Starting phenix.real_space_refine on Sat Jul 4 01:07:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g9x_29881/07_2026/8g9x_29881.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9x_29881/07_2026/8g9x_29881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g9x_29881/07_2026/8g9x_29881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9x_29881/07_2026/8g9x_29881.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8g9x_29881/07_2026/8g9x_29881.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g9x_29881/07_2026/8g9x_29881.cif" model { file = "/net/cci-nas-00/data/ceres_data/8g9x_29881/07_2026/8g9x_29881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9x_29881/07_2026/8g9x_29881.cif" } resolution = 4.46 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= 0.010 sd= 0.053 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 115 5.16 5 C 10610 2.51 5 N 2809 2.21 5 O 3502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s 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: 17036 Number of models: 1 Model: "" Number of chains: 53 Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "E" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "G" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "H" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 933 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 100} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "P" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 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: "C" 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: "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: 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: "S" 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: "T" 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: "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: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: 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: 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: "g" 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: "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: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: 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: "s" 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: "t" 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: "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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.44, per 1000 atoms: 0.20 Number of scatterers: 17036 At special positions: 0 Unit cell: (126.644, 149.182, 133.083, 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 115 16.00 O 3502 8.00 N 2809 7.00 C 10610 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS P 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.02 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS O 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.02 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.02 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 598 " - pdb=" SG CYS O 604 " distance=2.02 Simple disulfide: pdb=" SG CYS P 54 " - pdb=" SG CYS P 74 " distance=2.03 Simple disulfide: pdb=" SG CYS P 119 " - pdb=" SG CYS P 205 " distance=2.03 Simple disulfide: pdb=" SG CYS P 126 " - pdb=" SG CYS P 196 " distance=2.03 Simple disulfide: pdb=" SG CYS P 131 " - pdb=" SG CYS P 157 " distance=2.03 Simple disulfide: pdb=" SG CYS P 201 " - pdb=" SG CYS P 433 " distance=2.03 Simple disulfide: pdb=" SG CYS P 218 " - pdb=" SG CYS P 247 " distance=2.02 Simple disulfide: pdb=" SG CYS P 228 " - pdb=" SG CYS P 239 " distance=2.03 Simple disulfide: pdb=" SG CYS P 296 " - pdb=" SG CYS P 331 " distance=2.03 Simple disulfide: pdb=" SG CYS P 378 " - pdb=" SG CYS P 445 " distance=2.02 Simple disulfide: pdb=" SG CYS P 385 " - pdb=" SG CYS P 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA a 3 " - " MAN a 4 " " BMA n 3 " - " MAN n 4 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " 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 a 2 " - " BMA a 3 " " 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 e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " NAG-ASN " NAG A 1 " - " ASN E 88 " " NAG B 701 " - " ASN B 637 " " NAG C 1 " - " ASN E 156 " " NAG D 701 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 339 " " NAG E 603 " - " ASN E 355 " " NAG E 604 " - " ASN E 276 " " NAG F 1 " - " ASN E 160 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 339 " " NAG G 603 " - " ASN G 355 " " NAG G 604 " - " ASN G 276 " " NAG I 1 " - " ASN E 197 " " NAG J 1 " - " ASN E 234 " " NAG K 1 " - " ASN E 262 " " NAG M 1 " - " ASN E 295 " " NAG N 1 " - " ASN E 301 " " NAG O 701 " - " ASN O 637 " " NAG P 601 " - " ASN P 133 " " NAG P 602 " - " ASN P 339 " " NAG P 603 " - " ASN P 355 " " NAG P 604 " - " ASN P 276 " " NAG Q 1 " - " ASN E 332 " " NAG R 1 " - " ASN E 363 " " NAG S 1 " - " ASN E 386 " " NAG T 1 " - " ASN E 392 " " NAG U 1 " - " ASN E 448 " " NAG V 1 " - " ASN G 88 " " NAG W 1 " - " ASN G 156 " " NAG X 1 " - " ASN G 160 " " NAG Y 1 " - " ASN G 197 " " NAG Z 1 " - " ASN G 234 " " NAG a 1 " - " ASN G 262 " " NAG b 1 " - " ASN G 295 " " NAG c 1 " - " ASN G 301 " " NAG d 1 " - " ASN G 332 " " NAG e 1 " - " ASN G 363 " " NAG f 1 " - " ASN G 386 " " NAG g 1 " - " ASN G 392 " " NAG h 1 " - " ASN G 448 " " NAG i 1 " - " ASN P 88 " " NAG j 1 " - " ASN P 156 " " NAG k 1 " - " ASN P 160 " " NAG l 1 " - " ASN P 197 " " NAG m 1 " - " ASN P 234 " " NAG n 1 " - " ASN P 262 " " NAG o 1 " - " ASN P 295 " " NAG p 1 " - " ASN P 301 " " NAG q 1 " - " ASN P 332 " " NAG r 1 " - " ASN P 363 " " NAG s 1 " - " ASN P 386 " " NAG t 1 " - " ASN P 392 " " NAG u 1 " - " ASN P 448 " Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 881.8 milliseconds 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 41 sheets defined 20.4% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.773A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 595 removed outlier: 3.864A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 641 through 664 removed outlier: 3.672A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.724A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 595 removed outlier: 3.764A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.549A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 664 removed outlier: 4.098A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 removed outlier: 3.681A pdb=" N GLU E 62 " --> pdb=" O LYS E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 115 removed outlier: 3.684A pdb=" N MET E 104 " --> pdb=" O MET E 100 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.818A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.714A pdb=" N LYS E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.313A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.883A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 removed outlier: 3.689A pdb=" N GLU G 62 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 115 removed outlier: 3.681A pdb=" N HIS G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.870A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 354 removed outlier: 3.710A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.337A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 3.828A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'O' and resid 529 through 534 Processing helix chain 'O' and resid 537 through 543 removed outlier: 3.752A pdb=" N ASN O 543 " --> pdb=" O VAL O 539 " (cutoff:3.500A) Processing helix chain 'O' and resid 572 through 595 removed outlier: 3.620A pdb=" N ALA O 578 " --> pdb=" O LYS O 574 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU O 581 " --> pdb=" O GLN O 577 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLU O 584 " --> pdb=" O VAL O 580 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP O 589 " --> pdb=" O ARG O 585 " (cutoff:3.500A) Processing helix chain 'O' and resid 627 through 636 removed outlier: 3.581A pdb=" N LYS O 633 " --> pdb=" O LEU O 629 " (cutoff:3.500A) Processing helix chain 'O' and resid 641 through 664 removed outlier: 3.870A pdb=" N GLU O 647 " --> pdb=" O TYR O 643 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU O 648 " --> pdb=" O GLY O 644 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN O 653 " --> pdb=" O SER O 649 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU O 663 " --> pdb=" O ASP O 659 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP O 664 " --> pdb=" O LEU O 660 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 62 removed outlier: 3.691A pdb=" N GLU P 62 " --> pdb=" O LYS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 115 removed outlier: 3.729A pdb=" N MET P 104 " --> pdb=" O MET P 100 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS P 105 " --> pdb=" O VAL P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 126 removed outlier: 3.811A pdb=" N LEU P 125 " --> pdb=" O LEU P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 354 removed outlier: 3.665A pdb=" N LYS P 347 " --> pdb=" O GLY P 343 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS P 352 " --> pdb=" O GLN P 348 " (cutoff:3.500A) Processing helix chain 'P' and resid 425 through 429 removed outlier: 4.349A pdb=" N ARG P 429 " --> pdb=" O MET P 426 " (cutoff:3.500A) Processing helix chain 'P' and resid 475 through 480 removed outlier: 3.734A pdb=" N TRP P 479 " --> pdb=" O MET P 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 604 removed outlier: 3.739A pdb=" N CYS B 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL G 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 603 through 604 removed outlier: 3.914A pdb=" N CYS D 604 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL P 38 " --> pdb=" O CYS D 604 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 495 through 499 removed outlier: 5.793A pdb=" N VAL O 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N VAL E 38 " --> pdb=" O THR O 606 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N THR O 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.768A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU E 86 " --> pdb=" O VAL E 242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 91 through 92 Processing sheet with id=AA6, first strand: chain 'E' and resid 154 through 155 Processing sheet with id=AA7, first strand: chain 'E' and resid 158 through 162 Processing sheet with id=AA8, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AA9, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.843A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.287A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.134A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.607A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG E 273 " --> pdb=" O LEU E 285 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.843A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 297 through 298 Processing sheet with id=AB3, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.673A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 330 through 334 Processing sheet with id=AB5, first strand: chain 'E' and resid 375 through 378 Processing sheet with id=AB6, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.676A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 