> pdb=" O SER A 707 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA A 709 " --> pdb=" O ASN A1070 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASN A1070 " --> pdb=" O ALA A 709 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLU A1068 " --> pdb=" O PRO A 711 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A1072 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A1074 " --> pdb=" O PHE A1091 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE A1091 " --> pdb=" O ALA A1074 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 730 through 732 Processing sheet with id=AB8, first strand: chain 'A' and resid 783 through 784 Processing sheet with id=AB9, first strand: chain 'A' and resid 1116 through 1118 Processing sheet with id=AC1, first strand: chain 'B' and resid 20 through 27 removed outlier: 7.623A pdb=" N ASN B 58 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N TYR B 265 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 191 " --> pdb=" O LYS B 198 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 44 through 52 removed outlier: 4.100A pdb=" N ASP B 283 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 81 through 82 removed outlier: 6.204A pdb=" N LEU B 138 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 81 through 82 removed outlier: 4.033A pdb=" N GLY B 100 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA B 239 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE B 98 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 127 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 164 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLU B 129 " --> pdb=" O CYS B 162 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N CYS B 162 " --> pdb=" O GLU B 129 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLN B 131 " --> pdb=" O ASN B 160 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N ASN B 160 " --> pdb=" O GLN B 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 307 through 315 removed outlier: 7.029A pdb=" N VAL B 591 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ASN B 313 " --> pdb=" O GLY B 589 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY B 589 " --> pdb=" O ASN B 313 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY B 590 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 321 through 324 removed outlier: 3.632A pdb=" N VAL B 535 " --> pdb=" O GLY B 546 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR B 549 " --> pdb=" O ASP B 582 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASP B 570 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY B 562 " --> pdb=" O ASP B 570 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N PHE B 561 " --> pdb=" O PHE C 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 350 through 354 removed outlier: 3.954A pdb=" N VAL B 391 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL B 508 " --> pdb=" O ASP B 394 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 448 through 450 Processing sheet with id=AC9, first strand: chain 'B' and resid 650 through 651 removed outlier: 6.044A pdb=" N GLU B 650 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N THR B 692 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE B 666 " --> pdb=" O ILE B 662 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 697 through 698 removed outlier: 6.719A pdb=" N ALA B 697 " --> pdb=" O ILE C 784 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 707 through 724 removed outlier: 6.551A pdb=" N SER B 707 " --> pdb=" O THR B1072 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR B1072 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA B 709 " --> pdb=" O ASN B1070 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN B1070 " --> pdb=" O ALA B 709 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU B1068 " --> pdb=" O PRO B 711 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLY B1055 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER B1051 " --> pdb=" O GLY B1055 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B1057 " --> pdb=" O PRO B1049 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B1059 " --> pdb=" O SER B1047 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER B1047 " --> pdb=" O LEU B1059 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL B1061 " --> pdb=" O LEU B1045 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 707 through 724 removed outlier: 6.551A pdb=" N SER B 707 " --> pdb=" O THR B1072 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR B1072 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA B 709 " --> pdb=" O ASN B1070 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN B1070 " --> pdb=" O ALA B 709 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU B1068 " --> pdb=" O PRO B 711 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B1074 " --> pdb=" O PHE B1091 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE B1091 " --> pdb=" O ALA B1074 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.470A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1116 through 1118 Processing sheet with id=AD6, first strand: chain 'C' and resid 20 through 27 removed outlier: 8.051A pdb=" N ASN C 58 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR C 265 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 60 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS C 191 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE C 199 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 222 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 44 through 52 removed outlier: 4.149A pdb=" N ASP C 283 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 81 through 82 removed outlier: 6.341A pdb=" N LEU C 138 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 81 through 82 removed outlier: 4.274A pdb=" N GLY C 100 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ALA C 239 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE C 98 