Starting phenix.real_space_refine on Sun Aug 24 05:36:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g9x_29881/08_2025/8g9x_29881.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9x_29881/08_2025/8g9x_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_29881/08_2025/8g9x_29881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9x_29881/08_2025/8g9x_29881.map" model { file = "/net/cci-nas-00/data/ceres_data/8g9x_29881/08_2025/8g9x_29881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9x_29881/08_2025/8g9x_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-2.0-5787/lib/python3.9/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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 12 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 dihedrals: 12 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 dihedrals: 3 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.37, per 1000 atoms: 0.26 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: 1.77 Conformation dependent library (CDL) restraints added in 650.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.63 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: 2.95 Time building geometry restraints manager: 2.22 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 - 21.91: 10675 21.91 - 43.83: 844 43.83 - 65.74: 158 65.74 - 87.65: 119 87.65 - 109.57: 63 Dihedral angle restraints: 11859 sinusoidal: 6158 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 11856 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: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.370 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 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 : 19.098 109.567 8065 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 aren 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 covalent geometry : bond 0.00814 (17352) covalent geometry : angle 1.32362 (23548) SS BOND : bond 0.00541 ( 38) SS BOND : angle 2.80276 ( 76) hydrogen bonds : bond 0.15427 ( 458) hydrogen bonds : angle 8.37158 ( 1209) link_ALPHA1-3 : bond 0.00393 ( 3) link_ALPHA1-3 : angle 1.79208 ( 9) link_BETA1-4 : bond 0.00842 ( 54) link_BETA1-4 : angle 2.54678 ( 162) link_NAG-ASN : bond 0.00954 ( 54) link_NAG-ASN : angle 3.88887 ( 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 : 0.849 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: 0.1196 time to fit residues: 11.7074 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 : 0.676 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2942 r_free = 0.2942 target = 0.028028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.021630 restraints weight = 305406.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.022321 restraints weight = 178310.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.022807 restraints weight = 122738.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.023126 restraints weight = 93147.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.023305 restraints weight = 76014.881| |-----------------------------------------------------------------------------| r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17501 Z= 0.263 Angle : 0.884 14.888 23957 Z= 0.426 Chirality : 0.047 0.256 2975 Planarity : 0.005 0.038 2855 Dihedral : 14.621 76.149 4403 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % 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 aren not related in a simple way. whole: -3.53 (0.17), residues: 1949 helix: -2.31 (0.22), residues: 421 sheet: -2.66 (0.20), residues: 489 loop : -2.14 (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 0.034 0.003 TRP G 427 HIS 0.006 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00516 (17352) covalent geometry : angle 0.83920 (23548) SS BOND : bond 0.00942 ( 38) SS BOND : angle 1.41808 ( 76) hydrogen bonds : bond 0.04370 ( 458) hydrogen bonds : angle 6.27763 ( 1209) link_ALPHA1-3 : bond 0.01168 ( 3) link_ALPHA1-3 : angle 2.27281 ( 9) link_BETA1-4 : bond 0.00546 ( 54) link_BETA1-4 : angle 2.27011 ( 162) link_NAG-ASN : bond 0.00644 ( 54) link_NAG-ASN : angle 2.59817 ( 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 : 0.712 Fit side-chains REVERT: D 530 MET cc_start: 0.8693 (mpp) cc_final: 0.8165 (mpp) REVERT: P 271 MET cc_start: 0.9131 (tpt) cc_final: 0.8700 (tpt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1234 time to fit residues: 10.9978 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 : 0.683 ------------------------------------------------------------------------------- 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: 0.5980 chunk 55 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.2920 r_free = 0.2920 target = 0.027560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.021178 restraints weight = 305840.