Starting phenix.real_space_refine on Tue Jan 21 21:47:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g9y_29882/01_2025/8g9y_29882.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9y_29882/01_2025/8g9y_29882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g9y_29882/01_2025/8g9y_29882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9y_29882/01_2025/8g9y_29882.map" model { file = "/net/cci-nas-00/data/ceres_data/8g9y_29882/01_2025/8g9y_29882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9y_29882/01_2025/8g9y_29882.cif" } resolution = 4.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 10664 2.51 5 N 2809 2.21 5 O 3547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 17135 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: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 10.47, per 1000 atoms: 0.61 Number of scatterers: 17135 At special positions: 0 Unit cell: (132.01, 129.863, 134.156, 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 3547 8.00 N 2809 7.00 C 10664 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=2.04 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=2.04 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=2.07 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 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=2.02 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 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=2.05 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS P 131 " - pdb=" SG CYS P 157 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS P 385 " - pdb=" SG CYS P 418 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA S 3 " - " MAN S 4 " " BMA a 3 " - " MAN a 4 " " BMA f 3 " - " MAN f 4 " " BMA n 3 " - " MAN n 4 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA f 3 " - " MAN f 5 " " BMA s 3 " - " MAN s 5 " 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 Q 2 " - " BMA Q 3 " " 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 d 2 " - " BMA d 3 " " 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 q 2 " - " BMA q 3 " " 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: 5.42 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 38 helices and 42 sheets defined 20.6% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 4.065A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 595 removed outlier: 3.548A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 3.749A 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: 3.659A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.831A 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: 3.854A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 595 removed outlier: 3.586A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 641 through 664 removed outlier: 3.689A pdb=" N GLN D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 removed outlier: 3.721A pdb=" N GLU E 62 " --> pdb=" O LYS E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 115 removed outlier: 3.531A pdb=" N MET E 104 " --> pdb=" O MET E 100 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.834A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.685A pdb=" N LYS E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG E 350 " --> pdb=" O VAL E 346 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.274A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.917A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 removed outlier: 3.658A pdb=" N GLU G 62 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 115 removed outlier: 3.594A pdb=" N HIS G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.873A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 354 removed outlier: 3.738A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG G 350 " --> pdb=" O VAL G 346 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.320A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 3.909A 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 'H' and resid 98 through 100B removed outlier: 4.248A pdb=" N SER H 100B" --> pdb=" O LYS H 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.584A pdb=" N PHE L 83 " --> pdb=" O THR L 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 529 through 534 Processing helix chain 'O' and resid 537 through 543 removed outlier: 3.994A pdb=" N ASN O 543 " --> pdb=" O VAL O 539 " (cutoff:3.500A) Processing helix chain 'O' and resid 572 through 595 removed outlier: 3.526A pdb=" N ALA O 578 " --> pdb=" O LYS O 574 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU O 581 " --> pdb=" O GLN O 577 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU O 584 " --> pdb=" O VAL O 580 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP O 589 " --> pdb=" O ARG O 585 " (cutoff:3.500A) Processing helix chain 'O' and resid 627 through 636 Processing helix chain 'O' and resid 641 through 664 removed outlier: 3.602A pdb=" N GLU O 647 " --> pdb=" O TYR O 643 