Starting phenix.real_space_refine on Sun Jul 5 06:10:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v79_31763/07_2026/7v79_31763.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v79_31763/07_2026/7v79_31763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v79_31763/07_2026/7v79_31763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v79_31763/07_2026/7v79_31763.map" model { file = "/net/cci-nas-00/data/ceres_data/7v79_31763/07_2026/7v79_31763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v79_31763/07_2026/7v79_31763.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7v79_31763/07_2026/7v79_31763.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v79_31763/07_2026/7v79_31763.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.067 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 16341 2.51 5 N 4135 2.21 5 O 5090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25677 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8110 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Chain: "B" Number of atoms: 8166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8166 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 53, 'TRANS': 990} Chain breaks: 7 Chain: "C" Number of atoms: 8158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 8158 Classifications: {'peptide': 1043} Link IDs: {'PTRANS': 53, 'TRANS': 989} Chain breaks: 7 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.32, per 1000 atoms: 0.21 Number of scatterers: 25677 At special positions: 0 Unit cell: (144.1, 147.4, 196.9, 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 5090 8.00 N 4135 7.00 C 16341 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, 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 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 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=2.04 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 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 E 2 " - " BMA E 3 " " 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 122 " " NAG A2003 " - " ASN A 603 " " NAG A2004 " - " ASN A 657 " " NAG A2005 " - " ASN A 20 " " NAG A2006 " - " ASN A 188 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 234 " " NAG B2004 " - " ASN B 331 " " NAG B2005 " - " ASN B 603 " " NAG B2006 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 122 " " NAG C2003 " - " ASN C 331 " " NAG C2004 " - " ASN C 603 " " NAG C2005 " - " ASN C 657 " " NAG C2007 " - " ASN C 188 " " NAG D 1 " - " ASN A 165 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 343 " " NAG I 1 " - " ASN A 616 " " NAG J 1 " - " ASN A 709 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 165 " " 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 B 20 " " NAG a 1 " - " ASN C 165 " " 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: 2.93 Conformation dependent library (CDL) restraints added in 969.9 milliseconds 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5848 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 47 sheets defined 25.0% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.430A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.831A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.324A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.575A 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: 4.203A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.623A 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 982 removed outlier: 3.800A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.857A 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 removed outlier: 3.565A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.436A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.172A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.553A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.695A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 633 through 638 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.976A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.721A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.675A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 898 through 908 removed outlier: 3.607A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.664A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.660A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) 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: 3.615A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.099A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.778A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.500A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.619A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.907A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.567A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 638 removed outlier: 4.025A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.550A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.546A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.850A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.781A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.828A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.605A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.028A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.088A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.360A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.613A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN C 540 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.148A 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: 3.651A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.841A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.755A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.165A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 573 through 576 removed