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.021831 restraints weight = 181548.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.022307 restraints weight = 125960.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.022639 restraints weight = 96275.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.022813 restraints weight = 79014.226| |-----------------------------------------------------------------------------| r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17501 Z= 0.239 Angle : 0.830 13.929 23957 Z= 0.401 Chirality : 0.047 0.268 2975 Planarity : 0.004 0.052 2855 Dihedral : 11.457 59.903 4403 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.12 % Allowed : 4.72 % Favored : 95.17 % 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 aren not related in a simple way. whole: -2.98 (0.18), residues: 1949 helix: -1.49 (0.25), residues: 418 sheet: -2.34 (0.21), residues: 450 loop : -2.01 (0.18), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 94 TYR 0.019 0.002 TYR E 318 PHE 0.028 0.002 PHE G 391 TRP 0.023 0.002 TRP G 96 HIS 0.005 0.001 HIS H 95 Details of bonding type rmsd covalent geometry : bond 0.00479 (17352) covalent geometry : angle 0.78840 (23548) SS BOND : bond 0.00558 ( 38) SS BOND : angle 1.35088 ( 76) hydrogen bonds : bond 0.03961 ( 458) hydrogen bonds : angle 5.92924 ( 1209) link_ALPHA1-3 : bond 0.01108 ( 3) link_ALPHA1-3 : angle 1.90206 ( 9) link_BETA1-4 : bond 0.00497 ( 54) link_BETA1-4 : angle 2.06120 ( 162) link_NAG-ASN : bond 0.00587 ( 54) link_NAG-ASN : angle 2.50914 ( 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 53 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.650 Fit side-chains REVERT: D 530 MET cc_start: 0.8638 (mpp) cc_final: 0.7836 (mpp) REVERT: E 271 MET cc_start: 0.9367 (tpt) cc_final: 0.8942 (tmm) REVERT: E 434 MET cc_start: 0.9263 (tpp) cc_final: 0.9030 (tpp) REVERT: P 161 MET cc_start: 0.8705 (tmm) cc_final: 0.8261 (tmm) REVERT: P 271 MET cc_start: 0.9105 (tpt) cc_final: 0.8796 (tpp) outliers start: 2 outliers final: 0 residues processed: 53 average time/residue: 0.1023 time to fit residues: 9.5936 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 : 0.674 ------------------------------------------------------------------------------- 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: 7.9990 chunk 77 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 478 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 GLN L 32 ASN L 92 ASN ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.027542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.021212 restraints weight = 298946.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.021858 restraints weight = 177239.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.022277 restraints weight = 124045.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.022636 restraints weight = 96014.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.022792 restraints weight = 78702.127| |-----------------------------------------------------------------------------| r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17501 Z= 0.198 Angle : 0.759 13.101 23957 Z= 0.366 Chirality : 0.045 0.263 2975 Planarity : 0.004 0.063 2855 Dihedral : 10.020 59.703 4403 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % 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 aren not related in a simple way. whole: -2.70 (0.18), residues: 1949 helix: -1.07 (0.25), residues: 407 sheet: -2.17 (0.22), residues: 450 loop : -1.90 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 192 TYR 0.021 0.002 TYR D 643 PHE 0.015 0.002 PHE G 391 TRP 0.020 0.002 TRP O 571 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00398 (17352) covalent geometry : angle 0.72042 (23548) SS BOND : bond 0.00404 ( 38) SS BOND : angle 1.28619 ( 76) hydrogen bonds : bond 0.03503 ( 458) hydrogen bonds : angle 5.72458 ( 1209) link_ALPHA1-3 : bond 0.01020 ( 3) link_ALPHA1-3 : angle 2.45357 ( 9) link_BETA1-4 : bond 0.00426 ( 54) link_BETA1-4 : angle 1.86092 ( 162) link_NAG-ASN : bond 0.00488 ( 54) link_NAG-ASN : angle 2.27133 ( 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: 0 poor density : 51 time to evaluate : 0.687 Fit side-chains REVERT: D 530 MET cc_start: 0.8680 (mpp) cc_final: 0.7938 (mpp) REVERT: E 271 MET cc_start: 0.9387 (tpt) cc_final: 0.8925 (tmm) REVERT: E 475 MET cc_start: 0.8533 (tpt) cc_final: 0.8116 (tmm) REVERT: P 271 MET cc_start: 0.9109 (tpt) cc_final: 0.8782 (tpp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1201 time to fit residues: 10.7276 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 : 0.696 ------------------------------------------------------------------------------- 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: 6.9990 chunk 127 optimal weight: 9.9990 chunk 191 optimal weight: 20.0000 chunk 148 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 178 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2897 r_free = 0.2897 target = 0.026904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.020605 restraints weight = 307481.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.021225 restraints weight = 183369.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.021698 restraints weight = 128140.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.022033 restraints weight = 97784.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.022206 restraints weight = 80834.877| |-----------------------------------------------------------------------------| r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17501 Z= 0.231 Angle : 0.788 13.232 23957 Z= 0.382 Chirality : 0.046 0.257 2975 Planarity : 0.004 0.036 2855 Dihedral : 9.713 59.907 4403 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % 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 aren not related in a simple way. whole: -2.48 (0.18), residues: 1949 helix: -0.69 (0.27), residues: 370 sheet: -2.07 (0.22), residues: 450 loop : -1.79 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 542 TYR 0.013 0.002 TYR O 638 PHE 0.020 0.002 PHE G 391 TRP 0.022 0.002 TRP B 571 HIS 0.005 0.001 HIS P 85 Details of bonding type rmsd covalent geometry : bond 0.00467 (17352) covalent geometry : angle 0.75304 (23548) SS BOND : bond 0.00424 ( 38) SS BOND : angle 1.18249 ( 76) hydrogen bonds : bond 0.03647 ( 458) hydrogen bonds : angle 5.79140 ( 1209) link_ALPHA1-3 : bond 0.00952 ( 3) link_ALPHA1-3 : angle 1.98042 ( 9) link_BETA1-4 : bond 0.00438 ( 54) link_BETA1-4 : angle 1.82493 ( 162) link_NAG-ASN : bond 0.00601 ( 54) link_NAG-ASN : angle 2.29281 ( 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 50 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.726 Fit side-chains REVERT: D 530 MET cc_start: 0.8780 (mpp) cc_final: 0.8198 (mpp) REVERT: E 271 MET cc_start: 0.9350 (tpt) cc_final: 0.9128 (tpt) REVERT: E 475 MET cc_start: 0.8594 (tpt) cc_final: 0.8169 (tmm) REVERT: P 161 MET cc_start: 0.8617 (tmm) cc_final: 0.8344 (tmm) REVERT: P 271 MET cc_start: 0.9060 (tpt) cc_final: 0.8663 (tpp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1191 time to fit residues: 10.4995 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 : 0.768 ------------------------------------------------------------------------------- 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: 10.0000 chunk 155 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 577 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 577 GLN ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.027115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.020847 restraints weight = 303164.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.021498 restraints weight = 180622.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.021963 restraints weight = 125948.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.022186 restraints weight = 95933.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.022480 restraints weight = 81035.438| |-----------------------------------------------------------------------------| r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17501 Z= 0.186 Angle : 0.731 13.282 23957 Z= 0.352 Chirality : 0.045 0.262 2975 Planarity : 0.004 0.036 2855 Dihedral : 9.307 59.386 4403 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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 aren not related in a simple way. whole: -2.34 (0.18), residues: 1949 helix: -0.54 (0.27), residues: 368 sheet: -1.96 (0.23), residues: 450 loop : -1.73 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 94 TYR 0.018 0.001 TYR O 638 PHE 0.014 0.002 PHE G 391 TRP 0.020 0.002 TRP D 571 HIS 0.004 0.001 HIS P 249 Details of bonding type rmsd covalent geometry : bond 0.00378 (17352) covalent geometry : angle 