Starting phenix.real_space_refine on Thu Oct 29 10:30:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xo0_67065/10_2026/9xo0_67065.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xo0_67065/10_2026/9xo0_67065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xo0_67065/10_2026/9xo0_67065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xo0_67065/10_2026/9xo0_67065.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xo0_67065/10_2026/9xo0_67065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xo0_67065/10_2026/9xo0_67065.map" } resolution = 2.13 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= 0.018 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 156 5.16 5 C 19920 2.51 5 N 5082 2.21 5 O 6219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31377 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 8472 Classifications: {'peptide': 1102} Link IDs: {'PTRANS': 40, 'TRANS': 1061} Chain breaks: 12 Chain: "F" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 881 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "G" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 743 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 8, 'TRANS': 93} Chain: "B" Number of atoms: 8472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 8472 Classifications: {'peptide': 1102} Link IDs: {'PTRANS': 40, 'TRANS': 1061} Chain breaks: 12 Chain: "D" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 881 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "H" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 743 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 8, 'TRANS': 93} Chain: "C" Number of atoms: 8472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 8472 Classifications: {'peptide': 1102} Link IDs: {'PTRANS': 40, 'TRANS': 1061} Chain breaks: 12 Chain: "E" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 881 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "I" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 743 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 8, 'TRANS': 93} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 190 Unusual residues: {'NAG': 11, 'PAM': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 190 Unusual residues: {'NAG': 11, 'PAM': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 190 Unusual residues: {'NAG': 11, 'PAM': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 6.84, per 1000 atoms: 0.22 Number of scatterers: 31377 At special positions: 0 Unit cell: (192.51, 205.53, 157.17, 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 156 16.00 O 6219 8.00 N 5082 7.00 C 19920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 234 " distance=2.04 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 373 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 473 " distance=2.03 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 589 " distance=2.04 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 599 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 830 " distance=2.04 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 819 " distance=2.04 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 931 " distance=2.04 Simple disulfide: pdb=" SG CYS A1122 " - pdb=" SG CYS A1133 " distance=2.03 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1226 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 67 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 148 " distance=2.04 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 307 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 473 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 589 " distance=2.03 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 599 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 700 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 808 " - pdb=" SG CYS B 830 " distance=2.04 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 819 " distance=2.04 Simple disulfide: pdb=" SG CYS B 920 " - pdb=" SG CYS B 931 " distance=2.04 Simple disulfide: pdb=" SG CYS B1122 " - pdb=" SG CYS B1133 " distance=2.03 Simple disulfide: pdb=" SG CYS B1173 " - pdb=" SG CYS B1226 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 67 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 148 " distance=2.04 Simple disulfide: pdb=" SG CYS C 196 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS C 230 " - pdb=" SG CYS C 234 " distance=2.04 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 373 " distance=2.04 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 473 " distance=2.03 Simple disulfide: pdb=" SG CYS C 543 " - pdb=" SG CYS C 589 " distance=2.04 Simple disulfide: pdb=" SG CYS C 572 " - pdb=" SG CYS C 599 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 700 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 808 " - pdb=" SG CYS C 830 " distance=2.04 Simple disulfide: pdb=" SG CYS C 813 " - pdb=" SG CYS C 819 " distance=2.04 Simple disulfide: pdb=" SG CYS C 920 " - pdb=" SG CYS C 931 " distance=2.04 Simple disulfide: pdb=" SG CYS C1122 " - pdb=" SG CYS C1133 " distance=2.03 Simple disulfide: pdb=" SG CYS C1173 " - pdb=" SG CYS C1226 " distance=2.04 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 115 " distance=2.03 Simple disulfide: pdb=" SG CYS I 40 " - pdb=" SG CYS I 108 " 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 ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA S 3 " - " MAN S 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA S 3 " - " MAN S 5 " " BMA X 3 " - " MAN X 5 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A1401 " - " ASN A 344 " " NAG A1402 " - " ASN A 726 " " NAG A1403 " - " ASN A 781 " " NAG A1404 " - " ASN A 514 " " NAG A1405 " - " ASN A 743 " " NAG A1406 " - " ASN A 787 " " NAG A1407 " - " ASN A1009 " " NAG A1409 " - " ASN A 300 " " NAG A1410 " - " ASN A 351 " " NAG A1411 " - " ASN A 556 " " NAG A1412 " - " ASN A 667 " " NAG B1401 " - " ASN B 344 " " NAG B1402 " - " ASN B 726 " " NAG B1403 " - " ASN B 781 " " NAG B1404 " - " ASN B 514 " " NAG B1405 " - " ASN B 743 " " NAG B1406 " - " ASN B 787 " " NAG B1407 " - " ASN B1009 " " NAG B1409 " - " ASN B 300 " " NAG B1410 " - " ASN B 351 " " NAG B1411 " - " ASN B 556 " " NAG B1412 " - " ASN B 667 " " NAG C1402 " - " ASN C 344 " " NAG C1403 " - " ASN C 726 " " NAG C1404 " - " ASN C 781 " " NAG C1405 " - " ASN C 514 " " NAG C1406 " - " ASN C 743 " " NAG C1407 " - " ASN C 787 " " NAG C1408 " - " ASN C1009 " " NAG C1410 " - " ASN C 300 " " NAG C1411 " - " ASN C 351 " " NAG C1412 " - " ASN C 556 " " NAG C1413 " - " ASN C 667 " " NAG J 1 " - " ASN A 216 " " NAG K 1 " - " ASN A 324 " " NAG L 1 " - " ASN A 688 " " NAG M 1 " - " ASN A 873 " " NAG N 1 " - " ASN A 264 " " NAG O 1 " - " ASN B 216 " " NAG P 1 " - " ASN B 324 " " NAG Q 1 " - " ASN B 688 " " NAG R 1 " - " ASN B 873 " " NAG S 1 " - " ASN B 264 " " NAG T 1 " - " ASN C 216 " " NAG U 1 " - " ASN C 324 " " NAG V 1 " - " ASN C 688 " " NAG W 1 " - " ASN C 873 " " NAG X 1 " - " ASN C 264 " Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.2 seconds 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7236 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 65 sheets defined 20.9% alpha, 40.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 325 through 333 removed outlier: 3.675A pdb=" N ILE A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 475 Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 807 through 814 Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.580A pdb=" N THR A 824 " --> pdb=" O LYS A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 852 Processing helix chain 'A' and resid 855 through 861 removed outlier: 3.764A pdb=" N LEU A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 878 removed outlier: 3.652A pdb=" N LEU A 878 " --> pdb=" O THR A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 917 through 922 removed outlier: 3.764A pdb=" N SER A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN A 922 " --> pdb=" O LYS A 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 917 through 922' Processing helix chain 'A' and resid 928 through 936 Processing helix chain 'A' and resid 946 through 961 removed outlier: 3.795A pdb=" N MET A 961 " --> pdb=" O LEU A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 986 removed outlier: 3.795A pdb=" N ALA A 977 " --> pdb=" O PRO A 973 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 985 " --> pdb=" O ARG A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1014 Processing helix chain 'A' and resid 1030 through 1045 Processing helix chain 'A' and resid 1046 through 1055 Processing helix chain 'A' and resid 1056 through 1058 No H-bonds generated for 'chain 'A' and resid 1056 through 1058' Processing helix chain 'A' and resid 1066 through 1074 Processing helix chain 'A' and resid 1075 through 1123 Processing helix chain 'A' and resid 1216 through 1218 No H-bonds generated for 'chain 'A' and resid 1216 through 1218' Processing helix chain 'F' and resid 106 through 110 removed outlier: 3.797A pdb=" N ALA F 110 " --> pdb=" O THR F 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 52 removed outlier: 3.560A pdb=" N TYR G 52 " --> pdb=" O GLY G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 103 removed outlier: 3.769A pdb=" N ASP G 102 " --> pdb=" O GLN G 99 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU G 103 " --> pdb=" O ALA G 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 99 through 103' Processing helix chain 'B' and resid 31 through 38 Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 233 through 241 removed outlier: 3.524A pdb=" N TYR