Starting phenix.real_space_refine on Thu Mar 5 22:43:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v7a_31764/03_2026/7v7a_31764.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7a_31764/03_2026/7v7a_31764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v7a_31764/03_2026/7v7a_31764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7a_31764/03_2026/7v7a_31764.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v7a_31764/03_2026/7v7a_31764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7a_31764/03_2026/7v7a_31764.map" } resolution = 3.4 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= -0.002 sd= 0.050 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 111 5.16 5 C 16279 2.51 5 N 4121 2.21 5 O 5068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25579 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8110 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Chain: "C" Number of atoms: 8158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 8158 Classifications: {'peptide': 1043} Link IDs: {'PTRANS': 53, 'TRANS': 989} Chain breaks: 7 Chain: "B" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8110 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" 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: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" 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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.97, per 1000 atoms: 0.27 Number of scatterers: 25579 At special positions: 0 Unit cell: (147.4, 154, 198, 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 111 16.00 O 5068 8.00 N 4121 7.00 C 16279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 165 " " NAG A2004 " - " ASN A 603 " " NAG A2005 " - " ASN A 657 " " NAG A2006 " - " ASN A 188 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 165 " " NAG B2004 " - " ASN B 603 " " NAG B2005 " - " ASN B 657 " " NAG B2006 " - " ASN B 20 " " NAG B2007 " - " ASN B 188 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 122 " " NAG C2003 " - " ASN C 165 " " NAG C2004 " - " ASN C 331 " " NAG C2005 " - " ASN C 603 " " NAG C2006 " - " ASN C 657 " " NAG C2007 " - " ASN C 20 " " NAG C2008 " - " ASN C 188 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 343 " " NAG H 1 " - " ASN A 616 " " NAG I 1 " - " ASN A 709 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN A 20 " " NAG P 1 " - " ASN C 234 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C 343 " " NAG S 1 " - " ASN C 616 " " NAG T 1 " - " ASN C 709 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1074 " " NAG X 1 " - " ASN C1098 " " NAG Y 1 " - " ASN C1134 " " NAG Z 1 " - " ASN B 234 " " NAG a 1 " - " ASN B 282 " " NAG b 1 " - " ASN B 331 " " NAG c 1 " - " ASN B 616 " " NAG d 1 " - " ASN B 709 " " NAG e 1 " - " ASN B 717 " " NAG f 1 " - " ASN B 801 " " NAG g 1 " - " ASN B1074 " " NAG h 1 " - " ASN B1098 " " NAG i 1 " - " ASN B1134 " Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5836 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 45 sheets defined 24.3% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.034A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.392A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.593A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.714A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 removed outlier: 4.062A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.535A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 898 through 909 removed outlier: 4.054A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.550A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.636A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.908A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.567A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.879A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.734A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.143A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 633 through 638 removed outlier: 3.794A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.911A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.543A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.640A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.781A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.213A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.562A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.275A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.330A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.026A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.842A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 766 " --> pdb=" O GLN B 762 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.510A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 