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL C 117 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 11.459A pdb=" N VAL C 123 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 10.145A pdb=" N GLU C 165 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 11.796A pdb=" N ILE C 125 " --> pdb=" O THR C 163 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N THR C 163 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL C 127 " --> pdb=" O ASN C 161 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ASN C 161 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLU C 129 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA C 159 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLN C 131 " --> pdb=" O SER C 157 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 307 through 315 removed outlier: 6.875A pdb=" N VAL C 591 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN C 313 " --> pdb=" O GLY C 589 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLY C 589 " --> pdb=" O ASN C 313 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY C 590 " --> pdb=" O GLN C 609 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 350 through 354 Processing sheet with id=AE3, first strand: chain 'C' and resid 448 through 450 Processing sheet with id=AE4, first strand: chain 'C' and resid 469 through 470 removed outlier: 3.522A pdb=" N TYR C 485 " --> pdb=" O TYR C 469 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 650 through 651 removed outlier: 6.038A pdb=" N GLU C 650 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N THR C 692 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE C 666 " --> pdb=" O ILE C 662 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 707 through 724 removed outlier: 6.704A pdb=" N GLN C1067 " --> pdb=" O THR C 712 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE C 714 " --> pdb=" O PRO C1065 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE C 716 " --> pdb=" O TYR C1063 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TYR C1063 " --> pdb=" O ILE C 716 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL C 718 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL C1061 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR C 720 " --> pdb=" O LEU C1059 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C1059 " --> pdb=" O THR C 720 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE C 722 " --> pdb=" O VAL C1057 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL C1057 " --> pdb=" O ILE C 722 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY C1055 " --> pdb=" O PRO C 724 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLY C1055 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N SER C1051 " --> pdb=" O GLY C1055 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C1057 " --> pdb=" O PRO C1049 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU C1059 " --> pdb=" O SER C1047 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER C1047 " --> pdb=" O LEU C1059 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C1061 " --> pdb=" O LEU C1045 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 729 through 732 removed outlier: 4.565A pdb=" N LYS C 729 " --> pdb=" O LEU C 857 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1116 through 1118 Processing sheet with id=AE9, first strand: chain 'C' and resid 1090 through 1093 1046 hydrogen bonds defined for protein. 2883 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: 5.85 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6686 1.33 - 1.46: 5844 1.46 - 1.58: 13204 1.58 - 1.70: 0 1.70 - 1.83: 147 Bond restraints: 25881 Sorted by residual: bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" N VAL C 123 " pdb=" CA VAL C 123 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.11e-02 8.12e+03 1.03e+01 bond pdb=" N ILE C 708 " pdb=" CA ILE C 708 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.11e-02 8.12e+03 9.11e+00 bond pdb=" CA SER B 704 " pdb=" CB SER B 704 " ideal model delta sigma weight residual 1.534 1.494 0.040 1.34e-02 5.57e+03 8.92e+00 bond pdb=" N ILE A 328 " pdb=" CA ILE A 328 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.29e-02 6.01e+03 8.73e+00 ... (remaining 25876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 34594 2.20 - 4.40: 568 4.40 - 6.60: 41 6.60 - 8.80: 13 8.80 - 11.00: 4 Bond angle restraints: 35220 Sorted by residual: angle pdb=" C ASN A 705 " pdb=" CA ASN A 705 " pdb=" CB ASN A 705 " ideal model delta sigma weight residual 109.56 101.14 8.42 1.65e+00 3.67e-01 2.60e+01 angle pdb=" N ASN C1070 " pdb=" CA ASN C1070 " pdb=" CB ASN C1070 " ideal model delta sigma weight residual 110.57 103.34 7.23 1.57e+00 4.06e-01 2.12e+01 angle pdb=" C ASN C1070 " pdb=" CA ASN C1070 " pdb=" CB ASN C1070 " ideal model delta sigma weight residual 109.72 117.03 -7.31 1.73e+00 3.34e-01 1.79e+01 angle pdb=" C ASN B 327 " pdb=" CA ASN B 327 " pdb=" CB ASN B 327 " ideal model delta sigma weight residual 109.13 115.55 -6.42 1.56e+00 4.11e-01 1.69e+01 angle pdb=" CA SER B 704 " pdb=" C SER B 704 " pdb=" O SER B 704 " ideal model delta sigma weight residual 121.14 117.11 4.03 1.03e+00 9.43e-01 1.53e+01 ... (remaining 35215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 14392 17.96 - 35.93: 1319 35.93 - 53.89: 321 53.89 - 71.86: 66 71.86 - 89.82: 30 Dihedral angle restraints: 16128 sinusoidal: 6966 harmonic: 9162 Sorted by residual: dihedral pdb=" CA LYS C1069 " pdb=" C LYS C1069 " pdb=" N ASN C1070 " pdb=" CA ASN C1070 " ideal model delta harmonic sigma weight residual -180.00 -152.40 -27.60 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA PRO B 326 " pdb=" C PRO B 326 " pdb=" N ASN B 327 " pdb=" CA ASN B 327 " ideal model delta harmonic sigma weight residual -180.00 -153.62 -26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CB CYS B 734 " pdb=" SG CYS B 734 " pdb=" SG CYS B 756 " pdb=" CB CYS B 756 " ideal model delta sinusoidal sigma weight residual -86.00 -42.49 -43.51 1 1.00e+01 1.00e-02 