B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 333 removed outlier: 3.706A pdb=" N ILE B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 475 Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'B' and resid 807 through 814 Processing helix chain 'B' and resid 816 through 825 removed outlier: 4.227A pdb=" N GLN B 825 " --> pdb=" O GLN B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 852 Processing helix chain 'B' and resid 855 through 860 Processing helix chain 'B' and resid 874 through 878 removed outlier: 3.596A pdb=" N LEU B 878 " --> pdb=" O THR B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 903 Processing helix chain 'B' and resid 917 through 922 removed outlier: 3.739A pdb=" N SER B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN B 922 " --> pdb=" O LYS B 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 917 through 922' Processing helix chain 'B' and resid 928 through 936 Processing helix chain 'B' and resid 946 through 961 removed outlier: 3.700A pdb=" N MET B 961 " --> pdb=" O LEU B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 986 removed outlier: 4.007A pdb=" N ALA B 977 " --> pdb=" O PRO B 973 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 985 " --> pdb=" O ARG B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1014 Processing helix chain 'B' and resid 1030 through 1045 Processing helix chain 'B' and resid 1046 through 1055 Processing helix chain 'B' and resid 1056 through 1058 No H-bonds generated for 'chain 'B' and resid 1056 through 1058' Processing helix chain 'B' and resid 1066 through 1074 Processing helix chain 'B' and resid 1075 through 1123 Processing helix chain 'B' and resid 1175 through 1177 No H-bonds generated for 'chain 'B' and resid 1175 through 1177' Processing helix chain 'B' and resid 1216 through 1218 No H-bonds generated for 'chain 'B' and resid 1216 through 1218' Processing helix chain 'D' and resid 106 through 110 removed outlier: 3.735A pdb=" N ALA D 110 " --> pdb=" O THR D 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 52 Processing helix chain 'H' and resid 99 through 103 removed outlier: 3.738A pdb=" N ASP H 102 " --> pdb=" O GLN H 99 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU H 103 " --> pdb=" O ALA H 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 99 through 103' Processing helix chain 'C' and resid 31 through 38 Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 233 through 241 Processing helix chain 'C' and resid 325 through 333 removed outlier: 3.692A pdb=" N ILE C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 577 through 581 removed outlier: 3.518A pdb=" N ASN C 580 " --> pdb=" O GLN C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 814 Processing helix chain 'C' and resid 816 through 825 removed outlier: 4.255A pdb=" N GLN C 825 " --> pdb=" O GLN C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 852 Processing helix chain 'C' and resid 855 through 860 Processing helix chain 'C' and resid 874 through 878 removed outlier: 3.578A pdb=" N LEU C 878 " --> pdb=" O THR C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 903 Processing helix chain 'C' and resid 917 through 922 removed outlier: 3.723A pdb=" N SER C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN C 922 " --> pdb=" O LYS C 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 917 through 922' Processing helix chain 'C' and resid 928 through 936 Processing helix chain 'C' and resid 946 through 961 removed outlier: 3.721A pdb=" N MET C 961 " --> pdb=" O LEU C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 986 removed outlier: 3.818A pdb=" N ALA C 977 " --> pdb=" O PRO C 973 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 985 " --> pdb=" O ARG C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1013 Processing helix chain 'C' and resid 1030 through 1045 Processing helix chain 'C' and resid 1046 through 1055 Processing helix chain 'C' and resid 1056 through 1058 No H-bonds generated for 'chain 'C' and resid 1056 through 1058' Processing helix chain 'C' and resid 1066 through 1074 Processing helix chain 'C' and resid 1075 through 1123 Processing helix chain 'C' and resid 1216 through 1218 No H-bonds generated for 'chain 'C' and resid 1216 through 1218' Processing helix chain 'E' and resid 106 through 110 removed outlier: 3.733A pdb=" N ALA E 110 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 52 Processing helix chain 'I' and resid 99 through 103 removed outlier: 3.505A pdb=" N ASP I 102 " --> pdb=" O GLN I 99 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU I 103 " --> pdb=" O ALA I 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 99 through 103' Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 49 removed outlier: 3.616A pdb=" N ALA A 45 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 74 removed outlier: 3.755A pdb=" N ALA A 74 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 192 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 91 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 124 " --> pdb=" O TYR A 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA4, first strand: chain 'A' and resid 270 through 286 removed outlier: 7.682A pdb=" N VAL A 273 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 453 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER A 275 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 451 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLN A 277 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA A 449 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LEU A 279 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL A 447 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL A 281 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASN A 445 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 440 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 414 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 286 removed outlier: 7.682A pdb=" N VAL A 273 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 453 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER A 275 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 451 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLN A 277 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA A 449 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LEU A 279 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL A 447 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL A 281 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASN A 445 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ASP A 448 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR A 463 " --> pdb=" O ASP A 448 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU A 450 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE A 461 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU A 452 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 295 through 298 removed outlier: 4.147A pdb=" N ILE A 335 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 348 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR A 371 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 390 " --> pdb=" O TYR A 371 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N CYS A 373 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 488 removed outlier: 3.714A pdb=" N GLY A 715 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 499 through 502 removed outlier: 4.466A pdb=" N VAL A 694 " --> pdb=" O THR A 666 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU A 684 " --> pdb=" O VAL A 697 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 536 removed outlier: 7.231A pdb=" N LEU A 529 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N GLY A 522 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA A 531 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 587 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY A 625 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 585 " --> pdb=" O GLY A 625 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 526 through 536 removed outlier: 7.231A pdb=" N LEU A 529 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N GLY A 522 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA A 531 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LYS A 614 " --> pdb=" O GLY A 605 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLY A 605 " --> pdb=" O LYS A 614 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR A 616 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 620 " --> pdb=" O CYS A 599 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 749 through 751 Processing sheet with id=AB3, first strand: chain 'A' and resid 780 through 798 removed outlier: 6.795A pdb=" N ASN A 781 " --> pdb=" O ILE A1167 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE A1167 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER A 783 " --> pdb=" O ASP A1165 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP A1165 " --> pdb=" O SER A 783 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE A1163 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN A 787 " --> pdb=" O GLY A1161 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A1141 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU A1158 " --> pdb=" O HIS A1139 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N HIS A1139 " --> pdb=" O LEU A1158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 780 through 798 removed outlier: 6.795A pdb=" N ASN A 781 " --> pdb=" O ILE A1167 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE A1167 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER A 783 " --> pdb=" O ASP A1165 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP A1165 " --> pdb=" O SER A 783 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE A1163 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN A 787 " --> pdb=" O GLY A1161 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE A1167 " --> pdb=" O THR A1191 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A1191 " --> pdb=" O ILE A1167 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A1189 " --> pdb=" O ILE A1169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 804 through 806 Processing sheet with id=AB6, first strand: chain 'A' and resid 1171 through 1174 Processing sheet with id=AB7, first strand: chain 'F' and resid 22 through 26 removed outlier: 3.648A pdb=" N THR F 97 " --> pdb=" O ASP F 92 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP F 92 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER F 90 " --> pdb=" O TYR F 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 77 through 79 removed outlier: 5.706A pdb=" N TRP F 66 " --> pdb=" O ARG F 57 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG F 57 " --> pdb=" O TRP F 66 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 22 through 24 Processing sheet with id=AC1, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AC2, first strand: chain 'G' and resid 65 through 68 removed outlier: 6.290A pdb=" N LEU G 66 " --> pdb=" O GLN G 57 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLN G 57 " --> pdb=" O LEU G 66 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET G 68 " --> pdb=" O TRP G 55 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER G 54 " --> pdb=" O LYS G 109 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL G 105 " --> pdb=" O GLN G 58 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 85 through 87 removed outlier: 3.616A pdb=" N GLY G 85 " --> pdb=" O ALA G 92 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 45 through 49 removed outlier: 3.514A pdb=" N ALA B 45 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.603A pdb=" N ALA B 74 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 91 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B 124 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE B 150 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N GLN B 127 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N CYS B 148 " --> pdb=" O GLN B 127 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.603A pdb=" N ALA B 74 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 91 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B 124 " --> pdb=" O TYR B 108 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AC8, first strand: chain 'B' and resid 270 through 286 removed outlier: 6.237A pdb=" N ASN B 445 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL B 281 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N SER B 443 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS B 283 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 441 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU B 285 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP B 439 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B 440 " --> pdb=" O ASN B 322 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP B 405 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 414 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 270 through 286 removed outlier: 6.237A pdb=" N ASN B 445 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL B 281 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N SER B 443 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS B 283 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 441 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU B 285 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP B 439 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ASP B 448 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR B 463 " --> pdb=" O ASP B 448 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU B 450 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE B 461 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU B 452 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 295 through 298 removed outlier: 4.133A pdb=" N ILE B 335 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 348 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR B 371 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL B 390 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N CYS B 373 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 483 through 488 removed outlier: 3.753A pdb=" N GLY B 715 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 499 through 502 removed outlier: 4.580A pdb=" N VAL B 694 " --> pdb=" O THR B 666 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LEU B 684 " --> pdb=" O VAL B 697 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 526 through 536 removed outlier: 7.040A pdb=" N LEU B 529 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N GLY B 522 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA B 531 " --> pdb=" O SER B 520 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 587 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY B 625 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE B 585 " --> pdb=" O GLY B 625 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 526 through 536 removed outlier: 7.040A pdb=" N LEU B 529 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N GLY B 522 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA B 531 " --> pdb=" O SER B 520 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B 603 " --> pdb=" O PHE B 615 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N SER B 617 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE B 601 " --> pdb=" O SER B 617 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 747 through 751 Processing sheet with id=AD7, first strand: chain 'B' and resid 780 through 798 removed outlier: 6.804A pdb=" N ASN B 781 " --> pdb=" O ILE B1167 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE B1167 " --> pdb=" O ASN B 781 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER B 783 " --> pdb=" O ASP B1165 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASP B1165 " --> pdb=" O SER B 783 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE B1163 " --> pdb=" O PRO B 785 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN B 787 " --> pdb=" O GLY B1161 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B1141 " --> pdb=" O THR B1156 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU B1158 " --> pdb=" O HIS B1139 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N HIS B1139 " --> pdb=" O LEU B1158 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 780 through 798 removed outlier: 6.804A pdb=" N ASN B 781 " --> pdb=" O ILE B1167 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE B1167 " --> pdb=" O ASN B 781 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER B 783 " --> pdb=" O ASP B1165 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASP B1165 " --> pdb=" O SER B 783 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE B1163 " --> pdb=" O PRO B 785 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN B 787 " --> pdb=" O GLY B1161 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE B1167 " --> pdb=" O THR B1191 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B1191 " --> pdb=" O ILE B1167 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU B1189 " --> pdb=" O ILE B1169 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 804 through 806 Processing sheet with id=AE1, first strand: chain 'B' and resid 1171 through 1174 Processing sheet with id=AE2, first strand: chain 'D' and resid 22 through 26 removed outlier: 3.578A pdb=" N LEU D 100 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 97 " --> pdb=" O ASP D 92 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR D 88 " --> pdb=" O GLN D 101 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 77 through 79 removed outlier: 6.712A pdb=" N TRP D 55 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY D 69 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE D 53 " --> pdb=" O GLY D 69 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 56 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR D 114 " --> pdb=" O VAL D 56 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 22 through 24 removed outlier: 3.522A pdb=" N ALA H 41 " --> pdb=" O ILE H 23 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE6, first strand: chain 'H' and resid 65 through 68 removed outlier: 6.002A pdb=" N LEU H 66 " --> pdb=" O GLN H 57 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN H 57 " --> pdb=" O LEU H 66 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET H 68 " --> pdb=" O TRP H 55 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER H 54 " --> pdb=" O LYS H 109 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS H 109 " --> pdb=" O SER H 54 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL H 105 " --> pdb=" O GLN H 58 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 85 through 87 removed outlier: 3.632A pdb=" N GLY H 85 " --> pdb=" O ALA H 92 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 45 through 49 removed outlier: 3.573A pdb=" N ALA C 45 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 73 through 75 removed outlier: 3.707A pdb=" N ALA C 74 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 192 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 124 " --> pdb=" O TYR C 