898 through 909 removed outlier: 3.768A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.613A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.763A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.465A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.674A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.904A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.527A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.166A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.662A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.250A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 573 through 576 removed outlier: 3.905A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.358A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.615A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.811A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.900A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.444A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.486A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.042A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.881A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 11.736A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.431A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.030A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 143 through 144 removed outlier: 5.783A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.810A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'C' and resid 361 through 362 removed outlier: 3.866A pdb=" N CYS C 525 " --> pdb=" O CYS C 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.776A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.680A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.929A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.993A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.509A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.071A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.747A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.213A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.210A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.114A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 711 through 712 Processing sheet with id=AE6, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.584A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'B' and resid 1081 through 1083 removed outlier: 4.831A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 1094 through 1097 981 hydrogen bonds defined for protein. 2652 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.75 Time building geometry restraints manager: 3.39 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: 8008 1.34 - 1.47: 6749 1.47 - 1.59: 11251 1.59 - 1.71: 0 1.71 - 1.84: 138 Bond restraints: 26146 Sorted by residual: bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C1 NAG g 1 " pdb=" O5 NAG g 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.33e+00 bond pdb=" C1 NAG W 1 " pdb=" O5 NAG W 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C1 NAG d 1 " pdb=" O5 NAG d 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.95e+00 bond pdb=" C1 NAG i 1 " pdb=" O5 NAG i 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.77e+00 ... (remaining 26141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 34914 2.01 - 4.01: 608 4.01 - 6.02: 50 6.02 - 8.02: 13 8.02 - 10.03: 2 Bond angle restraints: 35587 Sorted by residual: angle pdb=" N GLN B1002 " pdb=" CA GLN B1002 " pdb=" CB GLN B1002 " ideal model delta sigma weight residual 110.12 116.03 -5.91 1.47e+00 4.63e-01 1.62e+01 angle pdb=" N ILE C 805 " pdb=" CA ILE C 805 " pdb=" C ILE C 805 " ideal model delta sigma weight residual 113.53 110.01 3.52 9.80e-01 1.04e+00 1.29e+01 angle pdb=" CA GLN B1002 " pdb=" CB GLN B1002 " pdb=" CG GLN B1002 " ideal model delta sigma weight residual 114.10 120.76 -6.66 2.00e+00 2.50e-01 1.11e+01 angle pdb=" N GLY A 103 " pdb=" CA GLY A 103 " pdb=" C GLY A 103 " ideal model delta sigma weight residual 112.06 117.49 -5.43 1.66e+00 3.63e-01 1.07e+01 angle pdb=" N VAL A 729 " pdb=" CA VAL A 729 " pdb=" C VAL A 729 " ideal model delta sigma weight residual 113.71 110.68 3.03 9.50e-01 1.11e+00 1.02e+01 ... (remaining 35582 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.63: 15488 22.63 - 45.26: 916 45.26 - 67.89: 166 67.89 - 90.52: 44 90.52 - 113.15: 28 Dihedral angle restraints: 16642 sinusoidal: 7561 harmonic: 9081 Sorted by residual: dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -176.41 90.41 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -171.72 85.72 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -3.56 -82.44 1 1.00e+01 1.00e-02 8.34e+01 ... (remaining 