Starting phenix.real_space_refine on Sun Jul 5 04:38:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v7d_31767/07_2026/7v7d_31767.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7d_31767/07_2026/7v7d_31767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7v7d_31767/07_2026/7v7d_31767.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v7d_31767/07_2026/7v7d_31767.cif" model { file = "/net/cci-nas-00/data/ceres_data/7v7d_31767/07_2026/7v7d_31767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7d_31767/07_2026/7v7d_31767.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v7d_31767/07_2026/7v7d_31767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7d_31767/07_2026/7v7d_31767.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.038 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 16109 2.51 5 N 4113 2.21 5 O 5020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25353 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 8070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8070 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 53, 'TRANS': 978} Chain breaks: 7 Chain: "B" Number of atoms: 8065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8065 Classifications: {'peptide': 1031} Link IDs: {'PTRANS': 53, 'TRANS': 977} Chain breaks: 7 Chain: "C" Number of atoms: 8070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8070 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 53, 'TRANS': 978} Chain breaks: 7 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 6 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.75, per 1000 atoms: 0.23 Number of scatterers: 25353 At special positions: 0 Unit cell: (143, 151.8, 177.1, 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 5020 8.00 N 4113 7.00 C 16109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 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 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 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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 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=2.03 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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 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 j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 165 " " NAG A2003 " - " ASN A 234 " " NAG A2004 " - " ASN A 331 " " NAG A2005 " - " ASN A 603 " " NAG A2006 " - " ASN A 657 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 331 " " NAG B2003 " - " ASN B 603 " " NAG B2004 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 331 " " NAG C2003 " - " ASN C 603 " " NAG C2004 " - " ASN C 657 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 343 " " NAG G 1 " - " ASN A 616 " " NAG H 1 " - " ASN A 709 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 122 " " NAG O 1 " - " ASN B 165 " " NAG P 1 " - " ASN B 234 " " NAG Q 1 " - " ASN B 282 " " NAG R 1 " - " ASN B 343 " " NAG S 1 " - " ASN B 616 " " NAG T 1 " - " ASN B 709 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 801 " " NAG W 1 " - " ASN B1074 " " NAG X 1 " - " ASN B1098 " " NAG Y 1 " - " ASN B1134 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C 165 " " NAG b 1 " - " ASN C 234 " " NAG c 1 " - " ASN C 282 " " NAG d 1 " - " ASN C 343 " " NAG e 1 " - " ASN C 616 " " NAG f 1 " - " ASN C 709 " " NAG g 1 " - " ASN C 717 " " NAG h 1 " - " ASN C 801 " " NAG i 1 " - " ASN C1074 " " NAG j 1 " - " ASN C1098 " " NAG k 1 " - " ASN C1134 " Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 740.7 milliseconds 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5806 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 48 sheets defined 25.3% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 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 349 through 353 removed outlier: 3.581A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.816A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.879A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.506A 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 910 removed outlier: 3.676A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.503A 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: 3.606A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.635A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.931A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.424A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.563A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.340A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.568A 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: 3.759A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.671A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 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 