2.64e+01 ... (remaining 16125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3667 0.081 - 0.163: 443 0.163 - 0.244: 26 0.244 - 0.325: 2 0.325 - 0.407: 2 Chirality restraints: 4140 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN C 713 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C1070 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.76 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 705 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 4137 not shown) Planarity restraints: 4523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C1070 " 0.010 2.00e-02 2.50e+03 4.69e-02 2.75e+01 pdb=" CG ASN C1070 " -0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN C1070 " 0.056 2.00e-02 2.50e+03 pdb=" ND2 ASN C1070 " -0.036 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1306 " 0.047 2.00e-02 2.50e+03 3.83e-02 1.83e+01 pdb=" C7 NAG B1306 " -0.015 2.00e-02 2.50e+03 pdb=" C8 NAG B1306 " 0.036 2.00e-02 2.50e+03 pdb=" N2 NAG B1306 " -0.060 2.00e-02 2.50e+03 pdb=" O7 NAG B1306 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 101 " 0.027 2.00e-02 2.50e+03 2.53e-02 1.59e+01 pdb=" CG TRP A 101 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP A 101 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 101 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 101 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 101 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 101 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 101 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 101 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 101 " 0.004 2.00e-02 2.50e+03 ... (remaining 4520 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 224 2.60 - 3.18: 21264 3.18 - 3.75: 38061 3.75 - 4.33: 52494 4.33 - 4.90: 88590 Nonbonded interactions: 200633 Sorted by model distance: nonbonded pdb=" O ARG A 979 " pdb=" NH1 ARG A 979 " model vdw 2.026 3.120 nonbonded pdb=" OG1 THR B 319 " pdb=" OE1 GLU B 320 " model vdw 2.115 3.040 nonbonded pdb=" OD1 ASN C 536 " pdb=" OG1 THR C 545 " model vdw 2.144 3.040 nonbonded pdb=" OD1 ASN B1130 " pdb=" N2 NAG Q 1 " model vdw 2.172 3.120 nonbonded pdb=" OH TYR B 34 " pdb=" O LEU B 51 " model vdw 2.205 3.040 ... (remaining 200628 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' selection = chain 'B' selection = (chain 'C' and resid 14 through 1306) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } 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: 4.800 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: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.730 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 25974 Z= 0.215 Angle : 0.730 17.557 35457 Z= 0.354 Chirality : 0.049 0.407 4140 Planarity : 0.005 0.090 4488 Dihedral : 14.898 89.819 10098 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.33 % Allowed : 15.69 % Favored : 83.99 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.15), residues: 3093 helix: 2.50 (0.20), residues: 682 sheet: 0.64 (0.19), residues: 716 loop : -0.56 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1015 TYR 0.023 0.001 TYR C 792 PHE 0.036 0.001 PHE A 537 TRP 0.065 0.003 TRP A 101 HIS 0.006 0.001 HIS A 950 Details of bonding type rmsd covalent geometry : bond 0.00431 (25881) covalent geometry : angle 0.64325 (35220) SS BOND : bond 0.00247 ( 42) SS BOND : angle 0.94816 ( 84) hydrogen bonds : bond 0.19046 ( 1016) hydrogen bonds : angle 7.90792 ( 2883) link_BETA1-4 : bond 0.00459 ( 16) link_BETA1-4 : angle 2.06073 ( 48) link_NAG-ASN : bond 0.01175 ( 35) link_NAG-ASN : angle 6.20836 ( 105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ASN cc_start: 0.5779 (OUTLIER) cc_final: 0.3513 (t0) REVERT: C 166 TYR cc_start: 0.7881 (t80) cc_final: 0.7680 (t80) REVERT: C 736 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.7745 (tmm) outliers start: 9 outliers final: 1 residues processed: 148 average time/residue: 0.1367 time to fit residues: 34.8604 Evaluate side-chains 131 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain C residue 736 MET Chi-restraints excluded: chain C residue 1014 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.0060 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 ASN B 909 GLN C 169 GLN ** C 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 GLN C 909 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.135527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.076728 restraints weight = 60288.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.078449 restraints weight = 39657.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.078947 restraints weight = 25973.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.079322 restraints weight = 24013.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.079610 restraints weight = 21741.874| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 25974 Z= 0.226 Angle : 0.710 20.208 35457 Z= 0.349 Chirality : 0.048 0.339 4140 Planarity : 0.004 0.056 4488 Dihedral : 7.054 58.071 4441 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.98 % Allowed : 14.09 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.15), residues: 3093 helix: 2.35 (0.20), residues: 660 sheet: 0.49 (0.18), residues: 758 loop : -0.49 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1087 TYR 0.028 0.002 TYR A1063 PHE 0.028 0.002 PHE A 537 TRP 0.037 0.003 TRP A 101 HIS 0.006 0.001 HIS C1054 Details of bonding type rmsd covalent geometry : bond 0.00525 (25881) covalent geometry : angle 0.65106 (35220) SS BOND : bond 0.00251 ( 42) SS BOND : angle 1.05746 ( 84) hydrogen bonds : bond 0.05968 ( 1016) hydrogen bonds : angle 5.72358 ( 2883) link_BETA1-4 : bond 0.00603 ( 16) link_BETA1-4 : angle 1.22752 ( 48) link_NAG-ASN : bond 0.00789 ( 35) link_NAG-ASN : angle 5.16240 ( 105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 140 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TRP cc_start: 0.5432 (m-10) cc_final: 0.4948 (m-10) REVERT: A 173 MET cc_start: 0.2455 (mmm) cc_final: 