0.69583 (23548) SS BOND : bond 0.00338 ( 38) SS BOND : angle 1.19630 ( 76) hydrogen bonds : bond 0.03299 ( 458) hydrogen bonds : angle 5.62479 ( 1209) link_ALPHA1-3 : bond 0.01162 ( 3) link_ALPHA1-3 : angle 2.09241 ( 9) link_BETA1-4 : bond 0.00389 ( 54) link_BETA1-4 : angle 1.69908 ( 162) link_NAG-ASN : bond 0.00461 ( 54) link_NAG-ASN : angle 2.18124 ( 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 49 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.705 Fit side-chains REVERT: D 530 MET cc_start: 0.8804 (mpp) cc_final: 0.8212 (mpp) REVERT: E 271 MET cc_start: 0.9372 (tpt) cc_final: 0.9160 (tpt) REVERT: E 434 MET cc_start: 0.9409 (tpp) cc_final: 0.9133 (tpp) REVERT: E 475 MET cc_start: 0.8622 (tpt) cc_final: 0.8187 (tmm) REVERT: P 161 MET cc_start: 0.8653 (tmm) cc_final: 0.8291 (tmm) REVERT: P 271 MET cc_start: 0.9100 (tpt) cc_final: 0.8640 (tpp) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1167 time to fit residues: 10.2157 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 : 0.603 ------------------------------------------------------------------------------- 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: 2.9990 chunk 7 optimal weight: 7.9990 chunk 1 optimal weight: 0.0670 chunk 27 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 98 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 577 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 577 GLN ** P 203 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 = 0.2900 r_free = 0.2900 target = 0.027018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.020771 restraints weight = 302761.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.021405 restraints weight = 181164.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.021861 restraints weight = 126677.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.022199 restraints weight = 96397.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.022375 restraints weight = 79545.993| |-----------------------------------------------------------------------------| r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17501 Z= 0.170 Angle : 0.712 12.212 23957 Z= 0.342 Chirality : 0.044 0.260 2975 Planarity : 0.004 0.037 2855 Dihedral : 8.970 59.616 4403 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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 aren not related in a simple way. whole: -2.28 (0.18), residues: 1949 helix: -0.55 (0.27), residues: 380 sheet: -1.94 (0.23), residues: 447 loop : -1.68 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 94 TYR 0.016 0.001 TYR L 50 PHE 0.013 0.002 PHE P 288 TRP 0.018 0.002 TRP D 571 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00348 (17352) covalent geometry : angle 0.67914 (23548) SS BOND : bond 0.00317 ( 38) SS BOND : angle 1.19877 ( 76) hydrogen bonds : bond 0.03208 ( 458) hydrogen bonds : angle 5.48992 ( 1209) link_ALPHA1-3 : bond 0.00809 ( 3) link_ALPHA1-3 : angle 1.70194 ( 9) link_BETA1-4 : bond 0.00412 ( 54) link_BETA1-4 : angle 1.65499 ( 162) link_NAG-ASN : bond 0.00408 ( 54) link_NAG-ASN : angle 2.10171 ( 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 : 0.518 Fit side-chains REVERT: B 626 MET cc_start: 0.7791 (ppp) cc_final: 0.7391 (ppp) REVERT: D 530 MET cc_start: 0.8826 (mpp) cc_final: 0.8283 (mpp) REVERT: E 95 MET cc_start: 0.9424 (mmm) cc_final: 0.9154 (mmm) REVERT: E 271 MET cc_start: 0.9348 (tpt) cc_final: 0.8923 (tmm) REVERT: E 434 MET cc_start: 0.9370 (tpp) cc_final: 0.9123 (tpp) REVERT: G 426 MET cc_start: 0.9507 (ppp) cc_final: 0.9276 (ppp) REVERT: P 271 MET cc_start: 0.9103 (tpt) cc_final: 0.8592 (tpp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1128 time to fit residues: 10.1301 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 143 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 189 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 577 GLN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 577 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.026707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.020468 restraints weight = 306606.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.021065 restraints weight = 183659.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.021548 restraints weight = 129605.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.021878 restraints weight = 99945.