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU O 648 " --> pdb=" O GLY O 644 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN O 653 " --> pdb=" O SER O 649 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU O 663 " --> pdb=" O ASP O 659 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP O 664 " --> pdb=" O LEU O 660 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 62 removed outlier: 3.705A pdb=" N GLU P 62 " --> pdb=" O LYS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 115 removed outlier: 3.605A pdb=" N HIS P 105 " --> pdb=" O VAL P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 126 removed outlier: 3.879A pdb=" N LEU P 125 " --> pdb=" O LEU P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 354 removed outlier: 3.597A pdb=" N GLU P 340 " --> pdb=" O ALA P 336 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS P 347 " --> pdb=" O GLY P 343 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG P 350 " --> pdb=" O VAL P 346 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS P 351 " --> pdb=" O LYS P 347 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N HIS P 352 " --> pdb=" O GLN P 348 " (cutoff:3.500A) Processing helix chain 'P' and resid 425 through 429 removed outlier: 4.257A pdb=" N ARG P 429 " --> pdb=" O MET P 426 " (cutoff:3.500A) Processing helix chain 'P' and resid 475 through 480 removed outlier: 3.801A 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 609 removed outlier: 8.570A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL G 36 " --> pdb=" O VAL B 608 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 603 through 609 removed outlier: 7.989A pdb=" N THR D 606 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N VAL P 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL D 608 " --> pdb=" O VAL P 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 495 through 499 removed outlier: 3.805A pdb=" N VAL E 38 " --> pdb=" O CYS O 604 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N CYS O 604 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.547A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.553A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) 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 159 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 202 through 203 removed outlier: 6.865A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.804A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.937A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.747A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG E 273 " --> pdb=" O LEU E 285 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET E 271 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.804A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 297 through 298 Processing sheet with id=AB4, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.715A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 330 through 334 Processing sheet with id=AB6, first strand: chain 'E' and resid 375 through 378 Processing sheet with id=AB7, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.587A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 91 through 92 removed outlier: 3.512A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AC1, first strand: chain 'G' and resid 158 through 162 Processing sheet with id=AC2, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AC3, first strand: chain 'G' and resid 260 through 261 removed outlier: 3.635A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.987A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.201A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 11.788A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.054A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU G 285 " --> pdb=" O ARG G 273 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG G 273 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN G 287 " --> pdb=" O MET G 271 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 260 through 261 removed outlier: 3.635A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 297 through 298 Processing sheet with id=AC6, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.810A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 330 through 334 Processing sheet with id=AC8, first strand: chain 'G' and resid 375 through 378 Processing sheet with id=AC9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.069A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.069A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG H 94 " --> pdb=" O ALA H 101 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.976A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.348A pdb=" N LEU L 33 " --> pdb=" O LYS L 49 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS L 49 " --> pdb=" O GLN L 53 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.599A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 45 through 47 removed