0.2201 (mmm) REVERT: A 898 MET cc_start: 0.9531 (mmm) cc_final: 0.9286 (tpt) REVERT: B 105 THR cc_start: 0.5548 (OUTLIER) cc_final: 0.5213 (p) REVERT: B 216 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7723 (t80) REVERT: B 320 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7252 (pm20) REVERT: B 382 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7716 (mtmm) REVERT: B 555 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7702 (m-80) REVERT: B 896 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8557 (mtm) REVERT: C 23 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7978 (mp10) REVERT: C 93 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6538 (tp30) REVERT: C 149 MET cc_start: 0.5918 (ppp) cc_final: 0.5623 (ppp) REVERT: C 166 TYR cc_start: 0.7914 (t80) cc_final: 0.7616 (t80) REVERT: C 1134 TYR cc_start: 0.7722 (t80) cc_final: 0.7457 (t80) outliers start: 82 outliers final: 39 residues processed: 212 average time/residue: 0.1344 time to fit residues: 48.8053 Evaluate side-chains 165 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 896 MET Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain B residue 1119 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 325 PHE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 PHE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 1006 GLN Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 88 optimal weight: 0.8980 chunk 192 optimal weight: 0.0000 chunk 207 optimal weight: 6.9990 chunk 257 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 246 optimal weight: 0.2980 chunk 107 optimal weight: 10.0000 chunk 109 optimal weight: 30.0000 chunk 42 optimal weight: 50.0000 chunk 308 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.134673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.075858 restraints weight = 60292.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.078246 restraints weight = 35533.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.078041 restraints weight = 23892.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.079066 restraints weight = 21733.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.078881 restraints weight = 19663.374| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25974 Z= 0.157 Angle : 0.618 20.538 35457 Z= 0.299 Chirality : 0.045 0.227 4140 Planarity : 0.004 0.050 4488 Dihedral : 6.387 59.759 4436 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.40 % Allowed : 15.25 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.15), residues: 3093 helix: 2.62 (0.20), residues: 663 sheet: 0.48 (0.18), residues: 762 loop : -0.48 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 210 TYR 0.019 0.001 TYR A1063 PHE 0.023 0.001 PHE B 164 TRP 0.024 0.001 TRP A 101 HIS 0.004 0.001 HIS A 950 Details of bonding type rmsd covalent geometry : bond 0.00362 (25881) covalent geometry : angle 0.55955 (35220) SS BOND : bond 0.00294 ( 42) SS BOND : angle 0.87502 ( 84) hydrogen bonds : bond 0.05509 ( 1016) hydrogen bonds : angle 5.47979 ( 2883) link_BETA1-4 : bond 0.00267 ( 16) link_BETA1-4 : angle 1.14028 ( 48) link_NAG-ASN : bond 0.00716 ( 35) link_NAG-ASN : angle 4.78030 ( 105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 128 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 898 MET cc_start: 0.9584 (mmm) cc_final: 0.9339 (tpt) REVERT: B 896 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8531 (mtm) REVERT: B 1046 MET cc_start: 0.9113 (ptm) cc_final: 0.8804 (ptm) REVERT: C 93 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6708 (tp30) REVERT: C 166 TYR cc_start: 0.7917 (t80) cc_final: 0.7483 (t80) REVERT: C 880 SER cc_start: 0.9407 (m) cc_final: 0.9102 (p) REVERT: C 1109 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8333 (mt0) outliers start: 66 outliers final: 36 residues processed: 187 average time/residue: 0.1375 time to fit residues: 44.0419 Evaluate side-chains 157 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 896 MET Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 325 PHE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 561 PHE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain C residue 1109 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 49 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 299 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 283 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 226 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 245 optimal weight: 0.1980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.130051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.071617 restraints weight = 61861.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.073954 restraints weight = 37678.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.073764 restraints weight = 23648.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.074222 restraints weight = 22689.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.074339 restraints weight = 20475.217| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25974 Z= 0.172 Angle : 0.629 20.713 35457 Z= 0.303 Chirality : 0.045 0.238 4140 Planarity : 0.004 0.100 4488 Dihedral : 5.963 59.192 4436 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.98 % Allowed : 15.32 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.15), residues: 3093 helix: 2.55 (0.20), residues: 663 sheet: 0.46 (0.18), residues: 757 loop : -0.46 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 21 TYR 0.021 0.001 TYR A1063 PHE 0.020 0.001 PHE B 164 TRP 0.021 0.002 TRP B 349 HIS 0.004 0.001 HIS C1054 Details of bonding type rmsd covalent geometry : bond 0.00403 (25881) covalent geometry : angle 0.57281 (35220) SS BOND : bond 0.00233 ( 42) SS BOND : angle 0.93302 ( 84) hydrogen bonds : bond 0.05328 ( 1016) hydrogen bonds : angle 5.31297 ( 2883) link_BETA1-4 : bond 0.00237 ( 16) link_BETA1-4 : angle 1.08372 ( 48) link_NAG-ASN : bond 0.00694 ( 35) link_NAG-ASN : angle 4.72564 ( 105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 