91 through 92 Processing sheet with id=AB8, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AB9, first strand: chain 'G' and resid 158 through 162 Processing sheet with id=AC1, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AC2, first strand: chain 'G' and resid 260 through 261 removed outlier: 6.906A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 12.018A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG G 273 " --> pdb=" O LEU G 285 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 260 through 261 removed outlier: 6.906A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 297 through 298 Processing sheet with id=AC5, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.757A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 330 through 334 Processing sheet with id=AC7, first strand: chain 'G' and resid 375 through 378 Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.657A pdb=" N LEU H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.644A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG H 94 " --> pdb=" O ALA H 101 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.016A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.574A pdb=" N LEU L 33 " --> pdb=" O LYS L 49 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 45 through 47 removed outlier: 3.666A pdb=" N ILE P 225 " --> pdb=" O VAL P 245 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL P 242 " --> pdb=" O LEU P 86 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU P 86 " --> pdb=" O VAL P 242 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 91 through 93 removed outlier: 3.701A pdb=" N GLY P 237 " --> pdb=" O PHE P 93 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 154 through 155 Processing sheet with id=AD7, first strand: chain 'P' and resid 159 through 162 Processing sheet with id=AD8, first strand: chain 'P' and resid 181 through 183 Processing sheet with id=AD9, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.725A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLY P 451 " --> pdb=" O THR P 290 " (cutoff:3.500A) removed outlier: 10.922A pdb=" N THR P 290 " --> pdb=" O GLY P 451 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N ILE P 453 " --> pdb=" O PHE P 288 " (cutoff:3.500A) removed outlier: 11.783A pdb=" N PHE P 288 " --> pdb=" O ILE P 453 " (cutoff:3.500A) removed outlier: 10.102A pdb=" N THR P 455 " --> pdb=" O VAL P 286 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N VAL P 286 " --> pdb=" O THR P 455 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG P 273 " --> pdb=" O LEU P 285 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.725A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG P 360 " --> pdb=" O PHE P 468 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 297 through 298 Processing sheet with id=AE3, first strand: chain 'P' and resid 304 through 312 removed outlier: 6.746A pdb=" N GLN P 315 " --> pdb=" O ILE P 309 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 330 through 334 Processing sheet with id=AE5, first strand: chain 'P' and resid 375 through 378 468 hydrogen bonds defined for protein. 1209 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: 2.87 Time building geometry restraints manager: 2.26 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: 5279 1.34 - 1.47: 4442 1.47 - 1.59: 7477 1.59 - 1.72: 0 1.72 - 1.84: 154 Bond restraints: 17352 Sorted by residual: bond pdb=" CG GLU O 584 " pdb=" CD GLU O 584 " ideal model delta sigma weight residual 1.516 1.451 0.065 2.50e-02 1.60e+03 6.73e+00 bond pdb=" CG MET P 426 " pdb=" SD MET P 426 " ideal model delta sigma weight residual 1.803 1.747 0.056 2.50e-02 1.60e+03 5.00e+00 bond pdb=" C1 MAN K 4 " pdb=" C2 MAN K 4 " ideal model delta sigma weight residual 1.526 1.568 -0.042 2.00e-02 2.50e+03 4.39e+00 bond pdb=" C1 BMA t 3 " pdb=" C2 BMA t 3 " ideal model delta sigma weight residual 1.519 1.560 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" CG MET E 426 " pdb=" SD MET E 426 " ideal model delta sigma weight residual 1.803 1.752 0.051 2.50e-02 1.60e+03 4.17e+00 ... (remaining 17347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 23251 4.66 - 9.32: 283 9.32 - 13.98: 12 13.98 - 18.64: 1 18.64 - 23.30: 1 Bond angle restraints: 23548 Sorted by residual: angle pdb=" CB MET E 95 " pdb=" CG MET E 95 " pdb=" SD MET E 95 " ideal model delta sigma weight residual 112.70 89.40 23.30 3.00e+00 1.11e-01 6.03e+01 angle pdb=" N GLY E 152 " pdb=" CA GLY E 152 " pdb=" C GLY E 152 " ideal model delta sigma weight residual 113.18 98.92 14.26 2.37e+00 1.78e-01 3.62e+01 angle pdb=" N GLU O 657 " pdb=" CA GLU O 657 " pdb=" CB GLU O 657 " ideal model delta sigma weight residual 110.28 118.41 -8.13 1.55e+00 4.16e-01 2.75e+01 angle pdb=" CA MET E 95 " pdb=" CB MET E 95 " pdb=" CG MET E 95 " ideal model delta sigma weight residual 114.10 124.59 -10.49 2.00e+00 2.50e-01 2.75e+01 angle pdb=" C MET E 95 " pdb=" N TRP E 96 " pdb=" CA TRP E 96 " ideal model delta sigma weight residual 122.60 112.86 9.74 1.88e+00 2.83e-01 2.68e+01 ... (remaining 23543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 8440 16.92 - 33.83: 898 33.83 - 50.75: 169 50.75 - 67.66: 30 67.66 - 84.58: 27 Dihedral angle restraints: 9564 sinusoidal: 3863 harmonic: 5701 Sorted by residual: dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -154.08 68.08 1 1.00e+01 1.00e-02 6.02e+01 dihedral pdb=" CB CYS P 119 " pdb=" SG CYS P 119 " pdb=" SG CYS P 205 " pdb=" CB CYS P 205 " ideal model delta sinusoidal sigma weight residual -86.00 -154.06 68.06 1 1.00e+01 1.00e-02 