outlier: 3.932A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.097A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.610A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.572A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.759A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.852A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.575A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.065A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.572A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.585A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 326 through 328 removed outlier: 5.700A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.313A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.271A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD3, first strand: chain 'B' and resid 717 through 719 Processing sheet with id=AD4, first strand: chain 'B' and resid 722 through 728 removed outlier: 3.530A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.544A 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: 5.038A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.465A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.970A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.999A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.537A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.595A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 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: 3.512A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.744A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.565A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.565A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.547A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 988 hydrogen bonds defined for protein. 2685 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: 5.30 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8030 1.34 - 1.46: 6653 1.46 - 1.58: 11426 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 26247 Sorted by residual: bond pdb=" C1 NAG W 1 " pdb=" O5 NAG W 1 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.91e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.44e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.43e+00 bond pdb=" C1 NAG b 2 " pdb=" O5 NAG b 2 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.48e+00 bond pdb=" C1 NAG C2003 " pdb=" O5 NAG C2003 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.72e+00 ... (remaining 26242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 34476 1.60 - 3.21: 1114 3.21 - 4.81: 103 4.81 - 6.42: 23 6.42 - 8.02: 8 Bond angle restraints: 35724 Sorted by residual: angle pdb=" N GLY B 103 " pdb=" CA GLY B 103 " pdb=" C GLY B 103 " ideal model delta sigma weight residual 111.42 117.57 -6.15 1.42e+00 4.96e-01 1.88e+01 angle pdb=" N CYS A 525 " pdb=" CA CYS A 525 " pdb=" C CYS A 525 " ideal model delta sigma weight residual 108.14 113.62 -5.48 1.52e+00 4.33e-01 1.30e+01 angle pdb=" N GLY C 103 " pdb=" CA GLY C 103 " pdb=" C GLY C 103 " ideal model delta sigma weight residual 112.06 117.74 -5.68 1.66e+00 3.63e-01 1.17e+01 angle pdb=" C ASN C1074 " pdb=" N PHE C1075 " pdb=" CA PHE C1075 " ideal model delta sigma weight residual 122.36 127.38 -5.02 1.60e+00 3.91e-01 9.86e+00 angle pdb=" C ARG C 102 " pdb=" N GLY C 103 " pdb=" CA GLY C 103 " ideal model delta sigma weight residual 122.67 119.46 3.21 1.10e+00 8.26e-01 8.51e+00 ... (remaining 35719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 13436 17.74 - 35.47: 1165 35.47 - 53.21: 220 53.21 - 70.94: 31 70.94 - 88.68: 24 Dihedral angle restraints: 14876 sinusoidal: 5777 harmonic: 9099 Sorted by residual: dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual 93.00 173.73 -80.73 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 -6.95 -79.05 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -7.79 -78.21 1 1.00e+01 1.00e-02 7.64e+01 ... (remaining 14873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 4242 0.122 - 0.243: 53 0.243 - 0.365: 6 0.365 - 0.486: 2 0.486 - 0.608: 1 Chirality restraints: 4304 Sorted by residual: chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.23e+00 chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.40e+00 ... (remaining 4301 not shown) Planarity restraints: 4542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 81 " 0.057 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO A 82 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO A 987 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 906 " -0.018 2.00e-02 2.50e+03 1.70e-02 5.06e+00 pdb=" CG PHE B 906 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 906 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 906 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 906 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 906 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 906 " -0.001 2.00e-02 2.50e+03 ... (remaining 4539 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 406 2.66 - 3.22: 23896 3.22 - 3.78: 36977 3.78 - 4.34: 49031 4.34 - 4.90: 83072 Nonbonded interactions: 193382 Sorted by model distance: nonbonded pdb=" OD1 ASN A 125 " pdb=" O3 NAG A2002 " model vdw 2.099 3.040 nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.125 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.151 3.040 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.169 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.175 3.040 ... (remaining 193377 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 621 or resid 635 through 827 or resid 855 throu \ gh 2006)) selection = (chain 'C' and (resid 14 through 621 or resid 635 through 827 or resid 855 throu \ gh 2006)) } ncs_group { reference = chain 'D' 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: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.060 