outlier: 3.505A pdb=" N ILE P 225 " --> pdb=" O VAL P 245 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL P 242 " --> pdb=" O LEU P 86 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU P 86 " --> pdb=" O VAL P 242 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 154 through 155 Processing sheet with id=AD8, first strand: chain 'P' and resid 159 through 162 Processing sheet with id=AD9, first strand: chain 'P' and resid 181 through 184 removed outlier: 4.636A pdb=" N GLU P 190 " --> pdb=" O ILE P 184 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.899A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY P 451 " --> pdb=" O THR P 290 " (cutoff:3.500A) removed outlier: 11.072A pdb=" N THR P 290 " --> pdb=" O GLY P 451 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N ILE P 453 " --> pdb=" O PHE P 288 " (cutoff:3.500A) removed outlier: 11.854A pdb=" N PHE P 288 " --> pdb=" O ILE P 453 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N THR P 455 " --> pdb=" O VAL P 286 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N VAL P 286 " --> pdb=" O THR P 455 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG P 273 " --> pdb=" O LEU P 285 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.899A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG P 360 " --> pdb=" O PHE P 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 297 through 298 Processing sheet with id=AE4, first strand: chain 'P' and resid 304 through 312 removed outlier: 6.820A pdb=" N GLN P 315 " --> pdb=" O ILE P 309 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 330 through 334 Processing sheet with id=AE6, first strand: chain 'P' and resid 375 through 378 457 hydrogen bonds defined for protein. 1179 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: 4.90 Time building geometry restraints manager: 6.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 5307 1.35 - 1.49: 4824 1.49 - 1.63: 7166 1.63 - 1.77: 17 1.77 - 1.91: 137 Bond restraints: 17451 Sorted by residual: bond pdb=" CB CYS E 205 " pdb=" SG CYS E 205 " ideal model delta sigma weight residual 1.808 1.700 0.108 3.30e-02 9.18e+02 1.08e+01 bond pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " ideal model delta sigma weight residual 1.808 1.909 -0.101 3.30e-02 9.18e+02 9.32e+00 bond pdb=" CG MET O 530 " pdb=" SD MET O 530 " ideal model delta sigma weight residual 1.803 1.739 0.064 2.50e-02 1.60e+03 6.57e+00 bond pdb=" CG LEU E 116 " pdb=" CD2 LEU E 116 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.80e+00 bond pdb=" C1 NAG s 2 " pdb=" O5 NAG s 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.42e+00 ... (remaining 17446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.12: 23209 4.12 - 8.24: 442 8.24 - 12.36: 28 12.36 - 16.47: 3 16.47 - 20.59: 1 Bond angle restraints: 23683 Sorted by residual: angle pdb=" CA LEU G 494 " pdb=" CB LEU G 494 " pdb=" CG LEU G 494 " ideal model delta sigma weight residual 116.30 136.89 -20.59 3.50e+00 8.16e-02 3.46e+01 angle pdb=" C ASN G 295 " pdb=" CA ASN G 295 " pdb=" CB ASN G 295 " ideal model delta sigma weight residual 111.97 123.50 -11.53 1.99e+00 2.53e-01 3.36e+01 angle pdb=" C ASN P 332 " pdb=" CA ASN P 332 " pdb=" CB ASN P 332 " ideal model delta sigma weight residual 109.35 120.81 -11.46 1.98e+00 2.55e-01 3.35e+01 angle pdb=" CA CYS E 433 " pdb=" CB CYS E 433 " pdb=" SG CYS E 433 " ideal model delta sigma weight residual 114.40 127.38 -12.98 2.30e+00 1.89e-01 3.18e+01 angle pdb=" N CYS E 433 " pdb=" CA CYS E 433 " pdb=" CB CYS E 433 " ideal model delta sigma weight residual 111.21 102.01 9.20 1.67e+00 3.59e-01 3.04e+01 ... (remaining 23678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.73: 10799 21.73 - 43.45: 872 43.45 - 65.17: 154 65.17 - 86.90: 128 86.90 - 108.62: 77 Dihedral angle restraints: 12030 sinusoidal: 6329 harmonic: 5701 Sorted by residual: dihedral pdb=" CB CYS E 201 " pdb=" SG CYS E 201 " pdb=" SG CYS E 433 " pdb=" CB CYS E 433 " ideal model delta sinusoidal sigma weight residual -86.00 3.17 -89.17 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS G 126 " pdb=" SG CYS G 126 " pdb=" SG CYS G 196 " pdb=" CB CYS G 196 " ideal model delta sinusoidal sigma weight residual 93.00 160.57 -67.57 1 1.00e+01 1.00e-02 5.94e+01 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 -152.85 66.85 1 1.00e+01 1.00e-02 5.83e+01 ... (remaining 12027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2333 0.079 - 0.158: 552 0.158 - 0.237: 92 0.237 - 0.316: 33 0.316 - 0.395: 10 Chirality restraints: 3020 Sorted by residual: chirality pdb=" CB ILE E 326 " pdb=" CA ILE E 326 " pdb=" CG1 ILE E 326 " pdb=" CG2 ILE E 326 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CA ASN G 295 " pdb=" N ASN G 295 " pdb=" C ASN G 295 " pdb=" CB ASN G 295 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+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 -2.01 -0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 