6.01e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -151.75 65.75 1 1.00e+01 1.00e-02 5.66e+01 ... (remaining 9561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2542 0.095 - 0.190: 364 0.190 - 0.284: 53 0.284 - 0.379: 13 0.379 - 0.474: 3 Chirality restraints: 2975 Sorted by residual: chirality pdb=" CB ILE G 284 " pdb=" CA ILE G 284 " pdb=" CG1 ILE G 284 " pdb=" CG2 ILE G 284 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.61e+00 chirality pdb=" CB ILE E 284 " pdb=" CA ILE E 284 " pdb=" CG1 ILE E 284 " pdb=" CG2 ILE E 284 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN G 156 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.68e+00 ... (remaining 2972 not shown) Planarity restraints: 2909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 427 " 0.041 2.00e-02 2.50e+03 3.83e-02 3.67e+01 pdb=" CG TRP G 427 " -0.103 2.00e-02 2.50e+03 pdb=" CD1 TRP G 427 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP G 427 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP G 427 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 427 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 427 " 0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 427 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 427 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP G 427 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 427 " 0.032 2.00e-02 2.50e+03 3.81e-02 3.63e+01 pdb=" CG TRP P 427 " -0.101 2.00e-02 2.50e+03 pdb=" CD1 TRP P 427 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 TRP P 427 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP P 427 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP P 427 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP P 427 " 0.021 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 427 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 427 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP P 427 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 427 " -0.040 2.00e-02 2.50e+03 3.75e-02 3.52e+01 pdb=" CG TRP E 427 " 0.101 2.00e-02 2.50e+03 pdb=" CD1 TRP E 427 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP E 427 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP E 427 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 427 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 427 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 427 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 427 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 427 " 0.002 2.00e-02 2.50e+03 ... (remaining 2906 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1884 2.73 - 3.27: 17018 3.27 - 3.82: 28230 3.82 - 4.36: 32428 4.36 - 4.90: 55072 Nonbonded interactions: 134632 Sorted by model distance: nonbonded pdb=" OH TYR E 61 " pdb=" O CYS E 74 " model vdw 2.188 3.040 nonbonded pdb=" OH TYR P 61 " pdb=" O CYS P 74 " model vdw 2.210 3.040 nonbonded pdb=" O LEU P 369 " pdb=" OG1 THR P 373 " model vdw 2.232 3.040 nonbonded pdb=" OD1 ASN G 302 " pdb=" OG1 THR G 320 " model vdw 2.243 3.040 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.252 3.040 ... (remaining 134627 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 'F' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'u' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'j' selection = chain 'r' selection = chain 's' selection = chain 't' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'P' } ncs_group { reference = chain 'K' selection = chain 'a' selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.040 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 : 0.008 0.066 17501 Z= 0.404 Angle : 1.376 23.299 23957 Z= 0.701 Chirality : 0.072 0.474 2975 Planarity : 0.008 0.057 2855 Dihedral : 14.440 84.577 5770 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.98 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -4.84 (0.15), residues: 1949 helix: -4.56 (0.10), residues: 422 sheet: -2.76 (0.20), residues: 490 loop : -2.82 (0.16), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG G 327 TYR 0.034 0.003 TYR D 643 PHE 0.038 0.004 PHE P 288 TRP 0.103 0.005 TRP G 427 HIS 0.012 0.003 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00814 / 0.40 (17352) covalent geometry : angle 1.32362 / 0.69 (23548) SS BOND : bond 0.00541 / 0.35 ( 38) SS BOND : angle 2.80276 / 1.86 ( 76) hydrogen bonds : bond 0.15427 / 10.28 ( 458) hydrogen bonds : angle 8.37158 / 5.89 ( 1209) link_ALPHA1-3 : bond 0.00393 / 0.19 ( 3) link_ALPHA1-3 : angle 1.79208 / 1.11 ( 9) link_BETA1-4 : bond 0.00842 / 0.59 ( 54) link_BETA1-4 : angle 2.54678 / 1.66 ( 162) link_NAG-ASN : bond 0.00954 / 0.68 ( 54) link_NAG-ASN : angle 3.88887 / 2.53 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.498 Fit side-chains REVERT: B 626 MET cc_start: 0.8308 (ppp) cc_final: 0.7858 (ppp) REVERT: D 530 MET cc_start: 0.9099 (mpp) cc_final: 0.8555 (mpp) REVERT: E 271 MET cc_start: 0.9402 (tpt) cc_final: 0.9201 (tpp) REVERT: G 271 MET cc_start: 0.9445 (tpt) cc_final: 0.9068 (tpp) REVERT: G 475 MET cc_start: 0.9392 (mmm) cc_final: 0.8570 (mmm) REVERT: P 271 MET cc_start: 0.9155 (tpt) cc_final: 0.8743 (tpp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1061 time to fit residues: 10.2395 Evaluate side-chains 50 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN E 103 GLN E 289 ASN E 478 ASN G 103 GLN G 289 ASN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 GLN ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 289 ASN P 432 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.027988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.021598 restraints weight = 305764.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.022278 restraints weight = 178729.