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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 : 0.006 0.063 26372 Z= 0.255 Angle : 0.702 19.862 36059 Z= 0.339 Chirality : 0.050 0.608 4304 Planarity : 0.004 0.087 4492 Dihedral : 13.560 88.678 8908 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.49 (0.15), residues: 3077 helix: 1.39 (0.21), residues: 680 sheet: 0.26 (0.19), residues: 756 loop : -1.41 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1039 TYR 0.023 0.001 TYR A 873 PHE 0.039 0.002 PHE B 906 TRP 0.017 0.001 TRP B 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.26 (26247) covalent geometry : angle 0.65580 / 0.33 (35724) SS BOND : bond 0.00374 / 0.25 ( 40) SS BOND : angle 1.75935 / 1.18 ( 80) hydrogen bonds : bond 0.13078 / 8.40 ( 972) hydrogen bonds : angle 6.05231 / 4.15 ( 2685) link_BETA1-4 : bond 0.00405 / 0.24 ( 35) link_BETA1-4 : angle 1.87338 / 1.17 ( 105) link_NAG-ASN : bond 0.00555 / 0.42 ( 50) link_NAG-ASN : angle 3.45019 / 2.38 ( 150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4929 (pmm) cc_final: 0.3533 (tmm) REVERT: A 187 LYS cc_start: 0.7014 (mmmm) cc_final: 0.6801 (tptp) REVERT: A 210 ILE cc_start: 0.8373 (tp) cc_final: 0.8085 (tp) REVERT: A 224 GLU cc_start: 0.7489 (pp20) cc_final: 0.6894 (pp20) REVERT: A 241 LEU cc_start: 0.6761 (mt) cc_final: 0.6513 (mt) REVERT: A 309 GLU cc_start: 0.7613 (mp0) cc_final: 0.7331 (pm20) REVERT: A 529 LYS cc_start: 0.8435 (mmpt) cc_final: 0.8122 (mmmt) REVERT: A 663 ASP cc_start: 0.8346 (m-30) cc_final: 0.8125 (m-30) REVERT: A 675 GLN cc_start: 0.5109 (pp30) cc_final: 0.4884 (tm-30) REVERT: A 950 ASP cc_start: 0.7768 (m-30) cc_final: 0.7218 (m-30) REVERT: A 1092 GLU cc_start: 0.7659 (tp30) cc_final: 0.7454 (pt0) REVERT: B 41 LYS cc_start: 0.7728 (mttt) cc_final: 0.7430 (mttm) REVERT: B 101 ILE cc_start: 0.7432 (mm) cc_final: 0.7184 (mp) REVERT: B 314 GLN cc_start: 0.8702 (tt0) cc_final: 0.8222 (mt0) REVERT: B 461 LEU cc_start: 0.8118 (mt) cc_final: 0.7876 (mt) REVERT: B 950 ASP cc_start: 0.7757 (m-30) cc_final: 0.7386 (m-30) REVERT: B 969 ASN cc_start: 0.8003 (t0) cc_final: 0.7798 (t0) REVERT: B 988 GLU cc_start: 0.7284 (pm20) cc_final: 0.6961 (pm20) REVERT: B 1114 ILE cc_start: 0.8737 (mt) cc_final: 0.8482 (tt) REVERT: C 429 PHE cc_start: 0.8192 (t80) cc_final: 0.7822 (t80) REVERT: C 564 GLN cc_start: 0.7268 (mm110) cc_final: 0.6848 (mm-40) REVERT: C 581 THR cc_start: 0.7969 (m) cc_final: 0.6821 (m) REVERT: C 740 MET cc_start: 0.7742 (tpt) cc_final: 0.7356 (mtt) REVERT: C 1002 GLN cc_start: 0.7610 (tp-100) cc_final: 0.7366 (mt0) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.1546 time to fit residues: 58.8503 Evaluate side-chains 173 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.0050 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 2.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 394 ASN C 856 ASN C 901 GLN C1106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.193872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.147283 restraints weight = 33399.151| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 3.92 r_work: 0.3552 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26372 Z= 0.182 Angle : 0.655 19.904 36059 Z= 0.319 Chirality : 0.049 0.390 4304 Planarity : 0.004 0.063 4492 Dihedral : 4.367 23.151 3355 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.09 % Rotamer: Outliers : 0.84 % Allowed : 7.11 % Favored : 92.05 % 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: -0.54 (0.15), residues: 3077 helix: 1.36 (0.21), residues: 671 sheet: 0.26 (0.19), residues: 744 loop : -1.43 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1039 TYR 0.027 0.001 TYR C 453 PHE 0.032 0.002 PHE B 238 TRP 0.010 0.001 TRP C 104 HIS 0.006 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.18 (26247) covalent geometry : angle 0.61471 / 0.31 (35724) SS BOND : bond 0.00376 / 0.23 ( 40) SS BOND : angle 1.66096 / 1.09 ( 80) hydrogen bonds : bond 0.05895 / 3.94 ( 972) hydrogen bonds : angle 5.10425 / 3.50 ( 2685) link_BETA1-4 : bond 0.00542 / 0.35 ( 35) link_BETA1-4 : angle 1.51818 / 0.98 ( 105) link_NAG-ASN : bond 0.00529 / 0.40 ( 50) link_NAG-ASN : angle 3.18180 / 2.21 ( 150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5143 (pmm) cc_final: 0.3759 (tmm) REVERT: A 187 LYS cc_start: 0.7285 (mmmm) cc_final: 0.7067 (tptp) REVERT: A 210 ILE cc_start: 0.8547 (tp) cc_final: 0.8281 (tp) REVERT: A 529 LYS cc_start: 0.8545 (mmpt) cc_final: 0.8330 (mmmt) REVERT: A 663 ASP cc_start: 0.8463 (m-30) cc_final: 0.8156 (m-30) REVERT: A 675 GLN cc_start: 0.5547 (pp30) cc_final: 0.5336 (tm-30) REVERT: A 754 LEU cc_start: 0.8314 (pp) cc_final: 0.7952 (mt) REVERT: A 878 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7640 (tt) REVERT: A 950 ASP cc_start: 0.8214 (m-30) cc_final: 0.7936 (m-30) REVERT: A 1092 GLU cc_start: 0.7843 (tp30) cc_final: 0.7631 (pt0) REVERT: A 1132 ILE cc_start: 0.8664 (pt) cc_final: 0.8455 (pt) REVERT: B 101 ILE cc_start: 0.7999 (mm) cc_final: 0.7684 (mp) REVERT: B 175 PHE cc_start: 0.8103 (m-80) cc_final: 0.7839 (m-10) REVERT: B 351 TYR cc_start: 0.7497 (p90) cc_final: 0.6781 (p90) REVERT: B 357 ARG cc_start: 0.7331 (mtp-110) cc_final: 0.7122 (ttm170) REVERT: B 950 ASP cc_start: 0.8294 (m-30) cc_final: 0.8078 (m-30) REVERT: C 564 GLN cc_start: 0.7610 (mm110) cc_final: 0.7291 (mm-40) REVERT: C 740 MET cc_start: 0.8198 (tpt) cc_final: 0.7810 (mtt) REVERT: C 814 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8657 (mmmt) REVERT: C 950 ASP cc_start: 0.8339 (t70) cc_final: 0.7902 (m-30) REVERT: C 1002 GLN cc_start: 0.8241 (tp-100) cc_final: 0.8035 (tt0) outliers start: 23 outliers final: 16 residues processed: 195 average time/residue: 0.1606 time to fit residues: 51.8179 Evaluate side-chains 176 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 84 optimal weight: 3.9990 chunk 296 optimal weight: 0.9980 chunk 