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.022052 restraints weight = 81689.630| |-----------------------------------------------------------------------------| r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17501 Z= 0.182 Angle : 0.729 14.560 23957 Z= 0.349 Chirality : 0.044 0.258 2975 Planarity : 0.004 0.035 2855 Dihedral : 8.824 59.861 4403 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % 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 aren not related in a simple way. whole: -2.24 (0.18), residues: 1949 helix: -0.46 (0.27), residues: 380 sheet: -1.97 (0.23), residues: 441 loop : -1.64 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 94 TYR 0.015 0.001 TYR O 638 PHE 0.014 0.002 PHE P 288 TRP 0.019 0.002 TRP D 571 HIS 0.004 0.001 HIS P 249 Details of bonding type rmsd covalent geometry : bond 0.00372 (17352) covalent geometry : angle 0.69622 (23548) SS BOND : bond 0.00331 ( 38) SS BOND : angle 1.33337 ( 76) hydrogen bonds : bond 0.03185 ( 458) hydrogen bonds : angle 5.48105 ( 1209) link_ALPHA1-3 : bond 0.00821 ( 3) link_ALPHA1-3 : angle 1.73276 ( 9) link_BETA1-4 : bond 0.00398 ( 54) link_BETA1-4 : angle 1.65588 ( 162) link_NAG-ASN : bond 0.00450 ( 54) link_NAG-ASN : angle 2.11011 ( 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 50 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: B 626 MET cc_start: 0.7882 (ppp) cc_final: 0.7653 (ppp) REVERT: D 530 MET cc_start: 0.8949 (mpp) cc_final: 0.8582 (mpp) REVERT: E 271 MET cc_start: 0.9340 (tpt) cc_final: 0.8841 (tmm) REVERT: E 434 MET cc_start: 0.9372 (tpp) cc_final: 0.9156 (tpp) REVERT: G 475 MET cc_start: 0.9465 (mmm) cc_final: 0.8908 (mmm) REVERT: P 271 MET cc_start: 0.9103 (tpt) cc_final: 0.8612 (tpp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1155 time to fit residues: 10.1082 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 : 0.729 ------------------------------------------------------------------------------- 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: 10.0000 chunk 175 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 7 optimal weight: 0.0030 chunk 188 optimal weight: 9.9990 chunk 121 optimal weight: 50.0000 chunk 13 optimal weight: 40.0000 chunk 178 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 overall best weight: 4.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** O 577 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.026344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.020126 restraints weight = 308878.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.020726 restraints weight = 186459.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.021194 restraints weight = 131349.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.021518 restraints weight = 100505.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.021693 restraints weight = 83367.333| |-----------------------------------------------------------------------------| r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17501 Z= 0.212 Angle : 0.759 13.034 23957 Z= 0.364 Chirality : 0.044 0.259 2975 Planarity : 0.004 0.036 2855 Dihedral : 8.834 59.962 4403 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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 aren not related in a simple way. whole: -2.29 (0.18), residues: 1949 helix: -0.48 (0.27), residues: 380 sheet: -2.20 (0.22), residues: 462 loop : -1.57 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 94 TYR 0.014 0.002 TYR L 50 PHE 0.016 0.002 PHE G 391 TRP 0.020 0.002 TRP E 96 HIS 0.006 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00431 (17352) covalent geometry : angle 0.72617 (23548) SS BOND : bond 0.00356 ( 38) SS BOND : angle 1.26182 ( 76) hydrogen bonds : bond 0.03328 ( 458) hydrogen bonds : angle 5.56899 ( 1209) link_ALPHA1-3 : bond 0.00776 ( 3) link_ALPHA1-3 : angle 1.70817 ( 9) link_BETA1-4 : bond 0.00402 ( 54) link_BETA1-4 : angle 1.69305 ( 162) link_NAG-ASN : bond 0.00525 ( 54) link_NAG-ASN : angle 2.15848 ( 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 50 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: B 626 MET cc_start: 0.8161 (ppp) cc_final: 0.7755 (ppp) REVERT: D 530 MET cc_start: 0.8959 (mpp) cc_final: 0.8466 (mpp) REVERT: E 95 MET cc_start: 0.9701 (mmm) cc_final: 0.9369 (mmm) REVERT: E 271 MET cc_start: 0.9275 (tpt) cc_final: 0.8918 (tmm) REVERT: E 434 MET cc_start: 0.9339 (tpp) cc_final: 0.9138 (tpp) REVERT: P 271 MET cc_start: 0.9086 (tpt) cc_final: 0.8601 (tpp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1065 time to fit residues: 9.2671 Evaluate side-chains 43 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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: 10.0000 chunk 46 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 161 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 577 GLN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN H 39 GLN L 32 ASN L 38 GLN L 92 ASN O 577 GLN P 114 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.025875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.019721 restraints weight = 312918.