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE C 150 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N GLN C 127 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N CYS C 148 " --> pdb=" O GLN C 127 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 73 through 75 removed outlier: 3.707A pdb=" N ALA C 74 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 192 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 124 " --> pdb=" O TYR C 108 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AF3, first strand: chain 'C' and resid 270 through 286 removed outlier: 7.737A pdb=" N VAL C 273 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL C 453 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N SER C 275 " --> pdb=" O ILE C 451 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE C 451 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLN C 277 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA C 449 " --> pdb=" O GLN C 277 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU C 279 " --> pdb=" O VAL C 447 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL C 447 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL C 281 " --> pdb=" O ASN C 445 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN C 445 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR C 440 " --> pdb=" O ASN C 322 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP C 405 " --> pdb=" O THR C 401 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 414 " --> pdb=" O VAL C 406 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 270 through 286 removed outlier: 7.737A pdb=" N VAL C 273 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL C 453 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N SER C 275 " --> pdb=" O ILE C 451 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE C 451 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLN C 277 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA C 449 " --> pdb=" O GLN C 277 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU C 279 " --> pdb=" O VAL C 447 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL C 447 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL C 281 " --> pdb=" O ASN C 445 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN C 445 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ASP C 448 " --> pdb=" O TYR C 463 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR C 463 " --> pdb=" O ASP C 448 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU C 450 " --> pdb=" O ILE C 461 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE C 461 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLU C 452 " --> pdb=" O GLN C 459 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 295 through 298 removed outlier: 6.982A pdb=" N HIS C 338 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL C 422 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL C 336 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE C 424 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER C 334 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE C 335 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 348 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR C 371 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL C 390 " --> pdb=" O TYR C 371 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N CYS C 373 " --> pdb=" O LEU C 388 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 483 through 488 removed outlier: 3.760A pdb=" N GLY C 715 " --> pdb=" O ALA C 707 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 499 through 502 removed outlier: 5.028A pdb=" N LEU C 684 " --> pdb=" O VAL C 697 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 526 through 536 removed outlier: 7.062A pdb=" N LEU C 529 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLY C 522 " --> pdb=" O LEU C 529 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA C 531 " --> pdb=" O SER C 520 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 587 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY C 625 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE C 585 " --> pdb=" O GLY C 625 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 526 through 536 removed outlier: 7.062A pdb=" N LEU C 529 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLY C 522 " --> pdb=" O LEU C 529 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA C 531 " --> pdb=" O SER C 520 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C 603 " --> pdb=" O PHE C 615 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N SER C 617 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE C 601 " --> pdb=" O SER C 617 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR C 619 " --> pdb=" O CYS C 599 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N CYS C 599 " --> pdb=" O TYR C 619 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 749 through 751 Processing sheet with id=AG2, first strand: chain 'C' and resid 780 through 798 removed outlier: 6.789A pdb=" N ASN C 781 " --> pdb=" O ILE C1167 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE C1167 " --> pdb=" O ASN C 781 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N SER C 783 " --> pdb=" O ASP C1165 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASP C1165 " --> pdb=" O SER C 783 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE C1163 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C 787 " --> pdb=" O GLY C1161 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE C1141 " --> pdb=" O THR C1156 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU C1158 " --> pdb=" O HIS C1139 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS C1139 " --> pdb=" O LEU C1158 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 780 through 798 removed outlier: 6.789A pdb=" N ASN C 781 " --> pdb=" O ILE C1167 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE C1167 " --> pdb=" O ASN C 781 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N SER C 783 " --> pdb=" O ASP C1165 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASP C1165 " --> pdb=" O SER C 783 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE C1163 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C 787 " --> pdb=" O GLY C1161 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE C1167 " --> pdb=" O THR C1191 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR C1191 " --> pdb=" O ILE C1167 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU C1189 " --> pdb=" O ILE C1169 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 804 through 806 Processing sheet with id=AG5, first strand: chain 'C' and resid 1171 through 1174 Processing sheet with id=AG6, first strand: chain 'E' and resid 22 through 26 removed outlier: 3.676A pdb=" N SER E 90 " --> pdb=" O TYR E 99 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 77 through 79 removed outlier: 6.788A pdb=" N TRP E 55 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLY E 69 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE E 53 " --> pdb=" O GLY E 69 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL E 56 " --> pdb=" O TYR E 114 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 22 through 24 Processing sheet with id=AG9, first strand: chain 'I' and resid 35 through 37 Processing sheet with id=AH1, first strand: chain 'I' and resid 65 through 68 removed outlier: 6.113A pdb=" N LEU I 66 " --> pdb=" O GLN I 57 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLN I 57 " --> pdb=" O LEU I 66 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET I 68 " --> pdb=" O TRP I 55 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER I 54 " --> pdb=" O LYS I 109 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS I 109 " --> pdb=" O SER I 54 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL I 105 " --> pdb=" O GLN I 58 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE I 118 " --> pdb=" O LEU I 110 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 85 through 87 1324 hydrogen bonds defined for protein. 3678 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: 8.69 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9846 1.34 - 1.46: 8366 1.46 - 1.59: 13624 1.59 - 1.71: 0 1.71 - 1.83: 204 Bond restraints: 32040 Sorted by residual: bond pdb=" C ASN I 73 " pdb=" N ARG I 74 " ideal model delta sigma weight residual 1.331 1.370 -0.039 2.07e-02 2.33e+03 3.52e+00 bond pdb=" C VAL F 123 " pdb=" N ASN F 124 " ideal model delta sigma weight residual 1.332 1.308 0.024 1.40e-02 5.10e+03 3.06e+00 bond pdb=" CA VAL F 123 " pdb=" CB VAL F 123 " ideal model delta sigma weight residual 1.527 1.550 -0.023 1.31e-02 5.83e+03 3.01e+00 bond pdb=" CG MET C 777 " pdb=" SD MET C 777 " ideal model delta sigma weight residual 1.803 1.768 0.035 2.50e-02 1.60e+03 2.00e+00 bond pdb=" CB VAL A 945 " pdb=" CG2 VAL A 945 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.91e+00 ... (remaining 32035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 42307 1.85 - 3.70: 1061 3.70 - 5.55: 115 5.55 - 7.41: 17 7.41 - 9.26: 9 Bond angle restraints: 43509 Sorted by residual: angle pdb=" C ILE A1223 " pdb=" N GLU A1224 " pdb=" CA GLU A1224 " ideal model delta sigma weight residual 121.54 127.74 -6.20 1.91e+00 2.74e-01 1.05e+01 angle pdb=" C ILE B1223 " pdb=" N GLU B1224 " pdb=" CA GLU B1224 " ideal model delta sigma weight residual 121.54 127.59 -6.05 1.91e+00 2.74e-01 1.00e+01 angle pdb=" N ASP C 466 " pdb=" CA ASP C 466 " pdb=" C ASP C 466 " ideal model delta sigma weight residual 109.81 102.83 6.98 2.21e+00 2.05e-01 9.97e+00 angle pdb=" C ILE C1223 " pdb=" N GLU C1224 " pdb=" CA GLU C1224 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.77e+00 angle pdb=" C VAL A 638 " pdb=" N THR A 639 " pdb=" CA THR A 639 " ideal model delta sigma weight residual 121.54 127.43 -5.89 1.91e+00 2.74e-01 9.51e+00 ... (remaining 43504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.11: 18653 20.11 - 40.22: 912 40.22 - 60.33: 132 60.33 - 80.44: 34 80.44 - 100.55: 9 Dihedral angle restraints: 19740 sinusoidal: 8388 harmonic: 11352 Sorted by residual: dihedral pdb=" CB CYS A 283 " pdb=" SG CYS A 283 " pdb=" SG CYS A 307 " pdb=" CB CYS A 307 " ideal model delta sinusoidal sigma weight residual 93.00 168.83 -75.83 1 1.00e+01 1.00e-02 7.25e+01 dihedral pdb=" CB CYS C 283 " pdb=" SG CYS C 283 " pdb=" SG CYS C 307 " pdb=" CB CYS C 307 " ideal model delta sinusoidal sigma weight residual 93.00 167.59 -74.59 1 1.00e+01 1.00e-02 7.05e+01 dihedral pdb=" CB CYS B 283 " pdb=" SG CYS B 283 " pdb=" SG CYS B 307 " pdb=" CB CYS B 307 " ideal model delta sinusoidal sigma weight residual 93.00 167.09 -74.09 1 1.00e+01 1.00e-02 6.97e+01 ... (remaining 19737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 4859 0.107 - 0.214: 260 0.214 - 0.321: 7 0.321 - 0.428: 3 0.428 - 0.534: 1 Chirality restraints: 5130 Sorted by residual: chirality pdb=" C1 NAG B1411 " pdb=" ND2 ASN B 556 " pdb=" C2 NAG B1411 " pdb=" O5 NAG B1411 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.14e+00 chirality pdb=" C1 NAG B1402 " pdb=" ND2 ASN B 726 " pdb=" C2 NAG B1402 " pdb=" O5 NAG B1402 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" C1 NAG B1409 " pdb=" ND2 ASN B 300 " pdb=" C2 NAG B1409 " pdb=" O5 NAG B1409 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 5127 not shown) Planarity restraints: 5550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 572 " -0.049 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO C 573 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO C 573 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 573 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C1184 " 0.044 5.00e-02 4.00e+02 6.65e-02 7.08e+00 pdb=" N PRO C1185 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO C1185 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C1185 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 572 " 0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO A 573 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 573 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 573 " 0.036 5.00e-02 4.00e+02 ... (remaining 5547 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 16725 3.01 - 3.48: 29545 3.48 - 3.96: 52658 3.96 - 4.43: 59540 4.43 - 4.90: 96789 Nonbonded interactions: 255257 Sorted by model distance: nonbonded pdb=" O5 MAN S 4 " pdb=" O6 MAN S 4 " model vdw 2.540 2.432 nonbonded pdb=" O ARG B1183 " pdb=" CA GLU B1184 " model vdw 2.543 2.776 nonbonded pdb=" O4 NAG S 2 " pdb=" O2 BMA S 3 " model vdw 2.581 2.432 nonbonded pdb=" O5 NAG Q 1 " pdb=" O6 NAG Q 1 " model vdw 2.581 2.432 nonbonded pdb=" O4 NAG X 2 " pdb=" O2 BMA X 3 " model vdw 2.586 2.432 ... (remaining 255252 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 1231 or resid 1402 through 1407 or resid 1410 t \ hrough 1412)) selection = (chain 'B' and (resid 26 through 1231 or resid 1402 through 1407 or resid 1410 t \ hrough 1412)) selection = (chain 'C' and (resid 26 through 1231 or resid 1402 through 1407 or resid 1410 t \ hrough 1412)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'N' selection = chain 'S' selection = chain 'X' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.490 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 0.046 32166 Z= 0.184 Angle : 0.728 12.967 43833 Z= 0.373 Chirality : 0.052 0.534 5130 Planarity : 0.006 0.075 5502 Dihedral : 11.803 100.552 12342 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.29 (0.13), residues: 3873 helix: 1.13 (0.20), residues: 678 sheet: 0.05 (0.16), residues: 1044 loop : -0.72 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 314 TYR 0.031 0.002 TYR E 125 PHE 0.025 0.002 PHE A 411 TRP 0.011 0.001 TRP D 55 HIS 0.007 0.001 HIS C 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (32040) covalent geometry : angle 0.69811 / 0.37 (43509) SS BOND : bond 0.00438 / 0.27 ( 54) SS BOND : angle 1.61695 / 1.17 ( 108) hydrogen bonds : bond 0.18358 / 12.50 ( 1191) hydrogen bonds : angle 8.71862 / 6.04 ( 3678) link_ALPHA1-3 : bond 0.00766 / 0.39 ( 3) link_ALPHA1-3 : angle 1.29040 / 0.73 ( 9) link_ALPHA1-6 : bond 0.01332 / 0.67 ( 3) link_ALPHA1-6 : angle 1.59546 / 0.88 ( 9) link_BETA1-4 : bond 0.00274 / 0.19 ( 18) link_BETA1-4 : angle 2.18389 / 1.47 ( 54) link_NAG-ASN : bond 0.00514 / 0.33 ( 48) link_NAG-ASN : angle 3.16926 / 2.14 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 648 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 518 SER cc_start: 0.8215 (p) cc_final: 0.7826 (p) REVERT: B 1178 ILE cc_start: 0.8144 (mp) cc_final: 0.7903 (mp) REVERT: C 593 SER cc_start: 0.8411 (m) cc_final: 0.7904 (p) REVERT: C 1076 ILE cc_start: 0.8367 (tt) cc_final: 0.7964 (tt) outliers start: 0 outliers final: 0 residues processed: 648 average time/residue: 0.5664 time to fit residues: 442.9063 Evaluate side-chains 558 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 558 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: [197, 388, 215, 20, 132, 261, 248, 207, 155, 244, 183] chunk 197 optimal weight: 0.2980 chunk 388 optimal weight: 0.5980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN A 814 ASN A 860 GLN ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN A1175 ASN B 249 HIS B 470 GLN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN B 860 GLN B1082 GLN D 96 ASN C 270 HIS ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 GLN C 814 ASN C1051 GLN C1128 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.161812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.128742 restraints weight = 38045.505| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.79 r_work: 0.3618 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 32166 Z= 0.173 Angle : 0.614 11.680 43833 Z= 0.312 Chirality : 0.047 0.355 5130 Planarity : 0.004 0.052 5502 Dihedral : 7.594 101.432 5811 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.43 % Allowed : 6.21 % Favored : 92.35 % 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: -0.14 (0.13), residues: 3873 helix: 1.33 (0.20), residues: 693 sheet: 0.07 (0.16), residues: 1059 loop : -0.63 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 919 TYR 0.021 0.002 TYR C 676 PHE 0.015 0.001 PHE A 411 TRP 0.007 0.001 TRP D 55 HIS 0.005 0.001 HIS C 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (32040) covalent geometry : angle 0.58623 / 0.31 (43509) SS BOND : bond 0.00366 / 0.24 ( 54) SS BOND : angle 1.62764 / 1.34 ( 108) hydrogen bonds : bond 0.04927 / 3.29 ( 1191) hydrogen bonds : angle 6.15888 / 4.26 ( 3678) link_ALPHA1-3 : bond 0.00679 / 0.34 ( 3) link_ALPHA1-3 : angle 1.55377 / 0.86 ( 9) link_ALPHA1-6 : bond 0.00863 / 0.44 ( 3) link_ALPHA1-6 : angle 1.44082 / 0.88 ( 9) link_BETA1-4 : bond 0.00277 / 0.18 ( 18) link_BETA1-4 : angle 1.96220 / 1.34 ( 54) link_NAG-ASN : bond 0.00467 / 0.31 ( 48) link_NAG-ASN : angle 2.66462 / 1.78 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 591 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 347 PHE cc_start: 0.8248 (m-80) cc_final: 0.8041 (m-80) REVERT: B 518 SER cc_start: 0.8436 (p) cc_final: 0.8073 (m) REVERT: B 898 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8063 (mt-10) REVERT: C 593 SER cc_start: 0.8390 (m) cc_final: 0.8151 (p) outliers start: 48 outliers final: 29 residues processed: 603 average time/residue: 0.5880 time to fit residues: 427.0045 Evaluate side-chains 587 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 558 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 825 GLN Chi-restraints excluded: chain B residue 1075 ASP Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 543 CYS Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 825 GLN Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 972 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: [103, 113, 385, 92, 38, 95, 351, 317, 233, 171, 283] chunk 103 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 385 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 351 optimal weight: 0.8980 chunk 317 optimal weight: 1.9990 chunk 233 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 283 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN A 814 ASN A 860 GLN A 933 GLN A1039 GLN A1051 GLN ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN A1175 ASN B 301 GLN B 470 GLN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 GLN B 814 ASN B1059 ASN D 96 ASN C 257 ASN ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 814 ASN C1100 GLN I 99 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.160538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.127410 restraints weight = 38121.013| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.79 r_work: 0.3598 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 32166 Z= 0.205 Angle : 0.633 11.118 43833 Z= 0.321 Chirality : 0.048 0.331 5130 Planarity : 0.004 0.055 5502 Dihedral : 7.684 100.894 5811 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.91 % Allowed : 8.30 % Favored : 89.78 % 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: -0.12 (0.13), residues: 3873 helix: 1.38 (0.20), residues: 693 sheet: -0.09 (0.15), residues: 1134 loop : -0.53 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 314 TYR 0.023 0.002 TYR C 676 PHE 0.023 0.002 PHE C 347 TRP 0.008 0.001 