298 optimal weight: 0.6980 chunk 286 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 306 optimal weight: 0.9990 chunk 260 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.193639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.147438 restraints weight = 33463.844| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 3.92 r_work: 0.3534 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26372 Z= 0.159 Angle : 0.620 19.656 36059 Z= 0.300 Chirality : 0.047 0.372 4304 Planarity : 0.004 0.056 4492 Dihedral : 4.255 22.968 3355 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 1.54 % Allowed : 9.75 % Favored : 88.71 % 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: -0.48 (0.15), residues: 3077 helix: 1.43 (0.21), residues: 667 sheet: 0.37 (0.19), residues: 718 loop : -1.41 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1039 TYR 0.021 0.001 TYR C 453 PHE 0.022 0.002 PHE A1121 TRP 0.010 0.001 TRP B 353 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (26247) covalent geometry : angle 0.58044 / 0.29 (35724) SS BOND : bond 0.00374 / 0.24 ( 40) SS BOND : angle 1.50339 / 0.99 ( 80) hydrogen bonds : bond 0.05574 / 3.72 ( 972) hydrogen bonds : angle 4.93831 / 3.37 ( 2685) link_BETA1-4 : bond 0.00484 / 0.31 ( 35) link_BETA1-4 : angle 1.50837 / 0.96 ( 105) link_NAG-ASN : bond 0.00521 / 0.40 ( 50) link_NAG-ASN : angle 3.06715 / 2.13 ( 150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6557 (p90) cc_final: 0.5902 (p90) REVERT: A 153 MET cc_start: 0.5016 (pmm) cc_final: 0.3796 (tmm) REVERT: A 187 LYS cc_start: 0.7314 (mmmm) cc_final: 0.7082 (tptp) REVERT: A 210 ILE cc_start: 0.8610 (tp) cc_final: 0.8394 (tp) REVERT: A 334 ASN cc_start: 0.9193 (t0) cc_final: 0.8528 (t0) REVERT: A 529 LYS cc_start: 0.8538 (mmpt) cc_final: 0.8328 (mmmt) REVERT: A 663 ASP cc_start: 0.8476 (m-30) cc_final: 0.8206 (m-30) REVERT: A 754 LEU cc_start: 0.8296 (pp) cc_final: 0.8033 (mt) REVERT: A 878 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7650 (tt) REVERT: A 950 ASP cc_start: 0.8276 (m-30) cc_final: 0.8043 (m-30) REVERT: A 1132 ILE cc_start: 0.8708 (pt) cc_final: 0.8469 (pt) REVERT: B 101 ILE cc_start: 0.8010 (mm) cc_final: 0.7673 (mp) REVERT: B 351 TYR cc_start: 0.7630 (p90) cc_final: 0.7001 (p90) REVERT: C 168 PHE cc_start: 0.8231 (t80) cc_final: 0.8010 (t80) REVERT: C 551 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7877 (m) REVERT: C 564 GLN cc_start: 0.7611 (mm110) cc_final: 0.7312 (mm-40) REVERT: C 740 MET cc_start: 0.8327 (tpt) cc_final: 0.7946 (mtt) REVERT: C 814 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8672 (mmmt) REVERT: C 918 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: C 950 ASP cc_start: 0.8366 (t70) cc_final: 0.7981 (m-30) REVERT: C 1002 GLN cc_start: 0.8245 (tp-100) cc_final: 0.8023 (tt0) outliers start: 42 outliers final: 27 residues processed: 201 average time/residue: 0.1591 time to fit residues: 53.7557 Evaluate side-chains 195 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 114 optimal weight: 9.9990 chunk 250 optimal weight: 4.9990 chunk 256 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 29 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 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 = 0.4467 r_free = 0.4467 target = 0.192040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.147397 restraints weight = 33172.066| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 3.87 r_work: 0.3502 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 26372 Z= 0.196 Angle : 0.646 19.610 36059 Z= 0.315 Chirality : 0.048 0.378 4304 Planarity : 0.004 0.054 4492 Dihedral : 4.338 23.330 3355 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.57 % Rotamer: Outliers : 2.35 % Allowed : 11.32 % Favored : 86.33 % 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: -0.57 (0.15), residues: 3077 helix: 1.31 (0.21), residues: 667 sheet: 0.32 (0.19), residues: 714 loop : -1.45 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1039 TYR 0.028 0.001 TYR C 453 PHE 0.026 0.002 PHE C1121 TRP 0.009 0.001 TRP C 886 HIS 0.005 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (26247) covalent geometry : angle 0.60676 / 0.31 (35724) SS BOND : bond 0.00377 / 0.22 ( 40) SS BOND : angle 1.89128 / 1.21 ( 80) hydrogen bonds : bond 0.05960 / 3.99 ( 972) hydrogen bonds : angle 4.93909 / 3.38 ( 2685) link_BETA1-4 : bond 0.00508 / 0.32 ( 35) link_BETA1-4 : angle 1.52405 / 0.97 ( 105) link_NAG-ASN : bond 0.00482 / 0.38 ( 50) link_NAG-ASN : angle 3.02789 / 2.10 ( 150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 171 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6486 (p90) cc_final: 0.5879 (p90) REVERT: A 153 MET cc_start: 0.4867 (pmm) cc_final: 0.3652 (tmm) REVERT: A 187 LYS cc_start: 0.7357 (mmmm) cc_final: 0.7120 (tptp) REVERT: A 210 ILE cc_start: 0.8685 (tp) cc_final: 0.8462 (tp) REVERT: A 212 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6919 (tt) REVERT: A 334 ASN cc_start: 0.9213 (t0) cc_final: 0.8557 (t0) REVERT: A 529 LYS cc_start: 0.8540 (mmpt) cc_final: 0.8318 (mmmt) REVERT: A 663 ASP cc_start: 0.8510 (m-30) cc_final: 0.8265 (m-30) REVERT: A 754 LEU cc_start: 0.8308 (pp) cc_final: 0.7936 (mt) REVERT: A 817 PHE cc_start: 0.8356 (t80) cc_final: 0.8140 (t80) REVERT: A 878 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7575 (tt) REVERT: A 950 ASP cc_start: 0.8346 (m-30) cc_final: 0.8104 (m-30) REVERT: A 996 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8673 (mp) REVERT: A 1132 ILE cc_start: 0.8932 (pt) cc_final: 0.8683 (pt) REVERT: B 101 ILE cc_start: 0.8055 (mm) cc_final: 0.7687 (mp) REVERT: B 212 LEU cc_start: 0.5746 (OUTLIER) cc_final: 0.5535 (mp) REVERT: B 351 TYR cc_start: 0.7592 (p90) cc_final: 0.6989 (p90) REVERT: B 988 GLU cc_start: 0.7786 (pm20) cc_final: 0.7558 (pm20) REVERT: C 32 PHE cc_start: 0.7878 (m-10) cc_final: 0.7572 (m-80) REVERT: C 456 PHE cc_start: 0.8579 (m-80) cc_final: 0.8350 (m-80) REVERT: C 465 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7891 (tm-30) REVERT: C 551 VAL cc_start: 0.8083 (OUTLIER) cc_final: 0.7847 (m) REVERT: C 564 GLN cc_start: 0.7618 (mm110) cc_final: 0.7207 (mm-40) REVERT: C 740 MET cc_start: 0.8511 (tpt) cc_final: 0.8036 (mtt) REVERT: C 814 LYS cc_start: 0.8989 (mmtt) cc_final: 0.8677 (mmmt) REVERT: C 918 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: C 950 ASP cc_start: 0.8366 (t70) cc_final: 0.7998 (m-30) REVERT: C 1002 GLN cc_start: 0.8361 (tp-100) cc_final: 0.8149 (tt0) outliers start: 64 outliers final: 40 residues processed: 219 average time/residue: 0.1423 time to fit residues: 52.8660 Evaluate side-chains 210 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 65 optimal weight: 0.9990 chunk 244 optimal weight: 0.4980 chunk 47 optimal weight: 10.0000 chunk 210 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 229 optimal weight: 1.9990 chunk 303 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 308 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.193490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.145867 restraints weight = 32999.471| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 3.72 r_work: 0.3556 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26372 Z= 0.129 Angle : 0.591 19.472 36059 Z= 0.285 Chirality : 0.046 0.369 4304 Planarity : 0.004 0.052 4492 Dihedral : 4.134 21.473 3355 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.35 % Favored : 95.61 % Rotamer: Outliers : 2.24 % Allowed : 12.57 % Favored : 85.20 % 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: -0.43 (0.15), residues: 3077 helix: 1.52 (0.21), residues: 661 sheet: 0.39 (0.19), residues: 723 loop : -1.39 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.024 0.001 TYR C 453 PHE 0.028 0.001 PHE C 168 TRP 0.008 0.001 TRP A 886 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (26247) covalent geometry : angle 0.55279 / 0.28 (35724) SS BOND : bond 0.00317 / 0.19 ( 40) SS BOND : angle 1.50849 / 0.97 ( 80) hydrogen bonds : bond 0.05132 / 3.44 ( 972) hydrogen bonds : angle 4.74920 / 3.25 ( 2685) link_BETA1-4 : bond 0.00520 / 0.33 ( 35) link_BETA1-4 : angle 1.49419 / 0.95 ( 105) link_NAG-ASN : bond 0.00518 / 0.40 ( 50) link_NAG-ASN : angle 2.91179 / 2.03 ( 150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 173 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6566 (p90) cc_final: 0.5953 (p90) REVERT: A 153 MET cc_start: 0.4732 (pmm) cc_final: 0.3600 (tmm) REVERT: A 210 ILE cc_start: 0.8689 (tp) cc_final: 0.8477 (tp) REVERT: A 212 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6629 (tt) REVERT: A 234 ASN cc_start: 0.6519 (t0) cc_final: 0.6191 (t0) REVERT: A 334 ASN cc_start: 0.9221 (t0) cc_final: 0.8600 (t0) REVERT: A 529 LYS cc_start: 0.8517 (mmpt) cc_final: 0.8309 (mmmt) REVERT: A 563 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.6340 (mp10) REVERT: A 663 ASP cc_start: 0.8410 (m-30) cc_final: 0.8185 (m-30) REVERT: A 754 LEU cc_start: 0.8267 (pp) cc_final: 0.8041 (mt) REVERT: A 950 ASP cc_start: 0.8317 (m-30) cc_final: 0.8046 (m-30) REVERT: A 984 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8160 (pp) REVERT: A 996 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8594 (mp) REVERT: A 1132 ILE cc_start: 0.8866 (pt) cc_final: 0.8600 (pt) REVERT: B 101 ILE cc_start: 0.8032 (mm) cc_final: 0.7648 (mp) REVERT: B 212 LEU cc_start: 0.5749 (OUTLIER) cc_final: 0.5544 (mp) REVERT: B 351 TYR cc_start: 0.7617 (p90) cc_final: 0.7003 (p90) REVERT: C 32 PHE cc_start: 0.7884 (m-10) cc_final: 0.7456 (m-80) REVERT: C 347 PHE cc_start: 0.8162 (m-10) cc_final: 0.7876 (m-10) REVERT: C 551 VAL cc_start: 0.7970 (OUTLIER) cc_final: 0.7718 (m) REVERT: C 564 GLN cc_start: 0.7623 (mm110) cc_final: 0.7311 (mm-40) REVERT: C 569 ILE cc_start: 0.5789 (OUTLIER) cc_final: 0.5400 (mp) REVERT: C 740 MET cc_start: 0.8385 (tpt) cc_final: 0.8006 (mtt) REVERT: C 814 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8665 (mmmt) REVERT: C 918 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: C 950 ASP cc_start: 0.8324 (t70) cc_final: 0.7970 (m-30) outliers start: 61 outliers final: 33 residues processed: 220 average time/residue: 0.1460 time to fit residues: 54.2433 Evaluate side-chains 204 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 254 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 245 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 286 optimal weight: 0.3980 chunk 115 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 307 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.192776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.146112 restraints weight = 33178.646| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 3.87 r_work: 0.3528 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26372 Z= 0.165 Angle : 0.616 19.494 36059 Z= 0.298 Chirality : 0.047 0.376 4304 Planarity : 0.004 0.053 4492 Dihedral : 4.207 22.701 3355 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.71 % Allowed : 13.05 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.15), residues: 3077 helix: 1.42 (0.21), residues: 661 sheet: 0.35 (0.19), residues: 724 loop : -1.41 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 357 TYR 0.029 0.001 TYR C 453 PHE 0.024 0.002 PHE B1121 TRP 0.008 0.001 TRP A 886 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (26247) covalent geometry : angle 0.57920 / 0.29 (35724) SS BOND : bond 0.00343 / 0.20 ( 40) SS BOND : angle 1.57472 / 1.02 ( 80) hydrogen bonds : bond 0.05498 / 3.68 ( 972) hydrogen bonds : angle 4.77683 / 3.26 ( 2685) link_BETA1-4 : bond 0.00508 / 0.32 ( 35) link_BETA1-4 : angle 1.49613 / 0.95 ( 105) link_NAG-ASN : bond 0.00478 / 0.38 ( 50) link_NAG-ASN : angle 2.89091 / 2.01 ( 150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 167 