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.020333 restraints weight = 189847.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.020767 restraints weight = 134568.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.021014 restraints weight = 104498.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.021270 restraints weight = 86916.804| |-----------------------------------------------------------------------------| r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17501 Z= 0.244 Angle : 0.804 13.545 23957 Z= 0.387 Chirality : 0.045 0.257 2975 Planarity : 0.004 0.035 2855 Dihedral : 8.974 59.941 4403 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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 aren not related in a simple way. whole: -2.40 (0.18), residues: 1949 helix: -0.69 (0.26), residues: 390 sheet: -2.27 (0.22), residues: 462 loop : -1.59 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 192 TYR 0.015 0.002 TYR E 318 PHE 0.018 0.002 PHE G 391 TRP 0.024 0.002 TRP G 112 HIS 0.006 0.002 HIS P 216 Details of bonding type rmsd covalent geometry : bond 0.00492 (17352) covalent geometry : angle 0.77050 (23548) SS BOND : bond 0.00469 ( 38) SS BOND : angle 1.41103 ( 76) hydrogen bonds : bond 0.03526 ( 458) hydrogen bonds : angle 5.77708 ( 1209) link_ALPHA1-3 : bond 0.00638 ( 3) link_ALPHA1-3 : angle 1.69518 ( 9) link_BETA1-4 : bond 0.00415 ( 54) link_BETA1-4 : angle 1.75204 ( 162) link_NAG-ASN : bond 0.00613 ( 54) link_NAG-ASN : angle 2.25054 ( 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 48 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: D 530 MET cc_start: 0.8997 (mpp) cc_final: 0.8498 (mpp) REVERT: E 95 MET cc_start: 0.9717 (mmm) cc_final: 0.9393 (mmm) REVERT: E 271 MET cc_start: 0.9262 (tpt) cc_final: 0.8853 (tmm) REVERT: P 271 MET cc_start: 0.9084 (tpt) cc_final: 0.8598 (tpp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1210 time to fit residues: 9.8339 Evaluate side-chains 42 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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: 1.9990 chunk 99 optimal weight: 3.9990 chunk 170 optimal weight: 0.0020 chunk 119 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 577 GLN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 577 GLN O 656 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.026758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.020539 restraints weight = 303518.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.021186 restraints weight = 181190.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.021575 restraints weight = 126684.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.021940 restraints weight = 98701.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.022090 restraints weight = 80180.726| |-----------------------------------------------------------------------------| r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17501 Z= 0.138 Angle : 0.717 13.865 23957 Z= 0.340 Chirality : 0.045 0.268 2975 Planarity : 0.004 0.039 2855 Dihedral : 8.751 59.094 4403 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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 aren not related in a simple way. whole: -2.15 (0.18), residues: 1949 helix: -0.41 (0.27), residues: 390 sheet: -1.99 (0.23), residues: 435 loop : -1.55 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 94 TYR 0.016 0.001 TYR L 50 PHE 0.012 0.001 PHE P 288 TRP 0.019 0.002 TRP G 112 HIS 0.004 0.001 HIS P 216 Details of bonding type rmsd covalent geometry : bond 0.00290 (17352) covalent geometry : angle 0.68785 (23548) SS BOND : bond 0.00265 ( 38) SS BOND : angle 1.19770 ( 76) hydrogen bonds : bond 0.03033 ( 458) hydrogen bonds : angle 5.46692 ( 1209) link_ALPHA1-3 : bond 0.00692 ( 3) link_ALPHA1-3 : angle 1.51945 ( 9) link_BETA1-4 : bond 0.00417 ( 54) link_BETA1-4 : angle 1.55816 ( 162) link_NAG-ASN : bond 0.00340 ( 54) link_NAG-ASN : angle 1.99881 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2446.62 seconds wall clock time: 43 minutes 53.02 seconds (2633.02 seconds total)