16639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3669 0.067 - 0.135: 588 0.135 - 0.202: 18 0.202 - 0.269: 2 0.269 - 0.336: 8 Chirality restraints: 4285 Sorted by residual: chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C1 NAG C2002 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C2002 " pdb=" O5 NAG C2002 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C1 NAG B2001 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B2001 " pdb=" O5 NAG B2001 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 4282 not shown) Planarity restraints: 4534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.79e+00 pdb=" N PRO A 986 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO A 295 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 61 " 0.023 2.00e-02 2.50e+03 2.07e-02 5.37e+00 pdb=" CG ASN B 61 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN B 61 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 61 " -0.018 2.00e-02 2.50e+03 pdb=" C1 NAG B2001 " 0.021 2.00e-02 2.50e+03 ... (remaining 4531 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 629 2.69 - 3.24: 24297 3.24 - 3.79: 37674 3.79 - 4.35: 48125 4.35 - 4.90: 81809 Nonbonded interactions: 192534 Sorted by model distance: nonbonded pdb=" OG SER C 349 " pdb=" O LEU C 452 " model vdw 2.137 3.040 nonbonded pdb=" OG1 THR C 716 " pdb=" O GLN C1071 " model vdw 2.175 3.040 nonbonded pdb=" OG1 THR A 716 " pdb=" O GLN A1071 " model vdw 2.177 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.189 3.040 nonbonded pdb=" NZ LYS C 378 " pdb=" OH TYR C 380 " model vdw 2.211 3.120 ... (remaining 192529 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 14 through 2006) selection = (chain 'C' and (resid 14 through 621 or resid 635 through 827 or resid 855 throu \ gh 2006)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.180 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 0.080 26271 Z= 0.184 Angle : 0.663 16.131 35923 Z= 0.312 Chirality : 0.047 0.336 4285 Planarity : 0.004 0.060 4481 Dihedral : 14.861 113.148 10689 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.78 % Favored : 96.09 % Rotamer: Outliers : 0.04 % Allowed : 0.44 % Favored : 99.52 % 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: -0.10 (0.15), residues: 3071 helix: 1.94 (0.21), residues: 655 sheet: 0.38 (0.19), residues: 697 loop : -1.10 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 905 TYR 0.014 0.001 TYR C1067 PHE 0.014 0.001 PHE B 759 TRP 0.015 0.001 TRP C 436 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00371 (26146) covalent geometry : angle 0.60864 (35587) SS BOND : bond 0.00271 ( 39) SS BOND : angle 1.33227 ( 78) hydrogen bonds : bond 0.12362 ( 981) hydrogen bonds : angle 5.74563 ( 2652) link_BETA1-4 : bond 0.00543 ( 33) link_BETA1-4 : angle 2.06769 ( 99) link_NAG-ASN : bond 0.00598 ( 53) link_NAG-ASN : angle 3.58579 ( 159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 577 ARG cc_start: 0.7646 (ttm170) cc_final: 0.7303 (ttm-80) REVERT: A 969 ASN cc_start: 0.8878 (m110) cc_final: 0.8668 (m110) REVERT: C 31 SER cc_start: 0.9213 (t) cc_final: 0.8795 (p) REVERT: C 52 GLN cc_start: 0.8324 (pp30) cc_final: 0.7918 (pp30) REVERT: C 160 TYR cc_start: 0.8243 (p90) cc_final: 0.8039 (p90) REVERT: C 441 LEU cc_start: 0.9351 (mm) cc_final: 0.9150 (mm) REVERT: C 740 MET cc_start: 0.7754 (mtp) cc_final: 0.7517 (mtt) REVERT: C 776 LYS cc_start: 0.8892 (tmtt) cc_final: 0.8663 (ptmm) REVERT: C 886 TRP cc_start: 0.8592 (p90) cc_final: 0.8021 (p90) REVERT: C 900 MET cc_start: 0.7182 (mtt) cc_final: 0.6955 (mtp) REVERT: C 950 ASP cc_start: 0.8612 (t70) cc_final: 0.8351 (t0) REVERT: B 329 PHE cc_start: 0.7689 (m-10) cc_final: 0.7186 (m-10) REVERT: B 740 MET cc_start: 0.7738 (mtp) cc_final: 0.7432 (mtm) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.1564 time to fit residues: 52.5983 Evaluate side-chains 125 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.1980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 957 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN B 764 ASN B 777 ASN B 913 GLN B1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.160474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.099405 restraints weight = 42792.464| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.99 r_work: 0.3097 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26271 Z= 0.179 Angle : 0.671 15.427 35923 Z= 0.321 Chirality : 0.047 0.329 4285 Planarity : 0.004 0.059 4481 Dihedral : 10.428 97.150 5152 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.79 % Favored : 95.08 % Rotamer: Outliers : 0.62 % Allowed : 6.79 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.21 (0.15), residues: 3071 helix: 1.77 (0.21), residues: 641 sheet: 0.31 (0.19), residues: 713 