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.470A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.808A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.885A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.513A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.554A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 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 984 removed outlier: 3.625A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.168A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.537A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 8.370A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.098A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.092A 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: 3.575A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.163A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 4.420A 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 removed outlier: 3.548A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 567 removed outlier: 3.804A 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: 6.038A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.452A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.449A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.863A 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 1120 through 1125 removed outlier: 4.693A 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 'B' and resid 27 through 30 removed outlier: 8.044A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.364A pdb=" N ALA B 222 " --> 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=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.990A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.553A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.165A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.615A pdb=" N VAL B 551 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.533A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.223A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.252A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.610A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.610A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.431A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.786A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.817A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.549A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.816A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.819A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 143 through 144 removed outlier: 5.193A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.198A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.607A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 565 through 567 removed outlier: 3.735A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.972A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.571A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.571A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.594A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.941A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 991 hydrogen bonds defined for protein. 2712 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: 5.34 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7990 1.35 - 1.47: 6812 1.47 - 1.60: 10965 1.60 - 1.72: 0 1.72 - 1.85: 138 Bond restraints: 25905 Sorted by residual: bond pdb=" C1 NAG i 1 " pdb=" O5 NAG i 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.30e+00 bond pdb=" C PRO B 986 " pdb=" N PRO B 987 " ideal model delta sigma weight residual 1.334 1.375 -0.042 2.34e-02 1.83e+03 3.16e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" CA ILE C 569 " pdb=" CB ILE C 569 " ideal model delta sigma weight residual 1.553 1.540 0.013 7.40e-03 1.83e+04 2.90e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.71e+00 ... (remaining 25900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 34792 2.38 - 4.76: 429 4.76 - 7.15: 26 7.15 - 9.53: 4 9.53 - 11.91: 2 Bond angle restraints: 35253 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 125.61 -11.21 2.30e+00 1.89e-01 2.37e+01 angle pdb=" N ILE B 468 " pdb=" CA ILE B 468 " pdb=" C ILE B 468 " ideal model delta sigma weight residual 113.20 109.48 3.72 9.60e-01 1.09e+00 1.51e+01 angle pdb=" N CYS A 432 " pdb=" CA CYS A 432 " pdb=" C CYS A 432 " ideal model delta sigma weight residual 107.88 113.18 -5.30 1.41e+00 5.03e-01 1.41e+01 angle pdb=" C PHE A 377 " pdb=" N LYS A 378 " pdb=" CA LYS A 378 " ideal model delta sigma weight residual 122.77 117.51 5.26 1.41e+00 5.03e-01 1.39e+01 angle pdb=" CA LEU A 560 " pdb=" CB LEU A 560 " pdb=" CG LEU A 560 " ideal model delta sigma weight residual 116.30 128.21 -11.91 3.50e+00 