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.022769 restraints weight = 123194.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.023087 restraints weight = 93297.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.023305 restraints weight = 76332.745| |-----------------------------------------------------------------------------| r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17501 Z= 0.269 Angle : 0.859 14.478 23957 Z= 0.422 Chirality : 0.045 0.262 2975 Planarity : 0.005 0.037 2855 Dihedral : 6.354 36.086 2108 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.54 (0.17), residues: 1949 helix: -2.36 (0.22), residues: 421 sheet: -2.66 (0.20), residues: 489 loop : -2.13 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 192 TYR 0.017 0.002 TYR O 638 PHE 0.018 0.002 PHE G 391 TRP 0.039 0.003 TRP G 427 HIS 0.007 0.002 HIS E 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.27 (17352) covalent geometry : angle 0.81889 / 0.41 (23548) SS BOND : bond 0.00975 / 0.73 ( 38) SS BOND : angle 1.55462 / 1.08 ( 76) hydrogen bonds : bond 0.04607 / 3.01 ( 458) hydrogen bonds : angle 6.27917 / 4.38 ( 1209) link_ALPHA1-3 : bond 0.00724 / 0.36 ( 3) link_ALPHA1-3 : angle 1.73802 / 1.08 ( 9) link_BETA1-4 : bond 0.00471 / 0.35 ( 54) link_BETA1-4 : angle 1.88521 / 1.21 ( 162) link_NAG-ASN : bond 0.00671 / 0.46 ( 54) link_NAG-ASN : angle 2.60084 / 1.73 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.554 Fit side-chains REVERT: D 530 MET cc_start: 0.8724 (mpp) cc_final: 0.8197 (mpp) REVERT: E 161 MET cc_start: 0.8709 (tmm) cc_final: 0.8477 (tmm) REVERT: E 271 MET cc_start: 0.9417 (tpt) cc_final: 0.9194 (tpt) REVERT: P 271 MET cc_start: 0.9189 (tpt) cc_final: 0.8731 (tpt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1013 time to fit residues: 9.0370 Evaluate side-chains 45 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 38 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 181 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 543 ASN E 432 GLN G 432 GLN G 478 ASN ** O 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 478 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.027158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.020819 restraints weight = 310241.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.021453 restraints weight = 184381.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.021918 restraints weight = 128789.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.022249 restraints weight = 98306.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.022422 restraints weight = 81016.833| |-----------------------------------------------------------------------------| r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17501 Z= 0.287 Angle : 0.863 13.514 23957 Z= 0.422 Chirality : 0.045 0.256 2975 Planarity : 0.005 0.040 2855 Dihedral : 6.227 33.978 2108 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.06 % Allowed : 4.43 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.18 (0.18), residues: 1949 helix: -1.61 (0.24), residues: 422 sheet: -2.73 (0.19), residues: 516 loop : -1.91 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 542 TYR 0.020 0.002 TYR E 318 PHE 0.031 0.003 PHE G 391 TRP 0.024 0.003 TRP G 479 HIS 0.005 0.001 HIS P 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.29 (17352) covalent geometry : angle 0.82317 / 0.41 (23548) SS BOND : bond 0.00453 / 0.34 ( 38) SS BOND : angle 1.56075 / 1.09 ( 76) hydrogen bonds : bond 0.04237 / 2.75 ( 458) hydrogen bonds : angle 6.09661 / 4.24 ( 1209) link_ALPHA1-3 : bond 0.00698 / 0.32 ( 3) link_ALPHA1-3 : angle 1.55346 / 0.95 ( 9) link_BETA1-4 : bond 0.00476 / 0.35 ( 54) link_BETA1-4 : angle 1.82303 / 1.17 ( 162) link_NAG-ASN : bond 0.00931 / 0.64 ( 54) link_NAG-ASN : angle 2.67209 / 1.79 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: D 530 MET cc_start: 0.8675 (mpp) cc_final: 0.7846 (mpp) REVERT: E 271 MET cc_start: 0.9358 (tpt) cc_final: 0.8912 (tmm) REVERT: E 434 MET cc_start: 0.9309 (tpp) cc_final: 0.9068 (tpp) REVERT: P 161 MET cc_start: 0.8724 (tmm) cc_final: 0.8267 (tmm) REVERT: P 271 MET cc_start: 0.9131 (tpt) cc_final: 0.8781 (tpp) outliers start: 1 outliers final: 0 residues processed: 50 average time/residue: 0.0962 time to fit residues: 8.5765 Evaluate side-chains 44 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 94 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 85 optimal weight: 0.0980 chunk 139 optimal weight: 1.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 478 ASN G 315 GLN L 32 ASN L 92 ASN ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 478 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.028182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.021808 restraints weight = 295031.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.022497 restraints weight = 172945.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.022985 restraints weight = 118798.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.023277 restraints weight = 90687.