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6519 (p90) cc_final: 0.5943 (p90) REVERT: A 153 MET cc_start: 0.4761 (pmm) cc_final: 0.3582 (tmm) REVERT: A 212 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6807 (tt) REVERT: A 334 ASN cc_start: 0.9157 (t0) cc_final: 0.8518 (t0) REVERT: A 529 LYS cc_start: 0.8525 (mmpt) cc_final: 0.8309 (mmmt) REVERT: A 563 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.6398 (mp10) REVERT: A 663 ASP cc_start: 0.8478 (m-30) cc_final: 0.8246 (m-30) REVERT: A 754 LEU cc_start: 0.8294 (pp) cc_final: 0.7945 (mt) REVERT: A 878 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7620 (tt) REVERT: A 950 ASP cc_start: 0.8334 (m-30) cc_final: 0.8060 (m-30) REVERT: A 984 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8085 (pp) REVERT: A 996 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8649 (mp) REVERT: A 1132 ILE cc_start: 0.8951 (pt) cc_final: 0.8700 (pt) REVERT: B 101 ILE cc_start: 0.8045 (mm) cc_final: 0.7662 (mp) REVERT: B 212 LEU cc_start: 0.5855 (OUTLIER) cc_final: 0.5597 (mp) REVERT: B 351 TYR cc_start: 0.7571 (p90) cc_final: 0.6980 (p90) REVERT: B 358 ILE cc_start: 0.7225 (mt) cc_final: 0.6903 (mt) REVERT: B 569 ILE cc_start: 0.4405 (OUTLIER) cc_final: 0.4053 (mp) REVERT: B 988 GLU cc_start: 0.7777 (pm20) cc_final: 0.7369 (pm20) REVERT: C 347 PHE cc_start: 0.8154 (m-10) cc_final: 0.7810 (m-10) REVERT: C 465 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7883 (tm-30) REVERT: C 551 VAL cc_start: 0.8011 (OUTLIER) cc_final: 0.7803 (m) REVERT: C 556 ASN cc_start: 0.8114 (t0) cc_final: 0.7874 (t0) REVERT: C 569 ILE cc_start: 0.5939 (OUTLIER) cc_final: 0.5544 (mp) REVERT: C 740 MET cc_start: 0.8580 (tpt) cc_final: 0.8058 (mtt) REVERT: C 814 LYS cc_start: 0.8976 (mmtt) cc_final: 0.8679 (mmmt) REVERT: C 918 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: C 950 ASP cc_start: 0.8339 (t70) cc_final: 0.7987 (m-30) outliers start: 74 outliers final: 47 residues processed: 229 average time/residue: 0.1485 time to fit residues: 57.7568 Evaluate side-chains 221 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 164 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 116 optimal weight: 6.9990 chunk 227 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 159 optimal weight: 0.5980 chunk 152 optimal weight: 0.0670 chunk 108 optimal weight: 5.9990 chunk 197 optimal weight: 0.4980 chunk 155 optimal weight: 0.0770 chunk 41 optimal weight: 8.9990 chunk 150 optimal weight: 0.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 115 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.195976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.148125 restraints weight = 33000.871| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 3.70 r_work: 0.3595 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26372 Z= 0.105 Angle : 0.565 19.345 36059 Z= 0.270 Chirality : 0.045 0.366 4304 Planarity : 0.004 0.052 4492 Dihedral : 3.944 19.915 3355 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.02 % Allowed : 13.92 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.15), residues: 3077 helix: 1.67 (0.21), residues: 661 sheet: 0.43 (0.19), residues: 731 loop : -1.31 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.026 0.001 TYR C 453 PHE 0.022 0.001 PHE C 168 TRP 0.007 0.001 TRP A 886 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (26247) covalent geometry : angle 0.52885 / 0.26 (35724) SS BOND : bond 0.00321 / 0.21 ( 40) SS BOND : angle 1.28962 / 0.83 ( 80) hydrogen bonds : bond 0.04467 / 3.00 ( 972) hydrogen bonds : angle 4.58424 / 3.13 ( 2685) link_BETA1-4 : bond 0.00536 / 0.34 ( 35) link_BETA1-4 : angle 1.46677 / 0.93 ( 105) link_NAG-ASN : bond 0.00533 / 0.42 ( 50) link_NAG-ASN : angle 2.77660 / 1.94 ( 150) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 168 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4644 (pmm) cc_final: 0.3548 (tmm) REVERT: A 334 ASN cc_start: 0.9197 (t0) cc_final: 0.8580 (t0) REVERT: A 563 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.6370 (mp10) REVERT: A 663 ASP cc_start: 0.8300 (m-30) cc_final: 0.8088 (m-30) REVERT: A 878 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7780 (tt) REVERT: A 950 ASP cc_start: 0.8279 (m-30) cc_final: 0.8005 (m-30) REVERT: A 984 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8179 (pp) REVERT: A 1132 ILE cc_start: 0.8770 (pt) cc_final: 0.8520 (pt) REVERT: B 101 ILE cc_start: 0.8014 (mm) cc_final: 0.7635 (mp) REVERT: B 351 TYR cc_start: 0.7572 (p90) cc_final: 0.7027 (p90) REVERT: B 354 ASN cc_start: 0.7698 (t0) cc_final: 0.7419 (t0) REVERT: B 569 ILE cc_start: 0.4377 (OUTLIER) cc_final: 0.4032 (mp) REVERT: C 32 PHE cc_start: 0.7905 (m-10) cc_final: 0.7533 (m-80) REVERT: C 347 PHE cc_start: 0.8094 (m-10) cc_final: 0.7743 (m-10) REVERT: C 414 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7527 (mt0) REVERT: C 551 VAL cc_start: 0.7956 (OUTLIER) cc_final: 0.7736 (m) REVERT: C 569 ILE cc_start: 0.5933 (OUTLIER) cc_final: 0.5500 (mp) REVERT: C 740 MET cc_start: 0.8521 (tpt) cc_final: 0.7999 (mtt) REVERT: C 814 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8680 (mmmt) REVERT: C 918 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: C 950 ASP cc_start: 0.8243 (t70) cc_final: 0.7934 (m-30) outliers start: 55 outliers final: 32 residues processed: 213 average time/residue: 0.1528 time to fit residues: 55.1061 Evaluate side-chains 194 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 164 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 198 optimal weight: 0.5980 chunk 184 optimal weight: 0.5980 chunk 286 optimal weight: 0.7980 chunk 213 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN C 370 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.194825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.148223 restraints weight = 33019.158| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 