loop : -1.12 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.022 0.001 TYR B1067 PHE 0.025 0.002 PHE B 906 TRP 0.013 0.001 TRP B 104 HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00429 (26146) covalent geometry : angle 0.61841 (35587) SS BOND : bond 0.00356 ( 39) SS BOND : angle 1.61009 ( 78) hydrogen bonds : bond 0.05006 ( 981) hydrogen bonds : angle 4.95052 ( 2652) link_BETA1-4 : bond 0.00531 ( 33) link_BETA1-4 : angle 1.95946 ( 99) link_NAG-ASN : bond 0.00525 ( 53) link_NAG-ASN : angle 3.53055 ( 159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 52 GLN cc_start: 0.8304 (pp30) cc_final: 0.7979 (pp30) REVERT: C 441 LEU cc_start: 0.9385 (mm) cc_final: 0.9131 (mm) REVERT: C 495 TYR cc_start: 0.7567 (m-80) cc_final: 0.6961 (m-80) REVERT: C 900 MET cc_start: 0.8439 (mtt) cc_final: 0.8131 (mtt) REVERT: C 950 ASP cc_start: 0.8757 (t70) cc_final: 0.8506 (t0) outliers start: 17 outliers final: 11 residues processed: 145 average time/residue: 0.1399 time to fit residues: 35.3051 Evaluate side-chains 125 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 25 optimal weight: 0.0870 chunk 187 optimal weight: 3.9990 chunk 237 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN C 239 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN B 542 ASN B1106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.160981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.100907 restraints weight = 42672.414| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 4.00 r_work: 0.3105 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26271 Z= 0.135 Angle : 0.615 14.584 35923 Z= 0.292 Chirality : 0.046 0.334 4285 Planarity : 0.004 0.058 4481 Dihedral : 9.238 93.545 5152 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 1.21 % Allowed : 8.85 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3071 helix: 1.85 (0.21), residues: 633 sheet: 0.22 (0.19), residues: 732 loop : -1.08 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.019 0.001 TYR C1067 PHE 0.021 0.001 PHE C 429 TRP 0.013 0.001 TRP B 104 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00316 (26146) covalent geometry : angle 0.55766 (35587) SS BOND : bond 0.00409 ( 39) SS BOND : angle 1.48979 ( 78) hydrogen bonds : bond 0.04563 ( 981) hydrogen bonds : angle 4.71071 ( 2652) link_BETA1-4 : bond 0.00586 ( 33) link_BETA1-4 : angle 1.95580 ( 99) link_NAG-ASN : bond 0.00581 ( 53) link_NAG-ASN : angle 3.51752 ( 159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 369 TYR cc_start: 0.8742 (t80) cc_final: 0.8503 (t80) REVERT: A 856 ASN cc_start: 0.8404 (t0) cc_final: 0.7993 (t0) REVERT: C 52 GLN cc_start: 0.8282 (pp30) cc_final: 0.7927 (pp30) REVERT: C 239 GLN cc_start: 0.6661 (OUTLIER) cc_final: 0.6344 (pp30) REVERT: C 495 TYR cc_start: 0.7575 (m-80) cc_final: 0.6920 (m-80) REVERT: C 661 GLU cc_start: 0.7735 (tp30) cc_final: 0.7399 (tm-30) REVERT: C 900 MET cc_start: 0.8357 (mtt) cc_final: 0.8037 (mtt) REVERT: B 1031 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7696 (mp0) outliers start: 33 outliers final: 15 residues processed: 160 average time/residue: 0.1458 time to fit residues: 40.5846 Evaluate side-chains 131 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 142 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 182 optimal weight: 0.0670 chunk 101 optimal weight: 0.8980 chunk 288 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN C 125 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.160179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.098075 restraints weight = 42696.304| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.87 r_work: 0.3101 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26271 Z= 0.152 Angle : 0.622 14.656 35923 Z= 0.296 Chirality : 0.046 0.340 4285 Planarity : 0.004 0.056 4481 Dihedral : 8.601 88.865 5152 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 1.25 % Allowed : 11.13 % Favored : 87.62 % 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: -0.21 (0.15), residues: 3071 helix: 1.82 (0.21), residues: 633 sheet: 0.19 (0.19), residues: 740 loop : -1.09 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.019 0.001 TYR C1067 PHE 0.023 0.001 PHE C 429 TRP 0.011 0.001 TRP B 104 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00363 (26146) covalent geometry : angle 0.56706 (35587) SS BOND : bond 0.00449 ( 39) SS BOND : angle 1.61947 ( 78) hydrogen bonds : bond 0.04714 ( 981) hydrogen bonds : angle 4.69724 ( 2652) link_BETA1-4 : bond 0.00497 ( 33) link_BETA1-4 : angle 1.94657 ( 99) link_NAG-ASN : bond 0.00545 ( 53) link_NAG-ASN : angle 3.43063 ( 159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 369 TYR cc_start: 0.8647 (t80) cc_final: 0.8347 (t80) REVERT: C 52 GLN cc_start: 0.8288 (pp30) cc_final: 0.7935 (pp30) REVERT: C 242 LEU cc_start: 0.7298 (tp) cc_final: 0.7045 (tp) REVERT: C 495 TYR cc_start: 0.7649 (m-80) cc_final: 0.6987 (m-80) REVERT: C 900 MET cc_start: 0.8447 (mtt) cc_final: 0.8128 (mtp) REVERT: B 1031 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7676 (mp0) outliers start: 34 outliers final: 21 residues processed: 151 average time/residue: 0.1415 time to fit residues: 37.7042 Evaluate side-chains 140 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 130 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 265 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 chunk 43 optimal weight: 20.0000 chunk 140 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 264 optimal weight: 0.5980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.159635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.097582 restraints weight = 42595.741| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.83 r_work: 0.3094 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26271 Z= 0.161 Angle : 0.628 14.617 35923 Z= 0.299 Chirality : 0.046 0.340 4285 Planarity : 0.004 0.052 4481 Dihedral : 8.131 83.265 5152 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.69 % Favored : 95.21 % Rotamer: Outliers : 1.51 % Allowed : 11.90 % Favored : 86.60 % 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: -0.27 (0.15), residues: 3071 helix: 1.79 (0.21), residues: 631 sheet: 0.17 (0.19), residues: 739 loop : -1.13 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1039 TYR 0.020 0.001 TYR C1067 PHE 0.026 0.001 PHE C 429 TRP 0.012 0.001 TRP A 104 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00389 (26146) covalent geometry : angle 0.57437 (35587) SS BOND : bond 0.00386 ( 39) SS BOND : angle 1.64031 ( 78) hydrogen bonds : bond 0.04810 ( 981) hydrogen bonds : angle 4.73340 ( 2652) link_BETA1-4 : bond 0.00530 ( 33) link_BETA1-4 : angle 1.95494 ( 99) link_NAG-ASN : bond 0.00540 ( 53) link_NAG-ASN : angle 3.41183 ( 159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 212 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6446 (tt) REVERT: A 369 TYR cc_start: 0.8654 (t80) cc_final: 0.8359 (t80) REVERT: A 977 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7844 (tt) REVERT: C 52 GLN cc_start: 0.8297 (pp30) cc_final: 0.7919 (pp30) REVERT: C 242 LEU cc_start: 0.7222 (tp) cc_final: 0.6937 (tp) REVERT: C 495 TYR cc_start: 0.7542 (m-80) cc_final: 0.6841 (m-80) REVERT: C 900 MET cc_start: 0.8473 (mtt) cc_final: 0.8147 (mtp) REVERT: B 1031 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7677 (mp0) outliers start: 41 outliers final: 30 residues processed: 160 average time/residue: 0.1393 time to fit residues: 39.4676 Evaluate side-chains 151 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 28 optimal weight: 10.0000 chunk 123 optimal weight: 30.0000 chunk 12 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 305 optimal weight: 0.9990 chunk 307 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 288 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.160567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.102434 restraints weight = 42798.371| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.98 r_work: 0.3105 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26271 Z= 0.130 Angle : 0.603 14.153 35923 Z= 0.287 Chirality : 0.045 0.340 4285 Planarity : 0.004 0.050 4481 Dihedral : 7.735 79.575 5152 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.69 % Favored : 95.21 % Rotamer: Outliers : 1.87 % Allowed : 12.45 % Favored : 85.68 % 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: -0.19 (0.15), residues: 3071 helix: 1.85 (0.21), residues: 632 sheet: 0.22 (0.19), residues: 720 loop : -1.08 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1039 TYR 0.019 0.001 TYR C1067 PHE 0.028 0.001 PHE C 429 TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00305 (26146) covalent geometry : angle 0.54989 (35587) SS BOND : bond 0.00350 ( 39) SS BOND : angle 1.46603 ( 78) hydrogen bonds : bond 0.04510 ( 981) hydrogen bonds : angle 4.62959 ( 2652) link_BETA1-4 : bond 0.00513 ( 33) link_BETA1-4 : angle 1.95338 ( 99) link_NAG-ASN : bond 0.00550 ( 53) link_NAG-ASN : angle 3.32521 ( 159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 128 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 212 LEU cc_start: 0.6652 (OUTLIER) cc_final: 0.6421 (tt) REVERT: A 369 TYR cc_start: 0.8756 (t80) cc_final: 0.8451 (t80) REVERT: A 560 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8825 (mp) REVERT: A 759 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7553 (t80) REVERT: A 856 ASN cc_start: 0.8435 (t0) cc_final: 0.7950 (t0) REVERT: A 977 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7827 (tt) REVERT: C 52 GLN cc_start: 