8.16e-02 1.16e+01 ... (remaining 35248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 13412 17.92 - 35.85: 1088 35.85 - 53.77: 209 53.77 - 71.70: 49 71.70 - 89.62: 17 Dihedral angle restraints: 14775 sinusoidal: 5757 harmonic: 9018 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual 93.00 -177.38 -89.62 1 1.00e+01 1.00e-02 9.54e+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 -170.64 84.64 1 1.00e+01 1.00e-02 8.70e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -165.00 79.00 1 1.00e+01 1.00e-02 7.77e+01 ... (remaining 14772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 4069 0.103 - 0.205: 171 0.205 - 0.308: 3 0.308 - 0.411: 0 0.411 - 0.513: 3 Chirality restraints: 4246 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.59e+00 chirality pdb=" C1 NAG B2002 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B2002 " pdb=" O5 NAG B2002 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.05e+00 chirality pdb=" C1 NAG B2004 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B2004 " pdb=" O5 NAG B2004 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.42e+00 ... (remaining 4243 not shown) Planarity restraints: 4503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO A 295 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 294 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO C 295 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " 0.036 5.00e-02 4.00e+02 5.42e-02 4.69e+00 pdb=" N PRO C 986 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " 0.030 5.00e-02 4.00e+02 ... (remaining 4500 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 378 2.65 - 3.21: 23144 3.21 - 3.78: 36900 3.78 - 4.34: 49394 4.34 - 4.90: 82524 Nonbonded interactions: 192340 Sorted by model distance: nonbonded pdb=" OG SER B 349 " pdb=" O ARG B 452 " model vdw 2.088 3.040 nonbonded pdb=" OE2 GLU A 725 " pdb=" NE2 HIS A1064 " model vdw 2.138 3.120 nonbonded pdb=" O GLU B 661 " pdb=" OH TYR B 695 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.206 3.040 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.214 3.040 ... (remaining 192335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 263 or resid 265 through 2004)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 263 or resid 265 through 2004)) } ncs_group { reference = chain 'D' selection = 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' selection = chain 'j' selection = chain 'k' } 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: 5.330 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.450 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 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:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 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 : 0.005 0.053 26023 Z= 0.210 Angle : 0.665 11.997 35571 Z= 0.323 Chirality : 0.048 0.513 4246 Planarity : 0.004 0.058 4455 Dihedral : 13.592 88.551 8861 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.27 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.16), residues: 3047 helix: 2.06 (0.22), residues: 667 sheet: 0.81 (0.19), residues: 729 loop : -1.28 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1039 TYR 0.018 0.001 TYR A 873 PHE 0.028 0.001 PHE A 906 TRP 0.023 0.002 TRP C 886 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.21 (25905) covalent geometry : angle 0.63046 / 0.32 (35253) SS BOND : bond 0.00426 / 0.26 ( 36) SS BOND : angle 1.49628 / 0.94 ( 72) hydrogen bonds : bond 0.14746 / 9.95 ( 967) hydrogen bonds : angle 6.57541 / 4.54 ( 2712) link_BETA1-4 : bond 0.00445 / 0.29 ( 34) link_BETA1-4 : angle 2.18708 / 1.58 ( 102) link_NAG-ASN : bond 0.00440 / 0.27 ( 48) link_NAG-ASN : angle 2.70127 / 1.72 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8062 (p90) cc_final: 0.7376 (p90) REVERT: A 981 LEU cc_start: 0.9042 (mt) cc_final: 0.8829 (mp) REVERT: B 153 MET cc_start: 0.5047 (tpt) cc_final: 0.4689 (tpt) REVERT: C 390 LEU cc_start: 0.8913 (mt) cc_final: 0.8643 (mp) REVERT: C 392 PHE cc_start: 0.7920 (m-80) cc_final: 0.7640 (m-80) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.4929 time to fit residues: 64.6789 Evaluate side-chains 73 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 394 ASN B 804 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.084127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.053955 restraints weight = 95616.859| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 4.25 r_work: 0.2907 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26023 Z= 0.143 Angle : 0.601 11.233 35571 Z= 0.298 Chirality : 0.046 0.437 4246 Planarity : 0.004 0.062 4455 Dihedral : 3.902 19.540 3320 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.33 % Allowed : 5.75 % Favored : 93.92 % 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: 0.05 (0.16), residues: 3047 helix: 1.93 (0.21), residues: 700 sheet: 0.75 (0.19), residues: 722 loop : -1.21 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.017 0.001 TYR B1067 PHE 0.020 0.001 PHE B 429 TRP 0.023 0.002 TRP B 436 HIS 0.002 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (25905) covalent geometry : angle 0.57051 / 0.29 (35253) SS BOND : bond 0.00428 / 0.25 ( 36) SS BOND : angle 1.49687 / 0.98 ( 72) hydrogen bonds : bond 0.05604 / 3.78 ( 967) hydrogen bonds : angle 5.51716 / 3.79 ( 2712) link_BETA1-4 : bond 0.00357 / 0.23 ( 34) link_BETA1-4 : angle 1.81886 / 1.32 ( 102) link_NAG-ASN : bond 0.00435 / 0.28 ( 48) link_NAG-ASN : angle 2.46554 / 1.58 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.5737 (tpt) cc_final: 0.5158 (tpt) REVERT: B 387 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8622 (mm) REVERT: B 456 PHE cc_start: 0.9431 (OUTLIER) cc_final: 0.9206 (t80) REVERT: B 636 TYR cc_start: 0.2991 (OUTLIER) cc_final: -0.0964 (p90) REVERT: C 153 MET cc_start: 0.4222 (ppp) cc_final: 0.3642 (ppp) REVERT: C 390 LEU cc_start: 0.8486 (mt) cc_final: 0.8123 (mp) outliers start: 9 outliers final: 2 residues processed: 88 average time/residue: 0.5761 time to fit residues: 60.5911 Evaluate side-chains 79 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 620 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 255 optimal weight: 9.9990 chunk 119 optimal weight: 0.0010 chunk 45 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 227 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 286 optimal weight: 1.9990 chunk 307 optimal weight: 0.7980 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 901 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 955 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.084168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.054105 restraints weight = 94866.815| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 4.22 r_work: 0.2918 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26023 Z= 0.126 Angle : 0.570 10.957 35571 Z= 0.282 Chirality : 0.045 0.431 4246 Planarity : 0.004 0.064 4455 Dihedral : 3.798 19.615 3320 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.66 % Allowed : 8.07 % Favored : 91.27 % 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: 0.11 (0.16), residues: 3047 helix: 2.01 (0.21), residues: 690 sheet: 0.78 (0.19), residues: 727 loop : -1.17 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.020 0.001 TYR B 473 PHE 0.026 0.001 PHE A 238 TRP 0.024 0.001 TRP B 436 HIS 0.002 0.000 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (25905) covalent geometry : angle 0.54043 / 0.28 (35253) SS BOND : bond 0.00366 / 0.21 ( 36) SS BOND : angle 1.31723 / 0.87 ( 72) hydrogen bonds : bond 0.05157 / 3.49 ( 967) hydrogen bonds : angle 5.31639 / 3.65 ( 2712) link_BETA1-4 : bond 0.00403 / 0.27 ( 34) link_BETA1-4 : angle 1.79025 / 1.29 ( 102) link_NAG-ASN : bond 0.00435 / 0.27 ( 48) link_NAG-ASN : angle 2.35536 / 1.49 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8561 (tt) REVERT: A 957 GLN cc_start: 0.9242 (tt0) cc_final: 0.9039 (tp-100) REVERT: B 153 MET cc_start: 0.5566 (tpt) cc_final: 0.4967 (tpt) REVERT: B 387 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8595 (mm) REVERT: B 636 TYR cc_start: 0.3014 (OUTLIER) cc_final: -0.0957 (p90) REVERT: B 1029 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8484 (tpp) REVERT: C 153 MET cc_start: 0.4074 (ppp) cc_final: 0.3651 (ppp) REVERT: C 505 TYR cc_start: 0.7403 (t80) cc_final: 0.7178 (t80) REVERT: C 524 VAL cc_start: 0.6598 (OUTLIER) cc_final: 0.6295 (m) outliers start: 18 outliers final: 5 residues processed: 91 average time/residue: 0.5701 time to fit residues: 62.3068 Evaluate side-chains 82 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 40.0000 chunk 197 optimal weight: 0.0070 chunk 61 optimal weight: 7.9990 chunk 260 optimal weight: 0.6980 chunk 245 optimal weight: 20.0000 chunk 145 optimal weight: 30.0000 chunk 158 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 214 optimal weight: 20.0000 chunk 154 optimal weight: 1.9990 chunk 237 optimal weight: 9.9990 overall best weight: 3.