121 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 CYS cc_start: 0.2788 (OUTLIER) cc_final: 0.1009 (p) REVERT: A 580 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8286 (mt) REVERT: A 749 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9395 (tp) REVERT: A 898 MET cc_start: 0.9633 (mmm) cc_final: 0.9422 (tpt) REVERT: B 83 PHE cc_start: 0.6988 (t80) cc_final: 0.6618 (t80) REVERT: B 105 THR cc_start: 0.5808 (OUTLIER) cc_final: 0.5420 (p) REVERT: B 320 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7479 (pm20) REVERT: B 349 TRP cc_start: 0.6997 (p-90) cc_final: 0.6351 (p-90) REVERT: B 396 PHE cc_start: 0.7194 (p90) cc_final: 0.6877 (p90) REVERT: B 419 TYR cc_start: 0.5948 (OUTLIER) cc_final: 0.5708 (m-10) REVERT: B 525 LYS cc_start: 0.8616 (tptm) cc_final: 0.8414 (mmtm) REVERT: B 896 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8533 (mtp) REVERT: B 984 GLU cc_start: 0.8562 (mp0) cc_final: 0.8345 (mp0) REVERT: C 105 THR cc_start: 0.4247 (OUTLIER) cc_final: 0.3605 (m) REVERT: C 125 ILE cc_start: 0.8094 (mp) cc_final: 0.7783 (mp) REVERT: C 166 TYR cc_start: 0.8039 (t80) cc_final: 0.7552 (t80) REVERT: C 187 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7960 (mp0) REVERT: C 578 LEU cc_start: 0.9090 (mm) cc_final: 0.8867 (mm) REVERT: C 851 PHE cc_start: 0.7786 (m-80) cc_final: 0.7572 (m-80) REVERT: C 874 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8715 (tt) REVERT: C 880 SER cc_start: 0.9382 (m) cc_final: 0.9021 (p) REVERT: C 1109 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8377 (mt0) outliers start: 82 outliers final: 48 residues processed: 193 average time/residue: 0.1262 time to fit residues: 42.2138 Evaluate side-chains 169 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 111 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 419 TYR Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 743 THR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 896 MET Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 325 PHE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 561 PHE Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 1006 GLN Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain C residue 1109 GLN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 181 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 234 optimal weight: 3.9990 chunk 5 optimal weight: 30.0000 chunk 168 optimal weight: 1.9990 chunk 252 optimal weight: 40.0000 chunk 101 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN C 909 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.138140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.081061 restraints weight = 62763.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.083915 restraints weight = 36649.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.083736 restraints weight = 21282.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.084309 restraints weight = 19857.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.084285 restraints weight = 18984.074| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25974 Z= 0.179 Angle : 0.622 20.781 35457 Z= 0.302 Chirality : 0.045 0.261 4140 Planarity : 0.004 0.047 4488 Dihedral : 5.745 59.868 4436 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.16 % Allowed : 15.90 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.15), residues: 3093 helix: 2.47 (0.20), residues: 671 sheet: 0.43 (0.18), residues: 754 loop : -0.46 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 761 TYR 0.020 0.001 TYR A1063 PHE 0.020 0.001 PHE A 153 TRP 0.019 0.001 TRP A 101 HIS 0.004 0.001 HIS A 950 Details of bonding type rmsd covalent geometry : bond 0.00419 (25881) covalent geometry : angle 0.56642 (35220) SS BOND : bond 0.00338 ( 42) SS BOND : angle 0.93966 ( 84) hydrogen bonds : bond 0.05396 ( 1016) hydrogen bonds : angle 5.23683 ( 2883) link_BETA1-4 : bond 0.00238 ( 16) link_BETA1-4 : angle 1.10000 ( 48) link_NAG-ASN : bond 0.00702 ( 35) link_NAG-ASN : angle 4.65398 ( 105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 110 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 CYS cc_start: -0.0472 (OUTLIER) cc_final: -0.0870 (t) REVERT: A 749 LEU cc_start: 0.9694 (OUTLIER) cc_final: 0.9423 (tp) REVERT: A 898 MET cc_start: 0.9626 (mmm) cc_final: 0.9393 (tpt) REVERT: B 105 THR cc_start: 0.5619 (OUTLIER) cc_final: 0.5261 (p) REVERT: B 328 ILE cc_start: 0.9168 (mm) cc_final: 0.8866 (tp) REVERT: B 396 PHE cc_start: 0.7390 (p90) cc_final: 0.7148 (p90) REVERT: B 896 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8523 (mtp) REVERT: B 984 GLU cc_start: 0.8690 (mp0) cc_final: 0.8464 (mp0) REVERT: C 105 THR cc_start: 0.4793 (OUTLIER) cc_final: 0.4294 (m) REVERT: C 149 MET cc_start: 0.6549 (ppp) cc_final: 0.6179 (pmm) REVERT: C 166 TYR cc_start: 0.8520 (t80) cc_final: 0.8214 (t80) REVERT: C 736 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8040 (tmm) REVERT: C 880 SER cc_start: 0.9497 (m) cc_final: 0.9097 (p) REVERT: C 1109 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8426 (mt0) outliers start: 87 outliers final: 51 residues processed: 187 average time/residue: 0.1376 time to fit residues: 43.5957 Evaluate side-chains 155 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 97 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 896 MET Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 325 PHE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 561 PHE Chi-restraints excluded: chain C residue 736 MET Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 1006 GLN Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain C residue 1109 GLN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 134 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 307 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 131 optimal weight: 0.5980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 GLN ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 909 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.133735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.075341 restraints weight = 63290.