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.023528 restraints weight = 73768.533| |-----------------------------------------------------------------------------| r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17501 Z= 0.142 Angle : 0.712 13.798 23957 Z= 0.344 Chirality : 0.044 0.264 2975 Planarity : 0.004 0.044 2855 Dihedral : 5.864 32.557 2108 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.06 % Allowed : 3.97 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.74 (0.18), residues: 1949 helix: -1.13 (0.25), residues: 407 sheet: -2.20 (0.22), residues: 450 loop : -1.92 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 94 TYR 0.020 0.001 TYR D 643 PHE 0.013 0.001 PHE G 391 TRP 0.018 0.002 TRP D 571 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (17352) covalent geometry : angle 0.67635 / 0.34 (23548) SS BOND : bond 0.00328 / 0.22 ( 38) SS BOND : angle 1.34150 / 0.89 ( 76) hydrogen bonds : bond 0.03357 / 2.18 ( 458) hydrogen bonds : angle 5.63256 / 3.93 ( 1209) link_ALPHA1-3 : bond 0.00730 / 0.34 ( 3) link_ALPHA1-3 : angle 1.43767 / 0.90 ( 9) link_BETA1-4 : bond 0.00439 / 0.33 ( 54) link_BETA1-4 : angle 1.54452 / 1.00 ( 162) link_NAG-ASN : bond 0.00396 / 0.26 ( 54) link_NAG-ASN : angle 2.25581 / 1.50 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.497 Fit side-chains REVERT: D 530 MET cc_start: 0.8734 (mpp) cc_final: 0.8066 (mpp) REVERT: E 271 MET cc_start: 0.9380 (tpt) cc_final: 0.8934 (tmm) REVERT: P 271 MET cc_start: 0.9105 (tpt) cc_final: 0.8753 (tpp) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.0926 time to fit residues: 8.2941 Evaluate side-chains 44 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 112 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 191 optimal weight: 20.0000 chunk 148 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 0.0050 chunk 2 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 overall best weight: 3.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.027852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.021493 restraints weight = 295605.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.022149 restraints weight = 175052.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.022637 restraints weight = 121510.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.022989 restraints weight = 91853.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.023159 restraints weight = 75007.527| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17501 Z= 0.161 Angle : 0.711 14.317 23957 Z= 0.345 Chirality : 0.044 0.262 2975 Planarity : 0.004 0.037 2855 Dihedral : 5.704 33.222 2108 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.54 (0.18), residues: 1949 helix: -0.89 (0.26), residues: 400 sheet: -2.07 (0.22), residues: 450 loop : -1.81 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 192 TYR 0.016 0.001 TYR D 643 PHE 0.014 0.002 PHE G 391 TRP 0.018 0.002 TRP E 96 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (17352) covalent geometry : angle 0.67775 / 0.34 (23548) SS BOND : bond 0.00349 / 0.25 ( 38) SS BOND : angle 1.22394 / 0.82 ( 76) hydrogen bonds : bond 0.03325 / 2.15 ( 458) hydrogen bonds : angle 5.55631 / 3.87 ( 1209) link_ALPHA1-3 : bond 0.00638 / 0.29 ( 3) link_ALPHA1-3 : angle 1.38857 / 0.85 ( 9) link_BETA1-4 : bond 0.00412 / 0.31 ( 54) link_BETA1-4 : angle 1.54754 / 1.00 ( 162) link_NAG-ASN : bond 0.00434 / 0.30 ( 54) link_NAG-ASN : angle 2.19490 / 1.46 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.624 Fit side-chains REVERT: D 530 MET cc_start: 0.8752 (mpp) cc_final: 0.8171 (mpp) REVERT: E 271 MET cc_start: 0.9389 (tpt) cc_final: 0.8962 (tmm) REVERT: P 161 MET cc_start: 0.8558 (tmm) cc_final: 0.8333 (tmm) REVERT: P 271 MET cc_start: 0.9082 (tpt) cc_final: 0.8747 (tpp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0957 time to fit residues: 8.0466 Evaluate side-chains 44 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 183 optimal weight: 9.9990 chunk 155 optimal weight: 50.0000 chunk 178 optimal weight: 8.9990 chunk 81 optimal weight: 0.2980 chunk 139 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.028254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.021907 restraints weight = 290574.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.022597 restraints weight = 172189.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.023080 restraints weight = 119068.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.023395 restraints weight = 90485.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.023586 restraints weight = 73666.186| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17501 Z= 0.125 Angle : 0.671 13.774 23957 Z= 0.322 Chirality : 0.044 0.267 2975 Planarity : 0.004 0.035 2855 Dihedral : 5.508 32.662 2108 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.32 (0.18), residues: 1949 helix: -0.62 (0.26), residues: 400 sheet: -1.89 (0.23), residues: 454 loop : -1.74 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 94 TYR 0.016 0.001 TYR O 638 PHE 0.011 0.001 PHE P 288 TRP 0.019 0.002 TRP D 571 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (17352) covalent geometry : angle 0.64103 / 0.32 (23548) SS BOND : bond 0.00254 / 0.18 ( 38) SS BOND : angle 1.11173 / 0.77 ( 76) hydrogen bonds : bond 0.03015 / 1.94 ( 458) hydrogen bonds : angle 5.30827 / 3.69 ( 1209) link_ALPHA1-3 : bond 0.00612 / 0.27 ( 3) link_ALPHA1-3 : angle 1.39368 / 0.87 ( 9) link_BETA1-4 : bond 0.00437 / 0.32 ( 54) link_BETA1-4 : angle 1.42938 / 0.93 ( 162) link_NAG-ASN : bond 0.00307 / 0.22 ( 54) link_NAG-ASN : angle 2.03201 / 1.34 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: B 585 ARG cc_start: 0.9576 (ptm-80) cc_final: 0.9127 (ptm-80) REVERT: D 530 MET cc_start: 0.8713 (mpp) cc_final: 0.8187 (mpp) REVERT: E 271 MET cc_start: 0.9380 (tpt) cc_final: 0.9005 (tmm) REVERT: E 434 MET cc_start: 0.9304 (tpp) cc_final: 0.8993 (tpp) REVERT: P 161 MET cc_start: 0.8598 (tmm) cc_final: 0.8305 (tmm) REVERT: P 271 MET cc_start: 0.9113 (tpt) cc_final: 0.8778 (tpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0932 time to fit residues: 8.4284 Evaluate side-chains 45 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 111 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 577 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 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 = 0.2898 r_free = 0.2898 target = 0.027015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.020741 restraints weight = 305202.