0.8271 (pp30) cc_final: 0.7882 (pp30) REVERT: C 242 LEU cc_start: 0.7259 (tp) cc_final: 0.6969 (tp) REVERT: C 495 TYR cc_start: 0.7518 (m-80) cc_final: 0.6847 (m-80) REVERT: C 900 MET cc_start: 0.8424 (mtt) cc_final: 0.8092 (mtp) REVERT: C 957 GLN cc_start: 0.9337 (tp40) cc_final: 0.9090 (tp-100) REVERT: C 1072 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8336 (mp0) REVERT: B 204 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.6498 (m-80) REVERT: B 984 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8226 (pp) REVERT: B 1031 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7665 (mp0) outliers start: 51 outliers final: 27 residues processed: 172 average time/residue: 0.1402 time to fit residues: 42.7720 Evaluate side-chains 158 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 93 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 232 optimal weight: 0.1980 chunk 137 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 238 optimal weight: 6.9990 chunk 266 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.160681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.098721 restraints weight = 42779.235| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.95 r_work: 0.3103 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26271 Z= 0.134 Angle : 0.606 14.050 35923 Z= 0.288 Chirality : 0.045 0.337 4285 Planarity : 0.004 0.049 4481 Dihedral : 7.433 76.702 5152 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.59 % Favored : 95.31 % Rotamer: Outliers : 1.91 % Allowed : 12.85 % Favored : 85.24 % 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: -0.22 (0.15), residues: 3071 helix: 1.86 (0.21), residues: 630 sheet: 0.18 (0.19), residues: 732 loop : -1.10 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1039 TYR 0.019 0.001 TYR C1067 PHE 0.031 0.001 PHE C 429 TRP 0.020 0.001 TRP B 104 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00316 (26146) covalent geometry : angle 0.55339 (35587) SS BOND : bond 0.00350 ( 39) SS BOND : angle 1.42705 ( 78) hydrogen bonds : bond 0.04490 ( 981) hydrogen bonds : angle 4.58540 ( 2652) link_BETA1-4 : bond 0.00509 ( 33) link_BETA1-4 : angle 1.95487 ( 99) link_NAG-ASN : bond 0.00540 ( 53) link_NAG-ASN : angle 3.30945 ( 159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 132 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 212 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6403 (tt) REVERT: A 369 TYR cc_start: 0.8780 (t80) cc_final: 0.8446 (t80) REVERT: A 560 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8797 (mp) REVERT: A 759 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7609 (t80) REVERT: A 856 ASN cc_start: 0.8442 (t0) cc_final: 0.7947 (t0) REVERT: A 977 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7840 (tt) REVERT: A 1031 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: C 52 GLN cc_start: 0.8292 (pp30) cc_final: 0.7915 (pp30) REVERT: C 242 LEU cc_start: 0.7190 (tp) cc_final: 0.6903 (tp) REVERT: C 495 TYR cc_start: 0.7533 (m-80) cc_final: 0.6833 (m-80) REVERT: C 661 GLU cc_start: 0.7737 (tp30) cc_final: 0.7495 (tp30) REVERT: C 957 GLN cc_start: 0.9375 (tp40) cc_final: 0.9087 (tp-100) REVERT: C 1072 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8339 (mp0) REVERT: B 204 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.6393 (m-80) REVERT: B 902 MET cc_start: 0.8586 (tpp) cc_final: 0.8301 (tpt) REVERT: B 1031 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7706 (mp0) outliers start: 52 outliers final: 35 residues processed: 176 average time/residue: 0.1385 time to fit residues: 43.0234 Evaluate side-chains 158 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 203 optimal weight: 0.5980 chunk 303 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 126 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 230 optimal weight: 0.5980 chunk 251 optimal weight: 50.0000 chunk 123 optimal weight: 30.0000 chunk 214 optimal weight: 3.9990 chunk 255 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.161203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.099374 restraints weight = 42670.513| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.89 r_work: 0.3122 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26271 Z= 0.118 Angle : 0.602 13.722 35923 Z= 0.284 Chirality : 0.045 0.337 4285 Planarity : 0.004 0.050 4481 Dihedral : 7.212 73.957 5152 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.43 % Favored : 95.47 % Rotamer: Outliers : 1.76 % Allowed : 13.40 % Favored : 84.83 % 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: -0.16 (0.15), residues: 3071 helix: 1.92 (0.21), residues: 633 sheet: 0.22 (0.19), residues: 722 loop : -1.06 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 355 TYR 0.018 0.001 