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS B 914 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.081727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.051218 restraints weight = 95695.410| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 4.24 r_work: 0.2831 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 26023 Z= 0.285 Angle : 0.698 10.317 35571 Z= 0.347 Chirality : 0.048 0.423 4246 Planarity : 0.005 0.083 4455 Dihedral : 4.274 22.589 3320 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.44 % Allowed : 10.31 % Favored : 88.25 % 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: 3047 helix: 1.70 (0.20), residues: 690 sheet: 0.47 (0.19), residues: 703 loop : -1.36 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 509 TYR 0.023 0.002 TYR C 369 PHE 0.026 0.002 PHE C 906 TRP 0.034 0.002 TRP C 436 HIS 0.005 0.001 HIS B1071 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.28 (25905) covalent geometry : angle 0.66997 / 0.34 (35253) SS BOND : bond 0.00487 / 0.30 ( 36) SS BOND : angle 1.88399 / 1.24 ( 72) hydrogen bonds : bond 0.06782 / 4.59 ( 967) hydrogen bonds : angle 5.72064 / 3.94 ( 2712) link_BETA1-4 : bond 0.00321 / 0.22 ( 34) link_BETA1-4 : angle 1.80487 / 1.29 ( 102) link_NAG-ASN : bond 0.00446 / 0.29 ( 48) link_NAG-ASN : angle 2.51131 / 1.64 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 73 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 636 TYR cc_start: 0.3197 (OUTLIER) cc_final: 0.2163 (p90) REVERT: A 1132 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.9055 (tp) REVERT: B 153 MET cc_start: 0.6127 (tpt) cc_final: 0.5584 (tpt) REVERT: B 387 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8766 (mm) REVERT: B 456 PHE cc_start: 0.9466 (OUTLIER) cc_final: 0.9160 (t80) REVERT: B 563 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6225 (mt0) REVERT: B 636 TYR cc_start: 0.3425 (OUTLIER) cc_final: -0.0823 (p90) REVERT: B 900 MET cc_start: 0.9389 (OUTLIER) cc_final: 0.9145 (mtm) REVERT: B 1029 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8739 (tpp) REVERT: C 81 ASN cc_start: 0.7102 (OUTLIER) cc_final: 0.6188 (p0) REVERT: C 153 MET cc_start: 0.4341 (OUTLIER) cc_final: 0.3758 (ppp) REVERT: C 524 VAL cc_start: 0.6869 (OUTLIER) cc_final: 0.6583 (m) REVERT: C 1002 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8842 (mp10) outliers start: 39 outliers final: 10 residues processed: 101 average time/residue: 0.5111 time to fit residues: 63.2847 Evaluate side-chains 91 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 1002 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 162 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 188 optimal weight: 0.8980 chunk 219 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.083268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.053109 restraints weight = 94481.082| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 4.24 r_work: 0.2884 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26023 Z= 0.125 Angle : 0.586 10.542 35571 Z= 0.289 Chirality : 0.045 0.429 4246 Planarity : 0.004 0.062 4455 Dihedral : 3.967 19.717 3320 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.52 % Rotamer: Outliers : 1.62 % Allowed : 11.45 % Favored : 86.92 % 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: -0.05 (0.15), residues: 3047 helix: 1.98 (0.21), residues: 689 sheet: 0.62 (0.19), residues: 721 loop : -1.29 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.016 0.001 TYR C1067 PHE 0.020 0.001 PHE A 157 TRP 0.025 0.002 TRP B 436 HIS 0.002 0.000 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (25905) covalent geometry : angle 0.55748 / 0.28 (35253) SS BOND : bond 0.00367 / 0.22 ( 36) SS BOND : angle 1.48830 / 1.00 ( 72) hydrogen bonds : bond 0.05444 / 3.69 ( 967) hydrogen bonds : angle 5.32937 / 3.66 ( 2712) link_BETA1-4 : bond 0.00421 / 0.28 ( 34) link_BETA1-4 : angle 1.81923 / 1.32 ( 102) link_NAG-ASN : bond 0.00422 / 0.27 ( 48) link_NAG-ASN : angle 2.28423 / 1.46 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 75 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: B 153 MET cc_start: 0.6087 (tpt) cc_final: 0.5513 (tpt) REVERT: B 387 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8787 (mm) REVERT: B 456 PHE cc_start: 0.9435 (OUTLIER) cc_final: 0.9140 (t80) REVERT: B 563 GLN cc_start: 0.6662 (OUTLIER) cc_final: 0.6200 (mt0) REVERT: B 636 TYR cc_start: 0.3157 (OUTLIER) cc_final: -0.0933 (p90) REVERT: C 81 ASN cc_start: 0.6781 (OUTLIER) cc_final: 0.5896 (p0) REVERT: C 153 MET cc_start: 0.4228 (OUTLIER) cc_final: 0.3731 (ppp) REVERT: C 524 VAL cc_start: 0.6703 (OUTLIER) cc_final: 0.6428 (m) REVERT: C 1002 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8762 (mp10) outliers start: 44 outliers final: 14 residues processed: 108 average time/residue: 0.4729 time to fit residues: 62.6518 Evaluate side-chains 92 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1002 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 308 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 218 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 81 ASN C 955 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.081495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.051068 restraints weight = 95786.590| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 4.22 r_work: 0.2833 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 26023 Z= 0.285 Angle : 0.696 10.325 35571 Z= 0.344 Chirality : 0.048 0.422 4246 Planarity : 0.004 0.058 4455 Dihedral : 4.302 20.964 3320 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.32 % Favored : 94.62 % Rotamer: Outliers : 1.69 % Allowed : 12.67 % Favored : 85.64 % 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: -0.34 (0.15), residues: 3047 helix: 1.75 (0.20), residues: 687 sheet: 0.35 (0.19), residues: 702 loop : -1.41 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1039 TYR 0.020 0.002 TYR A 636 PHE 0.022 0.002 PHE B1121 TRP 0.027 0.002 TRP B 436 HIS 0.005 0.001 HIS B1071 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.29 (25905) covalent geometry : angle 0.66870 / 0.34 (35253) SS BOND : bond 0.00530 / 0.33 ( 36) SS BOND : angle 1.91895 / 1.24 ( 72) hydrogen bonds : bond 0.06628 / 4.48 ( 967) hydrogen bonds : angle 5.63296 / 3.88 ( 2712) link_BETA1-4 : bond 0.00320 / 0.22 ( 34) link_BETA1-4 : angle 1.83286 / 1.31 ( 102) link_NAG-ASN : bond 0.00435 / 0.28 ( 48) link_NAG-ASN : angle 2.43013 / 1.59 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 71 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 636 TYR cc_start: 0.3290 (OUTLIER) cc_final: 0.2547 (p90) REVERT: A 957 GLN cc_start: 0.9277 (tt0) cc_final: 0.9059 (tp-100) REVERT: B 153 MET cc_start: 0.6554 (tpt) cc_final: 0.5782 (tpt) REVERT: B 387 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8806 (mm) REVERT: B 456 PHE cc_start: 0.9459 (OUTLIER) cc_final: 0.9157 (t80) REVERT: B 563 GLN cc_start: 0.6826 (OUTLIER) cc_final: 0.6315 (mt0) REVERT: B 636 TYR cc_start: 0.3344 (OUTLIER) cc_final: -0.1042 (p90) REVERT: B 1072 GLU cc_start: 0.9263 (OUTLIER) cc_final: 0.8903 (mp0) REVERT: C 81 ASN cc_start: 0.7214 (OUTLIER) cc_final: 0.6260 (p0) REVERT: C 153 MET cc_start: 0.4134 (OUTLIER) cc_final: 0.3757 (ppp) REVERT: C 524 VAL cc_start: 0.6939 (OUTLIER) cc_final: 0.6692 (m) REVERT: C 1002 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8812 (mp10) outliers start: 46 outliers final: 21 residues processed: 107 average time/residue: 0.4793 time to fit residues: 62.6380 Evaluate side-chains 97 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1002 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 247 optimal weight: 30.0000 chunk 228 optimal weight: 0.4980 chunk 198 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 289 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1002 GLN B1106 GLN C 955 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.083403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.053366 restraints weight = 94655.928| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 4.24 r_work: 0.2895 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26023 Z= 0.116 Angle : 0.597 10.232 35571 Z= 0.291 Chirality : 0.045 0.427 4246 Planarity : 0.004 0.062 4455 Dihedral : 3.954 19.258 3320 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.55 % Rotamer: Outliers : 1.36 % Allowed : 13.74 % Favored : 84.90 % 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: -0.08 (0.15), residues: 3047 helix: 2.02 (0.21), residues: 689 sheet: 0.55 (0.19), residues: 720 loop : -1.31 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.019 0.001 TYR C 369 PHE 0.022 0.001 PHE A 157 TRP 0.032 0.002 TRP B 436 HIS 0.003 0.000 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (25905) covalent geometry : angle 0.57042 / 0.29 (35253) SS BOND : bond 0.00368 / 0.22 ( 36) SS BOND : angle 1.44668 / 0.97 ( 72) hydrogen bonds : bond 0.05139 / 3.49 ( 967) hydrogen bonds : angle 5.22196 / 3.59 ( 2712) link_BETA1-4 : bond 0.00444 / 0.30 ( 34) link_BETA1-4 : angle 1.85776 / 1.34 ( 102) link_NAG-ASN : bond 0.00429 / 0.27 ( 48) link_NAG-ASN : angle 2.21738 / 1.41 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 79 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 957 GLN cc_start: 0.9230 (tt0) cc_final: 0.9026 (tp-100) REVERT: B 153 MET cc_start: 0.6172 (tpt) cc_final: 0.5639 (tpt) REVERT: B 387 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8777 (mm) REVERT: B 456 PHE cc_start: 0.9430 (OUTLIER) cc_final: 0.9148 (t80) REVERT: B 563 GLN cc_start: 0.6576 (OUTLIER) cc_final: 0.6235 (mt0) REVERT: B 636 TYR cc_start: 0.2960 (OUTLIER) cc_final: -0.1213 (p90) REVERT: B 1002 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8380 (tm-30) REVERT: B 1072 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8838 (mp0) REVERT: C 153 MET cc_start: 0.3890 (OUTLIER) cc_final: 0.3444 (ppp) REVERT: C 524 VAL cc_start: 0.6643 (OUTLIER) cc_final: 0.6361 (m) outliers start: 37 outliers final: 14 residues processed: 107 average time/residue: 0.5085 time to fit residues: 66.2460 Evaluate side-chains 93 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 697 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 132 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 