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.021417 restraints weight = 181151.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.021882 restraints weight = 125594.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.022198 restraints weight = 95901.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.022412 restraints weight = 78702.342| |-----------------------------------------------------------------------------| r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17501 Z= 0.208 Angle : 0.742 12.008 23957 Z= 0.357 Chirality : 0.043 0.260 2975 Planarity : 0.004 0.035 2855 Dihedral : 5.593 30.918 2108 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.26 (0.18), residues: 1949 helix: -0.48 (0.27), residues: 375 sheet: -2.02 (0.22), residues: 474 loop : -1.61 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 192 TYR 0.015 0.002 TYR O 638 PHE 0.016 0.002 PHE G 391 TRP 0.019 0.002 TRP E 96 HIS 0.006 0.001 HIS P 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.21 (17352) covalent geometry : angle 0.71005 / 0.35 (23548) SS BOND : bond 0.00335 / 0.24 ( 38) SS BOND : angle 1.27051 / 0.87 ( 76) hydrogen bonds : bond 0.03303 / 2.12 ( 458) hydrogen bonds : angle 5.51063 / 3.82 ( 1209) link_ALPHA1-3 : bond 0.00587 / 0.28 ( 3) link_ALPHA1-3 : angle 1.45775 / 0.89 ( 9) link_BETA1-4 : bond 0.00404 / 0.30 ( 54) link_BETA1-4 : angle 1.58725 / 1.03 ( 162) link_NAG-ASN : bond 0.00552 / 0.38 ( 54) link_NAG-ASN : angle 2.18134 / 1.46 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.529 Fit side-chains REVERT: B 585 ARG cc_start: 0.9604 (ptm-80) cc_final: 0.9159 (ptm-80) REVERT: B 626 MET cc_start: 0.7813 (ppp) cc_final: 0.7345 (ppp) REVERT: D 530 MET cc_start: 0.8807 (mpp) cc_final: 0.8256 (mpp) REVERT: E 271 MET cc_start: 0.9380 (tpt) cc_final: 0.8918 (tmm) REVERT: E 434 MET cc_start: 0.9347 (tpp) cc_final: 0.9038 (tpp) REVERT: P 271 MET cc_start: 0.9138 (tpt) cc_final: 0.8662 (tpp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1023 time to fit residues: 8.8957 Evaluate side-chains 45 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 143 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 189 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 182 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 577 GLN D 577 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 216 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.025235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.017927 restraints weight = 272822.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.018424 restraints weight = 187862.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.018774 restraints weight = 144809.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.019047 restraints weight = 120254.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.019236 restraints weight = 104354.137| |-----------------------------------------------------------------------------| r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17501 Z= 0.177 Angle : 0.712 12.823 23957 Z= 0.343 Chirality : 0.043 0.265 2975 Planarity : 0.004 0.035 2855 Dihedral : 5.548 29.808 2108 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -2.13 (0.18), residues: 1949 helix: -0.33 (0.27), residues: 368 sheet: -1.86 (0.23), residues: 447 loop : -1.60 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 273 TYR 0.016 0.001 TYR O 638 PHE 0.013 0.002 PHE G 391 TRP 0.018 0.002 TRP D 571 HIS 0.004 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.18 (17352) covalent geometry : angle 0.68264 / 0.34 (23548) SS BOND : bond 0.00423 / 0.34 ( 38) SS BOND : angle 1.37247 / 0.91 ( 76) hydrogen bonds : bond 0.03162 / 2.02 ( 458) hydrogen bonds : angle 5.41461 / 3.76 ( 1209) link_ALPHA1-3 : bond 0.00533 / 0.25 ( 3) link_ALPHA1-3 : angle 1.46509 / 0.90 ( 9) link_BETA1-4 : bond 0.00400 / 0.29 ( 54) link_BETA1-4 : angle 1.45708 / 0.94 ( 162) link_NAG-ASN : bond 0.00404 / 0.28 ( 54) link_NAG-ASN : angle 2.03741 / 1.35 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: B 585 ARG cc_start: 0.9651 (ptm-80) cc_final: 0.9212 (ptm-80) REVERT: E 271 MET cc_start: 0.9347 (tpt) cc_final: 0.8945 (tmm) REVERT: E 434 MET cc_start: 0.9357 (tpp) cc_final: 0.9098 (tpp) REVERT: P 271 MET cc_start: 0.9082 (tpt) cc_final: 0.8571 (tpp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1032 time to fit residues: 8.8942 Evaluate side-chains 45 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 180 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 7 optimal weight: 0.0970 chunk 188 optimal weight: 5.9990 chunk 121 optimal weight: 50.0000 chunk 13 optimal weight: 40.0000 chunk 178 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 577 GLN D 577 GLN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.027478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.021203 restraints weight = 299254.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.021857 restraints weight = 177097.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.022345 restraints weight = 122977.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.022693 restraints weight = 92956.