TRP F 55 HIS 0.006 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (32040) covalent geometry : angle 0.60866 / 0.31 (43509) SS BOND : bond 0.00425 / 0.29 ( 54) SS BOND : angle 1.90578 / 1.47 ( 108) hydrogen bonds : bond 0.05025 / 3.34 ( 1191) hydrogen bonds : angle 5.78077 / 4.00 ( 3678) link_ALPHA1-3 : bond 0.00295 / 0.15 ( 3) link_ALPHA1-3 : angle 1.69502 / 0.94 ( 9) link_ALPHA1-6 : bond 0.00704 / 0.35 ( 3) link_ALPHA1-6 : angle 1.41956 / 0.84 ( 9) link_BETA1-4 : bond 0.00297 / 0.18 ( 18) link_BETA1-4 : angle 2.03526 / 1.38 ( 54) link_NAG-ASN : bond 0.00491 / 0.33 ( 48) link_NAG-ASN : angle 2.31618 / 1.63 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 582 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 SER cc_start: 0.8117 (m) cc_final: 0.7729 (t) REVERT: F 53 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7381 (mp) REVERT: G 28 MET cc_start: 0.4893 (ppp) cc_final: 0.4454 (pp-130) REVERT: B 347 PHE cc_start: 0.8279 (m-80) cc_final: 0.8057 (m-80) REVERT: B 518 SER cc_start: 0.8459 (p) cc_final: 0.8075 (m) REVERT: C 593 SER cc_start: 0.8422 (m) cc_final: 0.8185 (p) REVERT: E 89 MET cc_start: 0.7471 (tmm) cc_final: 0.7042 (ttm) outliers start: 64 outliers final: 37 residues processed: 605 average time/residue: 0.5724 time to fit residues: 418.6991 Evaluate side-chains 607 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 569 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 668 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1183 ARG Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 1075 ASP Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 543 CYS Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 972 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: [134, 34, 72, 37, 172, 76, 119, 279, 40, 224, 83] chunk 134 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 72 optimal weight: 0.0870 chunk 37 optimal weight: 0.9990 chunk 172 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 279 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 overall best weight: 0.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN A 814 ASN ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN A1175 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 814 ASN B1055 GLN B1059 ASN ** B1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 GLN C 814 ASN C1128 GLN I 99 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.160802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.127818 restraints weight = 37844.036| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.79 r_work: 0.3606 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 32166 Z= 0.167 Angle : 0.598 10.909 43833 Z= 0.302 Chirality : 0.046 0.316 5130 Planarity : 0.004 0.058 5502 Dihedral : 7.477 100.889 5811 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.03 % Allowed : 10.16 % Favored : 87.81 % 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: -0.07 (0.13), residues: 3873 helix: 1.49 (0.20), residues: 693 sheet: -0.05 (0.15), residues: 1119 loop : -0.52 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 919 TYR 0.022 0.001 TYR C 52 PHE 0.017 0.001 PHE C 411 TRP 0.008 0.001 TRP E 133 HIS 0.004 0.001 HIS C 951 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (32040) covalent geometry : angle 0.57153 / 0.30 (43509) SS BOND : bond 0.00396 / 0.29 ( 54) SS BOND : angle 1.85465 / 1.43 ( 108) hydrogen bonds : bond 0.04584 / 3.04 ( 1191) hydrogen bonds : angle 5.56189 / 3.85 ( 3678) link_ALPHA1-3 : bond 0.00539 / 0.27 ( 3) link_ALPHA1-3 : angle 1.59864 / 0.90 ( 9) link_ALPHA1-6 : bond 0.00885 / 0.44 ( 3) link_ALPHA1-6 : angle 1.41168 / 0.84 ( 9) link_BETA1-4 : bond 0.00273 / 0.18 ( 18) link_BETA1-4 : angle 1.92117 / 1.32 ( 54) link_NAG-ASN : bond 0.00458 / 0.30 ( 48) link_NAG-ASN : angle 2.41883 / 1.64 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 590 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 SER cc_start: 0.8182 (m) cc_final: 0.7785 (t) REVERT: F 53 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7350 (mp) REVERT: G 28 MET cc_start: 0.4926 (ppp) cc_final: 0.4570 (pp-130) REVERT: B 347 PHE cc_start: 0.8260 (m-80) cc_final: 0.8019 (m-80) REVERT: B 518 SER cc_start: 0.8483 (p) cc_final: 0.8102 (m) REVERT: C 245 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: C 425 ASN cc_start: 0.7845 (t0) cc_final: 0.7632 (t0) REVERT: C 593 SER cc_start: 0.8468 (m) cc_final: 0.8241 (p) REVERT: E 89 MET cc_start: 0.7503 (tmm) cc_final: 0.7048 (ttm) outliers start: 68 outliers final: 43 residues processed: 613 average time/residue: 0.5749 time to fit residues: 426.1637 Evaluate side-chains 622 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 577 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1128 GLN Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1183 ARG Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 543 CYS Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 825 GLN Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 972 LEU Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain I residue 99 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: [13, 346, 190, 296, 73, 364, 47, 386, 114, 49, 163] chunk 13 optimal weight: 0.8980 chunk 346 optimal weight: 0.1980 chunk 190 optimal weight: 0.7980 chunk 296 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 364 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 386 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 163 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN A 814 ASN A1059 ASN ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1175 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1055 GLN B1059 ASN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 814 ASN I 99 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.160577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.127672 restraints weight = 37904.136| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.79 r_work: 0.3606 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 32166 Z= 0.180 Angle : 0.603 9.674 43833 Z= 0.307 Chirality : 0.047 0.334 5130 Planarity : 0.004 0.059 5502 Dihedral : 7.435 100.549 5811 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.03 % Allowed : 11.38 % Favored : 86.59 % 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: -0.06 (0.14), residues: 3873 helix: 1.49 (0.20), residues: 693 sheet: -0.03 (0.15), residues: 1119 loop : -0.52 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 314 TYR 0.026 0.002 TYR C 52 PHE 0.019 0.001 PHE C 411 TRP 0.009 0.001 TRP E 133 HIS 0.004 0.001 HIS C 951 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (32040) covalent geometry : angle 0.57853 / 0.30 (43509) SS BOND : bond 0.00420 / 0.30 ( 54) SS BOND : angle 2.13703 / 1.62 ( 108) hydrogen bonds : bond 0.04604 / 3.05 ( 1191) hydrogen bonds : angle 5.48417 / 3.79 ( 3678) link_ALPHA1-3 : bond 0.00456 / 0.23 ( 3) link_ALPHA1-3 : angle 1.66514 / 0.93 ( 9) link_ALPHA1-6 : bond 0.00915 / 0.45 ( 3) link_ALPHA1-6 : angle 1.38247 / 0.82 ( 9) link_BETA1-4 : bond 0.00247 / 0.16 ( 18) link_BETA1-4 : angle 1.92646 / 1.32 ( 54) link_NAG-ASN : bond 0.00416 / 0.28 ( 48) link_NAG-ASN : angle 2.11195 / 1.49 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 594 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 SER cc_start: 0.8211 (m) cc_final: 0.7804 (t) REVERT: F 53 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7397 (mp) REVERT: G 28 MET cc_start: 0.4857 (ppp) cc_final: 0.4319 (pp-130) REVERT: B 347 PHE cc_start: 0.8251 (m-80) cc_final: 0.7993 (m-80) REVERT: B 371 TYR cc_start: 0.7610 (m-80) cc_final: 0.7304 (m-80) REVERT: B 593 SER cc_start: 0.8301 (m) cc_final: 0.7963 (p) REVERT: C 245 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: C 425 ASN cc_start: 0.7885 (t0) cc_final: 0.7668 (t0) REVERT: C 593 SER cc_start: 0.8479 (m) cc_final: 0.8253 (p) REVERT: E 53 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7430 (mp) REVERT: E 89 MET cc_start: 0.7469 (tmm) cc_final: 0.6674 (ttm) REVERT: I 28 MET cc_start: 0.3774 (pp-130) cc_final: 0.3415 (pp-130) REVERT: I 68 MET cc_start: 0.5242 (OUTLIER) cc_final: 0.4928 (tpt) outliers start: 68 outliers final: 48 residues processed: 617 average time/residue: 0.5744 time to fit residues: 429.8747 Evaluate side-chains 640 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 588 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1183 ARG Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 1075 ASP Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 543 CYS Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 825 GLN Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 972 LEU Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain I residue 68 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: [290, 10, 216, 144, 76, 185, 36, 379, 245, 134, 339] chunk 290 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 216 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 185 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 379 optimal weight: 6.9990 chunk 245 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 339 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 301 GLN ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN A 814 ASN A1039 GLN A1059 ASN ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1175 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 GLN B1058 HIS B1059 ASN C 470 GLN C 814 ASN C1128 GLN I 99 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.159945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.127023 restraints weight = 37732.607| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.78 r_work: 