chunk 254 optimal weight: 8.9990 chunk 248 optimal weight: 8.9990 chunk 160 optimal weight: 0.3980 chunk 220 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1106 GLN C 955 ASN ** C1005 GLN ** 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 = 0.3803 r_free = 0.3803 target = 0.082324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.052120 restraints weight = 95000.204| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 4.23 r_work: 0.2852 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 26023 Z= 0.196 Angle : 0.631 10.255 35571 Z= 0.309 Chirality : 0.046 0.422 4246 Planarity : 0.004 0.059 4455 Dihedral : 4.045 20.002 3320 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.86 % Favored : 95.08 % Rotamer: Outliers : 1.47 % Allowed : 14.07 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 3047 helix: 1.91 (0.21), residues: 689 sheet: 0.48 (0.19), residues: 719 loop : -1.33 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 408 TYR 0.018 0.001 TYR C 369 PHE 0.027 0.001 PHE B 338 TRP 0.033 0.002 TRP B 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (25905) covalent geometry : angle 0.60434 / 0.30 (35253) SS BOND : bond 0.00421 / 0.25 ( 36) SS BOND : angle 1.63940 / 1.08 ( 72) hydrogen bonds : bond 0.05749 / 3.88 ( 967) hydrogen bonds : angle 5.35241 / 3.68 ( 2712) link_BETA1-4 : bond 0.00362 / 0.25 ( 34) link_BETA1-4 : angle 1.81865 / 1.31 ( 102) link_NAG-ASN : bond 0.00391 / 0.24 ( 48) link_NAG-ASN : angle 2.27512 / 1.46 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 71 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 636 TYR cc_start: 0.3101 (OUTLIER) cc_final: 0.2505 (p90) REVERT: A 878 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9235 (tt) REVERT: A 957 GLN cc_start: 0.9254 (tt0) cc_final: 0.8998 (tp-100) REVERT: A 1132 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.9055 (tp) REVERT: B 153 MET cc_start: 0.6445 (tpt) cc_final: 0.5723 (tpt) REVERT: B 387 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8776 (mm) REVERT: B 456 PHE cc_start: 0.9434 (OUTLIER) cc_final: 0.9146 (t80) REVERT: B 563 GLN cc_start: 0.6649 (OUTLIER) cc_final: 0.6219 (mt0) REVERT: B 636 TYR cc_start: 0.3342 (OUTLIER) cc_final: -0.1004 (p90) REVERT: B 1072 GLU cc_start: 0.9219 (OUTLIER) cc_final: 0.8862 (mp0) REVERT: C 153 MET cc_start: 0.4108 (OUTLIER) cc_final: 0.3630 (ppp) REVERT: C 524 VAL cc_start: 0.6756 (OUTLIER) cc_final: 0.6474 (m) outliers start: 40 outliers final: 18 residues processed: 101 average time/residue: 0.4859 time to fit residues: 60.7847 Evaluate side-chains 93 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 705 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 235 optimal weight: 0.0470 chunk 113 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 237 optimal weight: 20.0000 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 501 ASN C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.082250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.052055 restraints weight = 95674.085| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 4.24 r_work: 0.2851 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26023 Z= 0.187 Angle : 0.632 10.218 35571 Z= 0.310 Chirality : 0.046 0.420 4246 Planarity : 0.004 0.059 4455 Dihedral : 4.090 21.339 3320 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.56 % Favored : 95.37 % Rotamer: Outliers : 1.36 % Allowed : 14.59 % Favored : 84.05 % 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: -0.20 (0.15), residues: 3047 helix: 1.87 (0.21), residues: 690 sheet: 0.47 (0.19), residues: 718 loop : -1.36 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 408 TYR 0.017 0.001 TYR B1067 PHE 0.028 0.001 PHE A 157 TRP 0.036 0.002 TRP B 436 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (25905) covalent geometry : angle 0.60583 / 0.30 (35253) SS BOND : bond 0.00414 / 0.25 ( 36) SS BOND : angle 1.65316 / 1.10 ( 72) hydrogen bonds : bond 0.05815 / 3.93 ( 967) hydrogen bonds : angle 5.34404 / 3.68 ( 2712) link_BETA1-4 : bond 0.00369 / 0.25 ( 34) link_BETA1-4 : angle 1.82991 / 1.32 ( 102) link_NAG-ASN : bond 0.00388 / 0.24 ( 48) link_NAG-ASN : angle 2.25082 / 1.45 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 70 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 563 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.6985 (mp10) REVERT: A 636 TYR cc_start: 0.3157 (OUTLIER) cc_final: 0.2604 (p90) REVERT: A 878 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9248 (tt) REVERT: A 957 GLN cc_start: 0.9231 (tt0) cc_final: 0.8981 (tp-100) REVERT: A 1132 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.9051 (tp) REVERT: B 387 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8769 (mm) REVERT: B 456 PHE cc_start: 0.9457 (OUTLIER) cc_final: 0.9164 (t80) REVERT: B 563 