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.022871 restraints weight = 75789.125| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17501 Z= 0.133 Angle : 0.685 14.262 23957 Z= 0.326 Chirality : 0.043 0.267 2975 Planarity : 0.004 0.035 2855 Dihedral : 5.430 28.821 2108 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -2.07 (0.18), residues: 1949 helix: -0.26 (0.27), residues: 398 sheet: -1.91 (0.23), residues: 441 loop : -1.55 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 94 TYR 0.015 0.001 TYR D 643 PHE 0.011 0.001 PHE P 288 TRP 0.017 0.002 TRP D 571 HIS 0.004 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (17352) covalent geometry : angle 0.65759 / 0.32 (23548) SS BOND : bond 0.00446 / 0.28 ( 38) SS BOND : angle 1.20952 / 0.82 ( 76) hydrogen bonds : bond 0.02930 / 1.87 ( 458) hydrogen bonds : angle 5.25329 / 3.65 ( 1209) link_ALPHA1-3 : bond 0.00544 / 0.24 ( 3) link_ALPHA1-3 : angle 1.38283 / 0.87 ( 9) link_BETA1-4 : bond 0.00412 / 0.30 ( 54) link_BETA1-4 : angle 1.40648 / 0.92 ( 162) link_NAG-ASN : bond 0.00332 / 0.23 ( 54) link_NAG-ASN : angle 1.94187 / 1.28 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: B 585 ARG cc_start: 0.9578 (ptm-80) cc_final: 0.9143 (ptm-80) REVERT: B 626 MET cc_start: 0.7904 (ppp) cc_final: 0.7597 (ppp) REVERT: E 95 MET cc_start: 0.9599 (mmm) cc_final: 0.9212 (mmt) REVERT: E 271 MET cc_start: 0.9321 (tpt) cc_final: 0.8956 (tmm) REVERT: E 434 MET cc_start: 0.9318 (tpp) cc_final: 0.9082 (tpp) REVERT: P 271 MET cc_start: 0.9099 (tpt) cc_final: 0.8615 (tpp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0997 time to fit residues: 8.7208 Evaluate side-chains 45 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 152 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 189 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 577 GLN D 577 GLN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.026397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.020198 restraints weight = 309190.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.020822 restraints weight = 186067.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.021276 restraints weight = 130539.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.021593 restraints weight = 100436.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.021767 restraints weight = 82366.500| |-----------------------------------------------------------------------------| r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17501 Z= 0.230 Angle : 0.786 13.323 23957 Z= 0.377 Chirality : 0.044 0.257 2975 Planarity : 0.004 0.035 2855 Dihedral : 5.661 28.234 2108 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -2.25 (0.18), residues: 1949 helix: -0.46 (0.26), residues: 399 sheet: -2.16 (0.22), residues: 462 loop : -1.56 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 192 TYR 0.014 0.002 TYR E 318 PHE 0.018 0.002 PHE E 176 TRP 0.022 0.002 TRP G 112 HIS 0.005 0.001 HIS G 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.23 (17352) covalent geometry : angle 0.75537 / 0.37 (23548) SS BOND : bond 0.00381 / 0.29 ( 38) SS BOND : angle 1.40164 / 0.94 ( 76) hydrogen bonds : bond 0.03385 / 2.17 ( 458) hydrogen bonds : angle 5.56964 / 3.86 ( 1209) link_ALPHA1-3 : bond 0.00493 / 0.24 ( 3) link_ALPHA1-3 : angle 1.46223 / 0.89 ( 9) link_BETA1-4 : bond 0.00399 / 0.29 ( 54) link_BETA1-4 : angle 1.60994 / 1.04 ( 162) link_NAG-ASN : bond 0.00627 / 0.43 ( 54) link_NAG-ASN : angle 2.19623 / 1.46 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 585 ARG cc_start: 0.9593 (ptm-80) cc_final: 0.9177 (ptm-80) REVERT: B 626 MET cc_start: 0.8096 (ppp) cc_final: 0.7710 (ppp) REVERT: D 530 MET cc_start: 0.8987 (mpp) cc_final: 0.8560 (mpp) REVERT: E 271 MET cc_start: 0.9347 (tpt) cc_final: 0.8893 (tmm) REVERT: E 434 MET cc_start: 0.9348 (tpp) cc_final: 0.9137 (tpp) REVERT: P 271 MET cc_start: 0.9113 (tpt) cc_final: 0.8603 (tpp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1158 time to fit residues: 9.7627 Evaluate side-chains 46 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 38 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 170 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 577 GLN D 577 GLN ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.027834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.021537 restraints weight = 295679.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.022223 restraints weight = 174227.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.022720 restraints weight = 120046.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.023050 restraints weight = 91332.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.023274 restraints weight = 74094.631| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17501 Z= 0.109 Angle : 0.686 14.797 23957 Z= 0.323 Chirality : 0.044 0.276 2975 Planarity : 0.004 0.038 2855 Dihedral : 5.387 27.647 2108 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -1.94 (0.19), residues: 1949 helix: -0.01 (0.28), residues: 380 sheet: -1.85 (0.23), residues: 446 loop : -1.49 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 94 TYR 0.020 0.001 TYR D 643 PHE 0.009 0.001 PHE O 522 TRP 0.018 0.002 TRP G 112 HIS 0.003 0.001 HIS P 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (17352) covalent geometry : angle 0.66226 / 0.32 (23548) SS BOND : bond 0.00252 / 0.18 ( 38) SS BOND : angle 1.17907 / 0.83 ( 76) hydrogen bonds : bond 0.02790 / 1.79 ( 458) hydrogen bonds : angle 5.13417 / 3.57 ( 1209) link_ALPHA1-3 : bond 0.00557 / 0.25 ( 3) link_ALPHA1-3 : angle 1.40509 / 0.91 ( 9) link_BETA1-4 : bond 0.00471 / 0.34 ( 54) link_BETA1-4 : angle 1.32663 / 0.87 ( 162) link_NAG-ASN : bond 0.00295 / 0.21 ( 54) link_NAG-ASN : angle 1.82612 / 1.19 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2175.07 seconds wall clock time: 39 minutes 0.94 seconds (2340.94 seconds total)