0.3593 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 32166 Z= 0.213 Angle : 0.632 11.999 43833 Z= 0.321 Chirality : 0.048 0.365 5130 Planarity : 0.004 0.060 5502 Dihedral : 7.572 100.700 5811 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.57 % Allowed : 11.50 % Favored : 85.93 % 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: -0.07 (0.14), residues: 3873 helix: 1.41 (0.20), residues: 693 sheet: -0.01 (0.15), residues: 1119 loop : -0.52 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 314 TYR 0.023 0.002 TYR C 52 PHE 0.023 0.002 PHE C 411 TRP 0.010 0.001 TRP E 133 HIS 0.005 0.001 HIS C 951 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (32040) covalent geometry : angle 0.60368 / 0.31 (43509) SS BOND : bond 0.00530 / 0.37 ( 54) SS BOND : angle 2.30076 / 1.75 ( 108) hydrogen bonds : bond 0.04820 / 3.19 ( 1191) hydrogen bonds : angle 5.48856 / 3.80 ( 3678) link_ALPHA1-3 : bond 0.00366 / 0.18 ( 3) link_ALPHA1-3 : angle 1.77316 / 0.99 ( 9) link_ALPHA1-6 : bond 0.00830 / 0.42 ( 3) link_ALPHA1-6 : angle 1.40850 / 0.85 ( 9) link_BETA1-4 : bond 0.00355 / 0.22 ( 18) link_BETA1-4 : angle 1.98539 / 1.35 ( 54) link_NAG-ASN : bond 0.00457 / 0.31 ( 48) link_NAG-ASN : angle 2.35009 / 1.60 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 591 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 52 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.6173 (pm20) REVERT: F 53 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7433 (mp) REVERT: B 347 PHE cc_start: 0.8276 (m-80) cc_final: 0.7992 (m-80) REVERT: B 371 TYR cc_start: 0.7602 (m-80) cc_final: 0.7293 (m-80) REVERT: B 593 SER cc_start: 0.8328 (m) cc_final: 0.8026 (p) REVERT: B 831 LYS cc_start: 0.8804 (tmtt) cc_final: 0.8599 (tptm) REVERT: D 53 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7534 (mp) REVERT: C 230 CYS cc_start: 0.4205 (OUTLIER) cc_final: 0.3960 (t) REVERT: C 425 ASN cc_start: 0.7866 (t0) cc_final: 0.7645 (t0) REVERT: C 593 SER cc_start: 0.8471 (m) cc_final: 0.8266 (p) REVERT: E 53 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7469 (mp) REVERT: E 89 MET cc_start: 0.7456 (tmm) cc_final: 0.6697 (ttm) REVERT: I 28 MET cc_start: 0.3981 (pp-130) cc_final: 0.3694 (pp-130) REVERT: I 68 MET cc_start: 0.5297 (OUTLIER) cc_final: 0.4877 (tpt) outliers start: 86 outliers final: 56 residues processed: 621 average time/residue: 0.5643 time to fit residues: 422.8614 Evaluate side-chains 642 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 580 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1183 ARG Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 GLN Chi-restraints excluded: chain B residue 1075 ASP Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 543 CYS Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 825 GLN Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 972 LEU Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain I residue 68 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: [73, 90, 27, 117, 194, 305, 249, 120, 115, 278, 210] chunk 73 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 305 optimal weight: 1.9990 chunk 249 optimal weight: 0.0040 chunk 120 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 chunk 210 optimal weight: 0.0050 overall best weight: 0.4406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 301 GLN A 409 ASN ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN A 814 ASN A1059 ASN ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1175 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 GLN B1059 ASN ** B1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 GLN C 814 ASN I 99 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.161127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.128528 restraints weight = 38058.984| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.77 r_work: 0.3613 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 32166 Z= 0.142 Angle : 0.604 15.486 43833 Z= 0.306 Chirality : 0.046 0.361 5130 Planarity : 0.004 0.058 5502 Dihedral : 7.319 99.714 5811 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.27 % Allowed : 12.25 % Favored : 85.48 % 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: -0.00 (0.14), residues: 3873 helix: 1.55 (0.20), residues: 693 sheet: 0.07 (0.15), residues: 1101 loop : -0.53 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 314 TYR 0.025 0.001 TYR B 52 PHE 0.014 0.001 PHE C 411 TRP 0.009 0.001 TRP D 55 HIS 0.003 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (32040) covalent geometry : angle 0.57420 / 0.30 (43509) SS BOND : bond 0.00606 / 0.44 ( 54) SS BOND : angle 2.55567 / 1.89 ( 108) hydrogen bonds : bond 0.04314 / 2.87 ( 1191) hydrogen bonds : angle 5.29994 / 3.67 ( 3678) link_ALPHA1-3 : bond 0.00658 / 0.33 ( 3) link_ALPHA1-3 : angle 1.53476 / 0.86 ( 9) link_ALPHA1-6 : bond 0.01025 / 0.51 ( 3) link_ALPHA1-6 : angle 1.42199 / 0.85 ( 9) link_BETA1-4 : bond 0.00299 / 0.19 ( 18) link_BETA1-4 : angle 1.81330 / 1.25 ( 54) link_NAG-ASN : bond 0.00509 / 0.33 ( 48) link_NAG-ASN : angle 2.27443 / 1.53 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 587 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 984 TYR cc_start: 0.7520 (t80) cc_final: 0.7290 (t80) REVERT: F 53 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7396 (mp) REVERT: B 347 PHE cc_start: 0.8219 (m-80) cc_final: 0.7885 (m-80) REVERT: B 371 TYR cc_start: 0.7574 (m-80) cc_final: 0.7272 (m-80) REVERT: B 593 SER cc_start: 0.8342 (m) cc_final: 0.8040 (p) REVERT: B 831 LYS cc_start: 0.8813 (tmtt) cc_final: 0.8610 (tptm) REVERT: D 53 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7553 (mp) REVERT: C 245 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: C 425 ASN cc_start: 0.7849 (t0) cc_final: 0.7632 (t0) REVERT: C 593 SER cc_start: 0.8521 (m) cc_final: 0.8319 (p) REVERT: E 53 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7478 (mp) REVERT: E 89 MET cc_start: 0.7428 (tmm) cc_final: 0.6607 (ttm) REVERT: I 28 MET cc_start: 0.4004 (pp-130) cc_final: 0.3695 (pp-130) REVERT: I 68 MET cc_start: 0.5315 (OUTLIER) cc_final: 0.4875 (tpt) outliers start: 76 outliers final: 56 residues processed: 622 average time/residue: 0.5794 time to fit residues: 435.6880 Evaluate side-chains 641 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 580 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 543 CYS Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 972 LEU Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain I residue 99 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: [184, 132, 278, 317, 298, 289, 74, 236, 212, 388, 392] chunk 184 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 278 optimal weight: 0.7980 chunk 317 optimal weight: 0.3980 chunk 298 optimal weight: 2.9990 chunk 289 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 236 optimal weight: 0.9990 chunk 212 optimal weight: 0.9990 chunk 388 optimal weight: 4.9990 chunk 392 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 301 GLN ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN A 814 ASN A1059 ASN ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1175 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN ** B1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 ASN C 814 ASN C1128 GLN I 99 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.160306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.127595 restraints weight = 37871.346| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.77 r_work: 0.3603 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 32166 Z= 0.189 Angle : 0.632 17.715 43833 Z= 0.320 Chirality : 0.047 0.357 5130 Planarity : 0.004 0.058 5502 Dihedral : 7.384 99.736 5811 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.18 % Allowed : 12.69 % Favored : 85.13 % 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: -0.02 (0.14), residues: 3873 helix: 1.49 (0.20), residues: 693 sheet: 0.10 (0.15), residues: 1101 loop : -0.54 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 314 TYR 0.031 0.002 TYR B 52 PHE 0.024 0.002 PHE C 411 TRP 0.009 0.001 TRP E 133 HIS 0.004 0.001 HIS C 951 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (32040) covalent geometry : angle 0.60487 / 0.31 (43509) SS BOND : bond 0.00629 / 0.46 ( 54) SS BOND : angle 2.60456 / 1.93 ( 108) hydrogen bonds : bond 0.04577 / 3.03 ( 1191) hydrogen bonds : angle 5.33275 / 3.69 ( 3678) link_ALPHA1-3 : bond 0.00488 / 0.24 ( 3) link_ALPHA1-3 : angle 1.72205 / 0.96 ( 9) link_ALPHA1-6 : bond 0.00916 / 0.46 ( 3) link_ALPHA1-6 : angle 1.41567 / 0.85 ( 9) link_BETA1-4 : bond 0.00296 / 0.19 ( 18) link_BETA1-4 : angle 1.91829 / 1.31 ( 54) link_NAG-ASN : bond 0.00399 / 0.27 ( 48) link_NAG-ASN : angle 2.04932 / 1.44 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 578 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 53 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7426 (mp) REVERT: F 70 SER cc_start: 0.8051 (t) cc_final: 0.7734 (m) REVERT: F 72 SER cc_start: 0.7733 (p) cc_final: 0.7513 (m) REVERT: B 347 PHE cc_start: 0.8238 (m-80) cc_final: 0.7890 (m-80) REVERT: B 371 TYR cc_start: 0.7573 (m-80) cc_final: 0.7264 (m-80) REVERT: B 593 SER cc_start: 0.8342 (m) cc_final: 0.8055 (p) REVERT: D 53 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7572 (mp) REVERT: C 206 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.7735 (m-80) REVERT: C 245 GLU cc_start: 0.7574 (mp0) cc_final: 0.7191 (mp0) REVERT: C 425 ASN cc_start: 0.7882 (t0) cc_final: 0.7666 (t0) REVERT: E 53 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7491 (mp) REVERT: I 28 MET cc_start: 0.3833 (pp-130) cc_final: 0.3548 (pp-130) REVERT: I 68 MET cc_start: 0.5349 (OUTLIER) cc_final: 0.4976 (tpt) outliers start: 73 outliers final: 51 residues processed: 610 average time/residue: 0.5888 time to fit residues: 432.5644 Evaluate side-chains 628 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 572 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 543 CYS Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 972 LEU Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain I residue 68 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: [190, 373, 103, 249, 351, 53, 261, 235, 138, 391, 315] chunk 190 optimal weight: 0.2980 chunk 373 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 249 optimal weight: 3.9990 chunk 351 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 235 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 391 optimal weight: 4.9990 chunk 315 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 233 ASN A 301 GLN ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN A 814 ASN A1059 ASN A1082 GLN A1175 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 GLN B1055 GLN B1059 ASN C 814 ASN C1128 GLN I 99 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.160725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.128002 restraints weight = 38011.401| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.78 r_work: 0.3612 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 32166 Z= 0.163 Angle : 0.626 17.007 43833 Z= 0.316 Chirality : 0.046 0.341 5130 Planarity : 0.004 0.058 5502 Dihedral : 7.272 99.192 5811 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.00 % Allowed : 13.05 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.03 (0.14), residues: 3873 helix: 1.54 (0.20), residues: 693 sheet: 0.19 (0.16), residues: 1074 loop : -0.56 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 314 TYR 0.032 0.001 TYR B 52 PHE 0.021 0.001 PHE C 411 TRP 0.010 0.001 TRP D 55 HIS 0.004 0.001 HIS C 951 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (32040) covalent geometry : angle 0.59620 / 0.31 (43509) SS BOND : bond 0.00667 / 0.49 ( 54) SS BOND : angle 2.67781 / 1.99 ( 108) hydrogen bonds : bond 0.04394 / 2.91 ( 1191) hydrogen bonds : angle 5.27622 / 3.65 ( 3678) link_ALPHA1-3 : bond 0.00614 / 0.31 ( 3) link_ALPHA1-3 : angle 1.60394 / 0.90 ( 9) link_ALPHA1-6 : bond 0.00931 / 0.47 ( 3) link_ALPHA1-6 : angle 1.39069 / 0.84 ( 9) link_BETA1-4 : bond 0.00258 / 0.17 ( 18) link_BETA1-4 : angle 1.84709 / 1.26 ( 54) link_NAG-ASN : bond 0.00539 / 0.34 ( 48) link_NAG-ASN : angle 2.19574 / 1.50 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 576 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 53 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7426 (mp) REVERT: F 70 SER cc_start: 0.8045 (t) cc_final: 0.7749 (m) REVERT: F 72 SER cc_start: 0.7731 (p) cc_final: 0.7518 (m) REVERT: B 347 PHE cc_start: 0.8224 (m-80) cc_final: 0.7841 (m-80) REVERT: B 509 ASP cc_start: 0.7935 (t70) cc_final: 0.7723 (t70) REVERT: B 593 SER cc_start: 0.8341 (m) cc_final: 0.8057 (p) REVERT: B 979 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7908 (tm130) REVERT: D 53 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7583 (mp) REVERT: C 245 GLU cc_start: 0.7560 (mp0) cc_final: 0.7181 (mp0) REVERT: C 425 ASN cc_start: 0.7885 (t0) cc_final: 0.7658 (t0) REVERT: E 53 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7486 (mp) REVERT: E 89 MET cc_start: 0.7501 (tmm) cc_final: 0.7101 (ttm) REVERT: I 28 MET cc_start: 0.3913 (pp-130) cc_final: 0.3639 (pp-130) REVERT: I 68 MET cc_start: 0.5374 (OUTLIER) cc_final: 0.5057 (tpt) outliers start: 67 outliers final: 50 residues processed: 606 average time/residue: 0.5894 time to fit residues: 429.8273 Evaluate side-chains 628 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 573 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 979 GLN Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 543 CYS Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 972 LEU Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain I residue 68 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: [122, 7, 371, 239, 34, 87, 213, 31, 12, 105, 202] chunk 122 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 371 optimal weight: 1.9990 chunk 239 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 87 optimal weight: 0.0970 chunk 213 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 202 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 301 GLN ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN A 814 ASN A1059 ASN A1175 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1055 GLN B1059 ASN C 470 GLN C 814 ASN I 99 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.160779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.128161 restraints weight = 38023.391| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.76 r_work: 0.3614 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 32166 Z= 0.160 Angle : 0.628 16.957 43833 Z= 0.317 Chirality : 0.047 0.353 5130 Planarity : 0.004 0.058 5502 Dihedral : 7.228 98.985 5811 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.82 % Allowed : 13.47 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.14), residues: 3873 helix: 1.52 (0.20), residues: 693 sheet: 0.19 (0.16), residues: 1074 loop : -0.54 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 314 TYR 0.031 0.001 TYR B 52 PHE 0.021 0.001 PHE C 411 TRP 0.009 0.001 TRP D 55 HIS 0.004 0.001 HIS C 951 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (32040) covalent geometry : angle 0.60118 / 0.31 (43509) SS BOND : bond 0.00701 / 0.52 ( 54) SS BOND : angle 2.57394 / 1.91 ( 108) hydrogen bonds : bond 0.04375 / 2.91 ( 1191) hydrogen bonds : angle 5.24519 / 3.64 ( 3678) link_ALPHA1-3 : bond 0.00624 / 0.31 ( 3) link_ALPHA1-3 : angle 1.61057 / 0.91 ( 9) link_ALPHA1-6 : bond 0.00952 / 0.48 ( 3) link_ALPHA1-6 : angle 1.38558 / 0.83 ( 9) link_BETA1-4 : bond 0.00235 / 0.16 ( 18) link_BETA1-4 : angle 1.83738 / 1.26 ( 54) link_NAG-ASN : bond 0.00543 / 0.35 ( 48) link_NAG-ASN : angle 2.11544 / 1.45 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7746 Ramachandran restraints generated. 3873 Oldfield, 0 Emsley, 3873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 577 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 53 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7423 (mp) REVERT: F 70 SER cc_start: 0.8039 (t) cc_final: 0.7749 (m) REVERT: F 72 SER cc_start: 0.7732 (p) cc_final: 0.7521 (m) REVERT: B 509 ASP cc_start: 0.7930 (t70) cc_final: 0.7714 (t70) REVERT: B 593 SER cc_start: 0.8327 (m) cc_final: 0.8052 (p) REVERT: D 53 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7554 (mp) REVERT: C 245 GLU cc_start: 0.7537 (mp0) cc_final: 0.7178 (mp0) REVERT: C 425 ASN cc_start: 0.7876 (t0) cc_final: 0.7659 (t0) REVERT: E 53 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7486 (mp) REVERT: E 89 MET cc_start: 0.7500 (tmm) cc_final: 0.7110 (ttm) REVERT: I 28 MET cc_start: 0.3893 (pp-130) cc_final: 0.3626 (pp-130) REVERT: I 68 MET cc_start: 0.5382 (OUTLIER) cc_final: 0.5058 (tpt) outliers start: 61 outliers final: 53 residues processed: 602 average time/residue: 0.6010 time to fit residues: 435.3907 Evaluate side-chains 633 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 576 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 543 CYS Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 972 LEU Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain I residue 99 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: [2, 313, 148, 228, 260, 157, 352, 338, 169, 244, 59] chunk 2 optimal weight: 0.9980 chunk 313 optimal weight: 0.0980 chunk 148 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 260 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 352 optimal weight: 0.1980 chunk 338 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 301 GLN ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN A 814 ASN A1059 ASN A1128 GLN A1175 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1055 GLN B1059 ASN C 470 GLN C 814 ASN C1128 GLN I 99 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.160912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.128253 restraints weight = 38078.635| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.77 r_work: 0.3619 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 32166 Z= 0.153 Angle : 0.618 16.666 43833 Z= 0.313 Chirality : 0.046 0.336 5130 Planarity : 0.004 0.057 5502 Dihedral : 7.143 98.691 5811 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.06 % Allowed : 13.14 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3873 helix: 1.55 (0.20), residues: 693 sheet: 0.22 (0.16), residues: 1071 loop : -0.54 (0.14), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 314 TYR 0.031 0.001 TYR B 52 PHE 0.027 0.001 PHE C 411 TRP 0.009 0.001 TRP D 55 HIS 0.003 0.001 HIS C 951 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (32040) covalent geometry : angle 0.59246 / 0.30 (43509) SS BOND : bond 0.00680 / 0.50 ( 54) SS BOND : angle 2.59186 / 1.90 ( 108) hydrogen bonds : bond 0.04290 / 2.85 ( 1191) hydrogen bonds : angle 5.20722 / 3.61 ( 3678) link_ALPHA1-3 : bond 0.00660 / 0.33 ( 3) link_ALPHA1-3 : angle 1.61182 / 0.91 ( 9) link_ALPHA1-6 : bond 0.00963 / 0.48 ( 3) link_ALPHA1-6 : angle 1.38746 / 0.84 ( 9) link_BETA1-4 : bond 0.00232 / 0.16 ( 18) link_BETA1-4 : angle 1.80373 / 1.24 ( 54) link_NAG-ASN : bond 0.00353 / 0.24 ( 48) link_NAG-ASN : angle 1.90025 / 1.34 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19738.87 seconds wall clock time: 334 minutes 1.69 seconds (20041.69 seconds total)