GLN cc_start: 0.6678 (OUTLIER) cc_final: 0.6257 (mt0) REVERT: B 636 TYR cc_start: 0.3452 (OUTLIER) cc_final: -0.0932 (p90) REVERT: B 1072 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8957 (mp0) REVERT: C 153 MET cc_start: 0.4117 (OUTLIER) cc_final: 0.3559 (ppp) REVERT: C 524 VAL cc_start: 0.6768 (OUTLIER) cc_final: 0.6505 (m) outliers start: 37 outliers final: 22 residues processed: 100 average time/residue: 0.5214 time to fit residues: 63.6177 Evaluate side-chains 100 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 166 optimal weight: 0.7980 chunk 178 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 287 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 302 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 301 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.083428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.053664 restraints weight = 94433.641| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 4.17 r_work: 0.2904 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26023 Z= 0.114 Angle : 0.592 10.930 35571 Z= 0.288 Chirality : 0.045 0.417 4246 Planarity : 0.004 0.062 4455 Dihedral : 3.871 23.323 3320 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.07 % Favored : 95.86 % Rotamer: Outliers : 1.29 % Allowed : 14.81 % Favored : 83.90 % 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: -0.04 (0.15), residues: 3047 helix: 2.01 (0.21), residues: 690 sheet: 0.58 (0.19), residues: 720 loop : -1.27 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 408 TYR 0.021 0.001 TYR B 453 PHE 0.027 0.001 PHE B 338 TRP 0.036 0.002 TRP B 436 HIS 0.003 0.000 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (25905) covalent geometry : angle 0.56665 / 0.28 (35253) SS BOND : bond 0.00363 / 0.21 ( 36) SS BOND : angle 1.32270 / 0.90 ( 72) hydrogen bonds : bond 0.04964 / 3.36 ( 967) hydrogen bonds : angle 5.12652 / 3.52 ( 2712) link_BETA1-4 : bond 0.00448 / 0.31 ( 34) link_BETA1-4 : angle 1.83907 / 1.33 ( 102) link_NAG-ASN : bond 0.00412 / 0.26 ( 48) link_NAG-ASN : angle 2.13920 / 1.35 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 563 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7204 (mp10) REVERT: A 878 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9219 (tt) REVERT: A 957 GLN cc_start: 0.9213 (tt0) cc_final: 0.9004 (tp-100) REVERT: A 1132 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.9010 (tp) REVERT: B 387 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8779 (mm) REVERT: B 456 PHE cc_start: 0.9442 (OUTLIER) cc_final: 0.9149 (t80) REVERT: B 563 GLN cc_start: 0.6395 (OUTLIER) cc_final: 0.6188 (mt0) REVERT: B 636 TYR cc_start: 0.3178 (OUTLIER) cc_final: -0.0997 (p90) REVERT: B 1072 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8873 (mp0) REVERT: C 153 MET cc_start: 0.3948 (OUTLIER) cc_final: 0.3535 (ppp) REVERT: C 524 VAL cc_start: 0.6533 (OUTLIER) cc_final: 0.6248 (m) outliers start: 35 outliers final: 20 residues processed: 101 average time/residue: 0.5084 time to fit residues: 62.8891 Evaluate side-chains 98 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1002 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 256 optimal weight: 3.9990 chunk 219 optimal weight: 20.0000 chunk 242 optimal weight: 10.0000 chunk 291 optimal weight: 0.2980 chunk 164 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 209 optimal weight: 7.9990 chunk 184 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.082317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.052327 restraints weight = 94757.987| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 4.19 r_work: 0.2857 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26023 Z= 0.188 Angle : 0.630 10.142 35571 Z= 0.309 Chirality : 0.046 0.412 4246 Planarity : 0.004 0.059 4455 Dihedral : 4.033 22.559 3320 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.73 % Favored : 95.21 % Rotamer: Outliers : 1.25 % Allowed : 14.70 % Favored : 84.05 % 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: 3047 helix: 1.90 (0.21), residues: 690 sheet: 0.50 (0.19), residues: 718 loop : -1.30 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 408 TYR 0.017 0.001 TYR B1067 PHE 0.026 0.001 PHE A 135 TRP 0.035 0.002 TRP B 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (25905) covalent geometry : angle 0.60484 / 0.30 (35253) SS BOND : bond 0.00401 / 0.24 ( 36) SS BOND : angle 1.55603 / 1.03 ( 72) hydrogen bonds : bond 0.05648 / 3.82 ( 967) hydrogen bonds : angle 5.27828 / 3.63 ( 2712) link_BETA1-4 : bond 0.00359 / 0.25 ( 34) link_BETA1-4 : angle 1.81667 / 1.30 ( 102) link_NAG-ASN : bond 0.00386 / 0.24 ( 48) link_NAG-ASN : angle 2.19881 / 1.41 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7238.69 seconds wall clock time: 124 minutes 46.35 seconds (7486.35 seconds total)