TYR C1067 PHE 0.030 0.001 PHE C 429 TRP 0.017 0.001 TRP B 104 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00272 (26146) covalent geometry : angle 0.54876 (35587) SS BOND : bond 0.00336 ( 39) SS BOND : angle 1.75674 ( 78) hydrogen bonds : bond 0.04273 ( 981) hydrogen bonds : angle 4.53298 ( 2652) link_BETA1-4 : bond 0.00560 ( 33) link_BETA1-4 : angle 1.97139 ( 99) link_NAG-ASN : bond 0.00553 ( 53) link_NAG-ASN : angle 3.24698 ( 159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 126 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 212 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6389 (tt) REVERT: A 369 TYR cc_start: 0.8776 (t80) cc_final: 0.8454 (t80) REVERT: A 560 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8763 (mp) REVERT: A 759 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7469 (t80) REVERT: A 856 ASN cc_start: 0.8438 (t0) cc_final: 0.7947 (t0) REVERT: A 977 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7805 (tt) REVERT: A 1031 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: A 1132 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8027 (pp) REVERT: C 52 GLN cc_start: 0.8285 (pp30) cc_final: 0.7882 (pp30) REVERT: C 242 LEU cc_start: 0.7308 (tp) cc_final: 0.7040 (tp) REVERT: C 495 TYR cc_start: 0.7532 (m-80) cc_final: 0.6845 (m-80) REVERT: C 581 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8560 (p) REVERT: C 900 MET cc_start: 0.8394 (mtt) cc_final: 0.8067 (mtt) REVERT: C 957 GLN cc_start: 0.9362 (tp40) cc_final: 0.9080 (tp-100) REVERT: C 1072 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8271 (mp0) REVERT: B 1031 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: B 1132 ILE cc_start: 0.8147 (pt) cc_final: 0.7795 (pt) outliers start: 48 outliers final: 30 residues processed: 166 average time/residue: 0.1433 time to fit residues: 41.7856 Evaluate side-chains 160 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 0.8980 chunk 281 optimal weight: 0.9990 chunk 239 optimal weight: 0.8980 chunk 284 optimal weight: 0.6980 chunk 248 optimal weight: 30.0000 chunk 157 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 93 optimal weight: 0.0270 chunk 155 optimal weight: 1.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.161662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.099947 restraints weight = 42871.019| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.86 r_work: 0.3107 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26271 Z= 0.116 Angle : 0.600 13.508 35923 Z= 0.285 Chirality : 0.045 0.336 4285 Planarity : 0.004 0.050 4481 Dihedral : 7.066 71.270 5152 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.43 % Favored : 95.47 % Rotamer: Outliers : 1.76 % Allowed : 13.59 % Favored : 84.65 % 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: -0.13 (0.15), residues: 3071 helix: 1.93 (0.21), residues: 634 sheet: 0.25 (0.19), residues: 727 loop : -1.05 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 214 TYR 0.018 0.001 TYR C1067 PHE 0.032 0.001 PHE C 429 TRP 0.016 0.001 TRP B 104 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00265 (26146) covalent geometry : angle 0.54876 (35587) SS BOND : bond 0.00324 ( 39) SS BOND : angle 1.61971 ( 78) hydrogen bonds : bond 0.04202 ( 981) hydrogen bonds : angle 4.49588 ( 2652) link_BETA1-4 : bond 0.00530 ( 33) link_BETA1-4 : angle 1.94469 ( 99) link_NAG-ASN : bond 0.00549 ( 53) link_NAG-ASN : angle 3.21590 ( 159) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 131 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 212 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6383 (tt) REVERT: A 369 TYR cc_start: 0.8732 (t80) cc_final: 0.8464 (t80) REVERT: A 560 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8763 (mp) REVERT: A 759 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7555 (t80) REVERT: A 856 ASN cc_start: 0.8439 (t0) cc_final: 0.7945 (t0) REVERT: A 977 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7839 (tt) REVERT: A 1031 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: A 1132 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8070 (pp) REVERT: C 52 GLN cc_start: 0.8283 (pp30) cc_final: 0.7884 (pp30) REVERT: C 242 LEU cc_start: 0.7364 (tp) cc_final: 0.7120 (tp) REVERT: C 495 TYR cc_start: 0.7548 (m-80) cc_final: 0.6869 (m-80) REVERT: C 581 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8560 (p) REVERT: C 661 GLU cc_start: 0.7730 (tp30) cc_final: 0.7482 (tp30) REVERT: C 900 MET cc_start: 0.8424 (mtt) cc_final: 0.8091 (mtt) REVERT: C 957 GLN cc_start: 0.9332 (tp40) cc_final: 0.9020 (tp-100) REVERT: C 1072 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8287 (mp0) REVERT: B 237 ARG cc_start: 0.7242 (mtp180) cc_final: 0.6449 (mtt90) REVERT: B 1031 