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.077606 restraints weight = 32427.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.079026 restraints weight = 22166.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.079798 restraints weight = 17841.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.080337 restraints weight = 15826.902| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 25974 Z= 0.302 Angle : 0.728 21.309 35457 Z= 0.358 Chirality : 0.048 0.270 4140 Planarity : 0.004 0.049 4488 Dihedral : 6.146 59.817 4436 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.27 % Allowed : 15.87 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 3093 helix: 2.13 (0.20), residues: 671 sheet: 0.24 (0.18), residues: 743 loop : -0.61 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 761 TYR 0.022 0.001 TYR A1063 PHE 0.026 0.002 PHE C 388 TRP 0.016 0.002 TRP B 61 HIS 0.007 0.001 HIS C1054 Details of bonding type rmsd covalent geometry : bond 0.00718 (25881) covalent geometry : angle 0.67513 (35220) SS BOND : bond 0.00329 ( 42) SS BOND : angle 1.11988 ( 84) hydrogen bonds : bond 0.06748 ( 1016) hydrogen bonds : angle 5.56471 ( 2883) link_BETA1-4 : bond 0.00279 ( 16) link_BETA1-4 : angle 1.25468 ( 48) link_NAG-ASN : bond 0.00667 ( 35) link_NAG-ASN : angle 4.95078 ( 105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 98 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 CYS cc_start: 0.0209 (OUTLIER) cc_final: -0.0449 (t) REVERT: A 187 GLU cc_start: 0.7921 (mt-10) cc_final: 0.6795 (mp0) REVERT: A 580 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8584 (mt) REVERT: A 749 LEU cc_start: 0.9730 (OUTLIER) cc_final: 0.9453 (tp) REVERT: A 898 MET cc_start: 0.9590 (mmm) cc_final: 0.9388 (tpt) REVERT: A 998 GLN cc_start: 0.8578 (mt0) cc_final: 0.8354 (tt0) REVERT: B 105 THR cc_start: 0.5650 (OUTLIER) cc_final: 0.5304 (p) REVERT: B 370 PHE cc_start: 0.7970 (m-80) cc_final: 0.7736 (m-80) REVERT: B 396 PHE cc_start: 0.7712 (p90) cc_final: 0.7385 (p90) REVERT: B 896 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8602 (mtp) REVERT: C 149 MET cc_start: 0.6551 (ppp) cc_final: 0.6294 (pmm) REVERT: C 325 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.7445 (m-10) REVERT: C 578 LEU cc_start: 0.8872 (mm) cc_final: 0.8658 (mm) REVERT: C 851 PHE cc_start: 0.7891 (m-80) cc_final: 0.7632 (m-80) REVERT: C 874 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9026 (tt) REVERT: C 1109 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8432 (mt0) outliers start: 90 outliers final: 56 residues processed: 180 average time/residue: 0.1328 time to fit residues: 40.8748 Evaluate side-chains 152 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 88 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 865 MET Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 419 TYR Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 896 MET Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 325 PHE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 561 PHE Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 1006 GLN Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain C residue 1109 GLN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 30 optimal weight: 40.0000 chunk 177 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 142 optimal weight: 0.9990 chunk 271 optimal weight: 0.9990 chunk 293 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 92 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 909 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.136481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.079363 restraints weight = 62544.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.082361 restraints weight = 33274.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.082866 restraints weight = 20968.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.083168 restraints weight = 17887.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.083414 restraints weight = 17045.589| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 25974 Z= 0.119 Angle : 0.609 21.165 35457 Z= 0.295 Chirality : 0.045 0.286 4140 Planarity : 0.004 0.040 4488 Dihedral : 5.716 59.508 4436 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.18 % Allowed : 17.43 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.15), residues: 3093 helix: 2.46 (0.20), residues: 677 sheet: 0.32 (0.18), residues: 750 loop : -0.49 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 453 TYR 0.030 0.001 TYR C 166 PHE 0.033 0.001 PHE B 851 TRP 0.018 0.001 TRP A 101 HIS 0.003 0.001 HIS B 203 Details of bonding type rmsd covalent geometry : bond 0.00258 (25881) covalent geometry : angle 0.55620 (35220) SS BOND : bond 0.00247 ( 42) SS BOND : angle 1.28976 ( 84) hydrogen bonds : bond 0.05014 ( 1016) hydrogen bonds : angle 5.12980 ( 2883) link_BETA1-4 : bond 0.00515 ( 16) link_BETA1-4 : angle 1.05943 ( 48) link_NAG-ASN : bond 0.00941 ( 35) link_NAG-ASN : angle 4.43962 ( 105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 103 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 CYS cc_start: 0.0141 (OUTLIER) cc_final: -0.0251 (t) REVERT: A 187 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7286 (mp0) REVERT: A 580 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8258 (tt) REVERT: A 898 MET cc_start: 0.9640 (mmm) cc_final: 0.9397 (tpt) REVERT: A 998 GLN cc_start: 0.8451 (mt0) cc_final: 0.8235 (tt0) REVERT: B 105 THR cc_start: 0.5767 (OUTLIER) cc_final: 0.5488 (p) REVERT: B 896 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8527 (mtp) REVERT: C 736 MET cc_start: 0.8651 (tmm) cc_final: 0.8243 (tmm) REVERT: C 851 PHE cc_start: 0.7827 (m-80) cc_final: 0.7525 (m-80) REVERT: C 1109 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8359 (mt0) outliers start: 60 outliers final: 41 residues processed: 155 average time/residue: 0.1344 time to fit residues: 36.0667 