3.45 r_work: 0.3570 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26372 Z= 0.126 Angle : 0.583 19.452 36059 Z= 0.280 Chirality : 0.046 0.365 4304 Planarity : 0.004 0.053 4492 Dihedral : 3.960 20.766 3355 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.09 % Allowed : 13.92 % Favored : 83.99 % 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: -0.32 (0.15), residues: 3077 helix: 1.65 (0.21), residues: 661 sheet: 0.41 (0.19), residues: 729 loop : -1.31 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 44 TYR 0.026 0.001 TYR C 453 PHE 0.019 0.001 PHE B1121 TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (26247) covalent geometry : angle 0.54864 / 0.27 (35724) SS BOND : bond 0.00308 / 0.19 ( 40) SS BOND : angle 1.36305 / 0.89 ( 80) hydrogen bonds : bond 0.04789 / 3.21 ( 972) hydrogen bonds : angle 4.58466 / 3.13 ( 2685) link_BETA1-4 : bond 0.00507 / 0.31 ( 35) link_BETA1-4 : angle 1.45088 / 0.93 ( 105) link_NAG-ASN : bond 0.00486 / 0.39 ( 50) link_NAG-ASN : angle 2.75912 / 1.93 ( 150) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 159 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6435 (p90) cc_final: 0.5915 (p90) REVERT: A 153 MET cc_start: 0.4482 (pmm) cc_final: 0.3449 (tmm) REVERT: A 234 ASN cc_start: 0.5886 (t0) cc_final: 0.5684 (t0) REVERT: A 334 ASN cc_start: 0.9218 (t0) cc_final: 0.8624 (t0) REVERT: A 563 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.6422 (mp10) REVERT: A 663 ASP cc_start: 0.8340 (m-30) cc_final: 0.8102 (m-30) REVERT: A 878 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7754 (tt) REVERT: A 950 ASP cc_start: 0.8293 (m-30) cc_final: 0.8037 (m-30) REVERT: A 984 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8203 (pp) REVERT: A 996 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8515 (mp) REVERT: A 1132 ILE cc_start: 0.8890 (pt) cc_final: 0.8672 (pt) REVERT: B 101 ILE cc_start: 0.8069 (mm) cc_final: 0.7697 (mp) REVERT: B 351 TYR cc_start: 0.7625 (p90) cc_final: 0.7077 (p90) REVERT: B 354 ASN cc_start: 0.7738 (t0) cc_final: 0.7463 (t0) REVERT: B 396 TYR cc_start: 0.7581 (m-10) cc_final: 0.6989 (m-10) REVERT: B 569 ILE cc_start: 0.4396 (OUTLIER) cc_final: 0.4029 (mp) REVERT: B 902 MET cc_start: 0.8043 (tpt) cc_final: 0.7753 (tpt) REVERT: B 988 GLU cc_start: 0.7856 (pm20) cc_final: 0.7561 (pm20) REVERT: C 347 PHE cc_start: 0.8121 (m-10) cc_final: 0.7766 (m-10) REVERT: C 414 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7566 (mt0) REVERT: C 551 VAL cc_start: 0.8013 (OUTLIER) cc_final: 0.7790 (m) REVERT: C 556 ASN cc_start: 0.8078 (t0) cc_final: 0.7810 (t0) REVERT: C 740 MET cc_start: 0.8554 (tpt) cc_final: 0.8043 (mtt) REVERT: C 814 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8676 (mmmt) REVERT: C 918 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: C 950 ASP cc_start: 0.8271 (t70) cc_final: 0.7967 (m-30) outliers start: 57 outliers final: 41 residues processed: 207 average time/residue: 0.1354 time to fit residues: 47.6955 Evaluate side-chains 205 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 270 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 20 optimal weight: 0.0670 chunk 304 optimal weight: 0.4980 chunk 309 optimal weight: 0.7980 chunk 199 optimal weight: 2.9990 chunk 281 optimal weight: 1.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 121 ASN ** 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 = 0.4486 r_free = 0.4486 target = 0.194520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.146712 restraints weight = 33151.472| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 3.75 r_work: 0.3569 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26372 Z= 0.133 Angle : 0.588 19.427 36059 Z= 0.283 Chirality : 0.046 0.370 4304 Planarity : 0.004 0.053 4492 Dihedral : 3.993 21.092 3355 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.20 % Allowed : 13.81 % Favored : 83.99 % 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: -0.32 (0.15), residues: 3077 helix: 1.61 (0.21), residues: 661 sheet: 0.43 (0.19), residues: 720 loop : -1.30 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 44 TYR 0.026 0.001 TYR C 453 PHE 0.020 0.001 PHE B1121 TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (26247) covalent geometry : angle 0.55341 / 0.28 (35724) SS BOND : bond 0.00327 / 0.19 ( 40) SS BOND : angle 1.40725 / 0.95 ( 80) hydrogen bonds : bond 0.04881 / 3.27 ( 972) hydrogen bonds : angle 4.59158 / 3.13 ( 2685) link_BETA1-4 : bond 0.00519 / 0.32 ( 35) link_BETA1-4 : angle 1.45171 / 0.93 ( 105) link_NAG-ASN : bond 0.00487 / 0.39 ( 50) link_NAG-ASN : angle 2.74755 / 1.92 ( 150) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 158 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4581 (pmm) cc_final: 0.3536 (tmm) REVERT: A 234 ASN cc_start: 0.5910 (t0) cc_final: 0.5701 (t0) REVERT: A 334 ASN cc_start: 0.9180 (t0) cc_final: 0.8550 (t0) REVERT: A 563 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.6415 (mp10) REVERT: A 663 ASP cc_start: 0.8362 (m-30) cc_final: 0.8122 (m-30) REVERT: A 878 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7740 (tt) REVERT: A 950 ASP cc_start: 0.8309 (m-30) cc_final: 0.8031 (m-30) REVERT: A 984 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8155 (pp) REVERT: A 996 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8503 (mp) REVERT: A 1132 ILE cc_start: 0.8882 (pt) cc_final: 0.8667 (pt) REVERT: B 101 ILE cc_start: 0.8064 (mm) cc_final: 0.7701 (mp) REVERT: B 342 PHE cc_start: 0.8770 (m-80) cc_final: 0.8496 (m-80) REVERT: B 351 TYR cc_start: 0.7590 (p90) cc_final: 0.7030 (p90) REVERT: B 354 ASN cc_start: 0.7747 (t0) cc_final: 0.7471 (t0) REVERT: B 396 TYR cc_start: 0.7529 (m-10) cc_final: 0.7105 (m-10) REVERT: B 569 ILE cc_start: 0.4371 (OUTLIER) cc_final: 0.4015 (mp) REVERT: C 52 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7621 (tm-30) REVERT: C 347 PHE cc_start: 0.8138 (m-10) cc_final: 0.7769 (m-10) REVERT: C 414 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7566 (mt0) REVERT: C 551 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7780 (m) REVERT: C 569 ILE cc_start: 0.5946 (OUTLIER) cc_final: 0.5511 (mp) REVERT: C 740 MET cc_start: 0.8558 (tpt) cc_final: 0.8038 (mtt) REVERT: C 814 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8680 (mmmt) REVERT: C 918 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: C 950 ASP cc_start: 0.8266 (t70) cc_final: 0.7968 (m-30) outliers start: 60 outliers final: 45 residues processed: 207 average time/residue: 0.1398 time to fit residues: 50.1474 Evaluate side-chains 211 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 158 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 50 optimal weight: 0.9980 chunk 150 optimal weight: 0.2980 chunk 214 optimal weight: 0.7980 chunk 273 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 191 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.195216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.148477 restraints weight = 33043.507| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 3.37 r_work: 0.3572 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26372 Z= 0.118 Angle : 0.576 19.418 36059 Z= 0.276 Chirality : 0.046 0.364 4304 Planarity : 0.004 0.053 4492 Dihedral : 3.940 20.499 3355 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.02 % Allowed : 14.18 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.15), residues: 3077 helix: 1.65 (0.21), residues: 661 sheet: 0.41 (0.19), residues: 729 loop : -1.29 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 765 TYR 0.026 0.001 TYR C 453 PHE 0.018 0.001 PHE C 168 TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (26247) covalent geometry : angle 0.54201 / 0.27 (35724) SS BOND : bond 0.00341 / 0.19 ( 40) SS BOND : angle 1.36038 / 0.92 ( 80) hydrogen bonds : bond 0.04671 / 3.13 ( 972) hydrogen bonds : angle 4.55078 / 3.10 ( 2685) link_BETA1-4 : bond 0.00523 / 0.33 ( 35) link_BETA1-4 : angle 1.44267 / 0.92 ( 105) link_NAG-ASN : bond 0.00492 / 0.39 ( 50) link_NAG-ASN : angle 2.71106 / 1.90 ( 150) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 162 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4526 (pmm) cc_final: 0.3484 (tmm) REVERT: A 334 ASN cc_start: 0.9190 (t0) cc_final: 0.8579 (t0) REVERT: A 563 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.6396 (mp10) REVERT: A 663 ASP cc_start: 0.8340 (m-30) cc_final: 0.8118 (m-30) REVERT: A 878 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7770 (tt) REVERT: A 950 ASP cc_start: 0.8302 (m-30) cc_final: 0.8036 (m-30) REVERT: A 984 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8139 (pp) REVERT: A 996 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8465 (mp) REVERT: B 101 ILE cc_start: 0.8095 (mm) cc_final: 0.7725 (mp) REVERT: B 342 PHE cc_start: 0.8765 (m-80) cc_final: 0.8482 (m-80) REVERT: B 351 TYR cc_start: 0.7589 (p90) cc_final: 0.7055 (p90) REVERT: B 354 ASN cc_start: 0.7697 (t0) cc_final: 0.7421 (t0) REVERT: B 396 TYR cc_start: 0.7555 (m-10) cc_final: 0.7131 (m-10) REVERT: B 569 ILE cc_start: 0.4445 (OUTLIER) cc_final: 0.4081 (mp) REVERT: C 32 PHE cc_start: 0.7938 (m-10) cc_final: 0.7513 (m-80) REVERT: C 52 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7686 (tm-30) REVERT: C 347 PHE cc_start: 0.8101 (m-10) cc_final: 0.7714 (m-10) REVERT: C 414 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7556 (mt0) REVERT: C 523 THR cc_start: 0.8342 (p) cc_final: 0.7938 (t) REVERT: C 551 VAL cc_start: 0.7981 (OUTLIER) cc_final: 0.7767 (m) REVERT: C 569 ILE cc_start: 0.5961 (OUTLIER) cc_final: 0.5523 (mp) REVERT: C 740 MET cc_start: 0.8547 (tpt) cc_final: 0.8035 (mtt) REVERT: C 814 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8687 (mmmt) REVERT: C 918 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: C 950 ASP cc_start: 0.8245 (t70) cc_final: 0.7948 (m-30) outliers start: 55 outliers final: 42 residues processed: 207 average time/residue: 0.1522 time to fit residues: 53.9141 Evaluate side-chains 208 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 102 optimal weight: 0.7980 chunk 222 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 251 optimal weight: 6.9990 chunk 246 optimal weight: 9.9990 chunk 182 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 286 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 121 ASN ** 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 = 0.4479 r_free = 0.4479 target = 0.193676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.146616 restraints weight = 32914.239| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 3.44 r_work: 0.3545 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26372 Z= 0.154 Angle : 0.605 19.428 36059 Z= 0.293 Chirality : 0.047 0.369 4304 Planarity : 0.004 0.054 4492 Dihedral : 4.047 22.202 3355 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.16 % Allowed : 14.25 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.15), residues: 3077 helix: 1.54 (0.21), residues: 661 sheet: 0.36 (0.19), residues: 727 loop : -1.32 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1039 TYR 0.026 0.001 TYR C 453 PHE 0.023 0.001 PHE B1121 TRP 0.009 0.001 TRP A 436 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.15 (26247) covalent geometry : angle 0.57202 / 0.29 (35724) SS BOND : bond 0.00374 / 0.21 ( 40) SS BOND : angle 1.54512 / 1.04 ( 80) hydrogen bonds : bond 0.05181 / 3.47 ( 972) hydrogen bonds : angle 4.63313 / 3.16 ( 2685) link_BETA1-4 : bond 0.00498 / 0.32 ( 35) link_BETA1-4 : angle 1.43261 / 0.91 ( 105) link_NAG-ASN : bond 0.00465 / 0.38 ( 50) link_NAG-ASN : angle 2.72536 / 1.90 ( 150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5813.79 seconds wall clock time: 100 minutes 48.29 seconds (6048.29 seconds total)