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: B 1132 ILE cc_start: 0.8137 (pt) cc_final: 0.7787 (pt) outliers start: 48 outliers final: 37 residues processed: 172 average time/residue: 0.1467 time to fit residues: 44.3075 Evaluate side-chains 167 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 231 optimal weight: 0.9980 chunk 274 optimal weight: 3.9990 chunk 296 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 226 optimal weight: 7.9990 chunk 204 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.158162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.094929 restraints weight = 42734.525| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.90 r_work: 0.3070 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 26271 Z= 0.215 Angle : 0.675 14.706 35923 Z= 0.326 Chirality : 0.047 0.333 4285 Planarity : 0.004 0.052 4481 Dihedral : 7.235 70.999 5152 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.50 % Favored : 94.37 % Rotamer: Outliers : 1.87 % Allowed : 13.55 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.40 (0.15), residues: 3071 helix: 1.57 (0.21), residues: 641 sheet: 0.10 (0.19), residues: 749 loop : -1.20 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1039 TYR 0.022 0.001 TYR C1067 PHE 0.032 0.002 PHE C 429 TRP 0.014 0.001 TRP B 104 HIS 0.007 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00524 (26146) covalent geometry : angle 0.62248 (35587) SS BOND : bond 0.00435 ( 39) SS BOND : angle 1.90425 ( 78) hydrogen bonds : bond 0.05389 ( 981) hydrogen bonds : angle 4.80729 ( 2652) link_BETA1-4 : bond 0.00465 ( 33) link_BETA1-4 : angle 1.94866 ( 99) link_NAG-ASN : bond 0.00499 ( 53) link_NAG-ASN : angle 3.47248 ( 159) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 120 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6460 (tt) REVERT: A 369 TYR cc_start: 0.8806 (t80) cc_final: 0.8501 (t80) REVERT: A 560 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8731 (mp) REVERT: A 759 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7703 (t80) REVERT: A 977 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7923 (tt) REVERT: A 1031 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: A 1132 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8357 (pp) REVERT: C 52 GLN cc_start: 0.8330 (pp30) cc_final: 0.7963 (pp30) REVERT: C 134 GLN cc_start: 0.8130 (tp40) cc_final: 0.7735 (tp40) REVERT: C 242 LEU cc_start: 0.7210 (tp) cc_final: 0.6921 (tp) REVERT: C 581 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8564 (p) REVERT: C 855 PHE cc_start: 0.6834 (m-10) cc_final: 0.6396 (m-10) REVERT: C 957 GLN cc_start: 0.9364 (tp40) cc_final: 0.9044 (tp-100) REVERT: C 1072 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8466 (mp0) REVERT: B 204 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.6463 (m-80) REVERT: B 237 ARG cc_start: 0.7102 (mtp180) cc_final: 0.6422 (mtt90) REVERT: B 1031 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7635 (mp0) outliers start: 51 outliers final: 36 residues processed: 163 average time/residue: 0.1508 time to fit residues: 43.3724 Evaluate side-chains 161 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 115 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 196 optimal weight: 0.6980 chunk 139 optimal weight: 0.4980 chunk 184 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 204 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 774 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.160543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.097708 restraints weight = 42371.677| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.86 r_work: 0.3121 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26271 Z= 0.123 Angle : 0.614 13.445 35923 Z= 0.292 Chirality : 0.045 0.336 4285 Planarity : 0.004 0.050 4481 Dihedral : 6.981 65.866 5152 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.40 % Favored : 95.47 % Rotamer: Outliers : 1.84 % Allowed : 13.66 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.15), residues: 3071 helix: 1.82 (0.21), residues: 638 sheet: 0.15 (0.19), residues: 721 loop : -1.10 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 357 TYR 0.018 0.001 TYR C1067 PHE 0.032 0.001 PHE C 429 TRP 0.016 0.001 TRP B 104 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00281 (26146) covalent geometry : angle 0.56360 (35587) SS BOND : bond 0.00331 ( 39) SS BOND : angle 1.59388 ( 78) hydrogen bonds : bond 0.04427 ( 981) hydrogen bonds : angle 4.57214 ( 2652) link_BETA1-4 : bond 0.00527 ( 33) link_BETA1-4 : angle 1.91173 ( 99) link_NAG-ASN : bond 0.00560 ( 53) link_NAG-ASN : angle 3.26512 ( 159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6993.42 seconds wall clock time: 120 minutes 19.85 seconds (7219.85 seconds total)