Evaluate side-chains 138 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 92 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1094 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 419 TYR Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 896 MET Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 561 PHE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 1006 GLN Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain C residue 1109 GLN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 40 optimal weight: 50.0000 chunk 190 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 31 optimal weight: 30.0000 chunk 214 optimal weight: 2.9990 chunk 294 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN B 758 GLN ** B 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 909 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.133838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.076641 restraints weight = 63005.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.079505 restraints weight = 34215.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.080068 restraints weight = 21802.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.080288 restraints weight = 17972.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.080573 restraints weight = 18139.347| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 25974 Z= 0.237 Angle : 0.673 21.045 35457 Z= 0.327 Chirality : 0.047 0.302 4140 Planarity : 0.004 0.046 4488 Dihedral : 5.907 59.995 4436 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.29 % Allowed : 17.50 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 3093 helix: 2.21 (0.20), residues: 684 sheet: 0.20 (0.18), residues: 755 loop : -0.54 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 761 TYR 0.021 0.001 TYR A1063 PHE 0.026 0.002 PHE B 851 TRP 0.018 0.001 TRP A 101 HIS 0.005 0.001 HIS C1054 Details of bonding type rmsd covalent geometry : bond 0.00563 (25881) covalent geometry : angle 0.62072 (35220) SS BOND : bond 0.00310 ( 42) SS BOND : angle 1.42403 ( 84) hydrogen bonds : bond 0.06018 ( 1016) hydrogen bonds : angle 5.35801 ( 2883) link_BETA1-4 : bond 0.00221 ( 16) link_BETA1-4 : angle 1.13713 ( 48) link_NAG-ASN : bond 0.00800 ( 35) link_NAG-ASN : angle 4.62108 ( 105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 94 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 CYS cc_start: 0.0253 (OUTLIER) cc_final: -0.0455 (t) REVERT: A 187 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7108 (mp0) REVERT: A 898 MET cc_start: 0.9611 (mmm) cc_final: 0.9366 (tpt) REVERT: B 105 THR cc_start: 0.5749 (OUTLIER) cc_final: 0.5488 (p) REVERT: B 896 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8574 (mtp) REVERT: C 173 MET cc_start: 0.6295 (pmm) cc_final: 0.6045 (tmm) REVERT: C 325 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7232 (m-10) REVERT: C 736 MET cc_start: 0.8693 (tmm) cc_final: 0.8314 (tmm) REVERT: C 851 PHE cc_start: 0.7949 (m-80) cc_final: 0.7643 (m-80) REVERT: C 1109 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8419 (mt0) outliers start: 63 outliers final: 44 residues processed: 148 average time/residue: 0.1509 time to fit residues: 38.3728 Evaluate side-chains 135 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 86 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1094 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 896 MET Chi-restraints excluded: chain B residue 964 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 325 PHE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 561 PHE Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 1006 GLN Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain C residue 1109 GLN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 189 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 105 optimal weight: 0.5980 chunk 250 optimal weight: 0.0270 chunk 92 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 266 optimal weight: 0.9990 chunk 228 optimal weight: 4.9990 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 758 GLN B 849 GLN ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 909 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.136271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.079625 restraints weight = 62913.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.082819 restraints weight = 34699.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.083150 restraints weight = 20619.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.083374 restraints weight = 17753.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.083697 restraints weight = 18818.067| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25974 Z= 0.112 Angle : 0.595 20.997 35457 Z= 0.286 Chirality : 0.044 0.300 4140 Planarity : 0.003 0.041 4488 Dihedral : 5.558 59.356 4436 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.82 % Allowed : 17.72 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.15), residues: 3093 helix: 2.60 (0.20), residues: 669 sheet: 0.29 (0.18), residues: 742 loop : -0.45 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 450 TYR 0.024 0.001 TYR C 166 PHE 0.018 0.001 PHE C 819 TRP 0.020 0.001 TRP A 101 HIS 0.003 0.001 HIS B 203 Details of bonding type rmsd covalent geometry : bond 0.00243 (25881) covalent geometry : angle 0.54433 (35220) SS BOND : bond 0.00196 ( 42) SS BOND : angle 1.03272 ( 84) hydrogen bonds : bond 0.04719 ( 1016) hydrogen bonds : angle 5.03022 ( 2883) link_BETA1-4 : bond 0.00443 ( 16) link_BETA1-4 : angle 0.97937 ( 48) link_NAG-ASN : bond 0.00847 ( 35) link_NAG-ASN : angle 4.33331 ( 105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 96 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 CYS cc_start: 0.0149 (OUTLIER) cc_final: -0.0373 (t) REVERT: A 187 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7067 (mp0) REVERT: A 898 MET cc_start: 0.9646 (mmm) cc_final: 0.9408 (tpt) REVERT: B 370 PHE cc_start: 0.8171 (m-80) cc_final: 0.7922 (m-80) REVERT: B 896 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8473 (mtp) REVERT: C 736 MET cc_start: 0.8653 (tmm) cc_final: 0.8240 (tmm) REVERT: C 851 PHE cc_start: 0.7854 (m-80) cc_final: 0.7495 (m-80) REVERT: C 1109 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8351 (mt0) outliers start: 50 outliers final: 39 residues processed: 141 average time/residue: 0.1537 time to fit residues: 37.0630 Evaluate side-chains 135 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 1094 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 896 MET Chi-restraints excluded: chain B residue 964 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 561 PHE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 1006 GLN Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain C residue 1109 GLN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 172 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 268 optimal weight: 2.9990 chunk 37 optimal weight: 30.0000 chunk 143 optimal weight: 20.0000 chunk 291 optimal weight: 7.9990 chunk 42 optimal weight: 50.0000 chunk 9 optimal weight: 30.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 998 GLN ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 909 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.134258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.077286 restraints weight = 62752.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.080309 restraints weight = 34148.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.080885 restraints weight = 20833.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.081106 restraints weight = 17310.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.081325 restraints weight = 17754.135| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 25974 Z= 0.191 Angle : 0.631 20.954 35457 Z= 0.305 Chirality : 0.046 0.309 4140 Planarity : 0.004 0.047 4488 Dihedral : 5.699 59.626 4436 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.85 % Allowed : 17.76 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 3093 helix: 2.44 (0.20), residues: 676 sheet: 0.24 (0.18), residues: 744 loop : -0.47 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 761 TYR 0.024 0.001 TYR B 419 PHE 0.027 0.001 PHE A 555 TRP 0.020 0.001 TRP A 101 HIS 0.005 0.001 HIS C1054 Details of bonding type rmsd covalent geometry : bond 0.00456 (25881) covalent geometry : angle 0.57984 (35220) SS BOND : bond 0.00200 ( 42) SS BOND : angle 1.16807 ( 84) hydrogen bonds : bond 0.05518 ( 1016) hydrogen bonds : angle 5.17680 ( 2883) link_BETA1-4 : bond 0.00274 ( 16) link_BETA1-4 : angle 1.07350 ( 48) link_NAG-ASN : bond 0.00768 ( 35) link_NAG-ASN : angle 4.46689 ( 105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6186 Ramachandran restraints generated. 3093 Oldfield, 0 Emsley, 3093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 85 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 CYS cc_start: 0.0424 (OUTLIER) cc_final: -0.0407 (t) REVERT: A 187 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7358 (mp0) REVERT: A 898 MET cc_start: 0.9630 (mmm) cc_final: 0.9385 (tpt) REVERT: B 896 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8570 (mtp) REVERT: C 238 LEU cc_start: 0.8563 (tp) cc_final: 0.8117 (mp) REVERT: C 325 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7245 (m-10) REVERT: C 851 PHE cc_start: 0.7885 (m-80) cc_final: 0.7507 (m-80) REVERT: C 1109 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8404 (mt0) outliers start: 51 outliers final: 41 residues processed: 130 average time/residue: 0.1546 time to fit residues: 35.5696 Evaluate side-chains 130 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 85 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1094 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 896 MET Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 325 PHE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 561 PHE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1006 GLN Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain C residue 1109 GLN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 212 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 124 optimal weight: 0.0060 chunk 75 optimal weight: 3.9990 chunk 184 optimal weight: 0.5980 chunk 31 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 120 optimal weight: 0.0000 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN C 909 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.136081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.079305 restraints weight = 62502.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.082581 restraints weight = 33248.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.082743 restraints weight = 22060.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.083109 restraints weight = 17642.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.083434 restraints weight = 17641.264| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25974 Z= 0.105 Angle : 0.578 20.879 35457 Z= 0.277 Chirality : 0.044 0.307 4140 Planarity : 0.003 0.038 4488 Dihedral : 5.402 59.364 4436 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.60 % Allowed : 17.90 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.15), residues: 3093 helix: 2.59 (0.20), residues: 681 sheet: 0.36 (0.18), residues: 742 loop : -0.40 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 315 TYR 0.021 0.001 TYR B 419 PHE 0.027 0.001 PHE B 396 TRP 0.021 0.001 TRP A 101 HIS 0.003 0.001 HIS B 203 Details of bonding type rmsd covalent geometry : bond 0.00226 (25881) covalent geometry : angle 0.52775 (35220) SS BOND : bond 0.00196 ( 42) SS BOND : angle 0.97851 ( 84) hydrogen bonds : bond 0.04428 ( 1016) hydrogen bonds : angle 4.91771 ( 2883) link_BETA1-4 : bond 0.00458 ( 16) link_BETA1-4 : angle 0.95565 ( 48) link_NAG-ASN : bond 0.00830 ( 35) link_NAG-ASN : angle 4.25141 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4090.87 seconds wall clock time: 71 minutes 35.58 seconds (4295.58 seconds total)