3017 not shown) Planarity restraints: 2909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 295 " -0.005 2.00e-02 2.50e+03 5.37e-02 3.61e+01 pdb=" CG ASN G 295 " 0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN G 295 " -0.062 2.00e-02 2.50e+03 pdb=" ND2 ASN G 295 " 0.063 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 427 " -0.025 2.00e-02 2.50e+03 2.83e-02 2.00e+01 pdb=" CG TRP G 427 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP G 427 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP G 427 " -0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP G 427 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP G 427 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP G 427 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 427 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 427 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP G 427 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 653 " -0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C GLN B 653 " 0.073 2.00e-02 2.50e+03 pdb=" O GLN B 653 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU B 654 " -0.025 2.00e-02 2.50e+03 ... (remaining 2906 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1913 2.73 - 3.28: 16983 3.28 - 3.82: 27716 3.82 - 4.36: 31756 4.36 - 4.90: 53916 Nonbonded interactions: 132284 Sorted by model distance: nonbonded pdb=" O SER L 43 " pdb=" NH1 ARG L 45 " model vdw 2.193 3.120 nonbonded pdb=" OD1 ASN P 302 " pdb=" OG1 THR P 320 " model vdw 2.231 3.040 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.245 3.040 nonbonded pdb=" OD1 ASN G 302 " pdb=" OG1 THR G 320 " model vdw 2.255 3.040 nonbonded pdb=" O LEU G 369 " pdb=" OG1 THR G 373 " model vdw 2.255 3.040 ... (remaining 132279 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 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'u' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'W' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'j' selection = chain 'q' selection = chain 'r' 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' } ncs_group { reference = chain 'S' selection = chain 'f' selection = chain 's' } 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 38.600 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.130 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 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 0.108 17451 Z= 0.502 Angle : 1.336 20.593 23683 Z= 0.687 Chirality : 0.074 0.395 3020 Planarity : 0.008 0.058 2855 Dihedral : 19.158 108.624 8236 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.65 % Favored : 90.25 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.83 (0.15), residues: 1949 helix: -4.60 (0.10), residues: 414 sheet: -2.87 (0.20), residues: 448 loop : -2.79 (0.15), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.004 TRP G 427 HIS 0.013 0.002 HIS E 105 PHE 0.025 0.003 PHE P 288 TYR 0.020 0.003 TYR L 36 ARG 0.021 0.001 ARG E 327 *********************** 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 61 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9076 (mpp) cc_final: 0.8851 (mpp) REVERT: D 530 MET cc_start: 0.9175 (mmp) cc_final: 0.8492 (mmp) REVERT: D 535 MET cc_start: 0.9454 (mpp) cc_final: 0.9182 (mpp) REVERT: E 95 MET cc_start: 0.9143 (ppp) cc_final: 0.8791 (ppp) REVERT: G 104 MET cc_start: 0.9213 (ppp) cc_final: 0.8958 (ppp) REVERT: H 3 MET cc_start: 0.8684 (tmm) cc_final: 0.8462 (tmm) REVERT: O 530 MET cc_start: 0.9157 (mmp) cc_final: 0.8727 (mmp) REVERT: O 535 MET cc_start: 0.9495 (mmp) cc_final: 0.9260 (mmp) REVERT: O 632 ASP cc_start: 0.9108 (m-30) cc_final: 0.8896 (m-30) REVERT: P 95 MET cc_start: 0.9649 (ptm) cc_final: 0.8002 (ppp) REVERT: P 434 MET cc_start: 0.9084 (tmm) cc_final: 0.8518 (tmm) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2904 time to fit residues: 29.1575 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 : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 0.0010 chunk 153 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 GLN ** P 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.027165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.020763 restraints weight = 240868.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.021358 restraints weight = 154503.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.021783 restraints weight = 114458.315| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17451 Z= 0.248 Angle : 0.771 13.963 23683 Z= 0.379 Chirality : 0.047 0.353 3020 Planarity : 0.005 0.034 2855 Dihedral : 14.651 73.501 4574 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.31 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.17), residues: 1949 helix: -2.74 (0.20), residues: 403 sheet: -2.63 (0.20), residues: 507 loop : -2.19 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 427 HIS 0.004 0.001 HIS P 374 PHE 0.014 0.002 PHE G 288 TYR 0.013 0.001 TYR G 177 ARG 0.005 0.001 ARG E 298 *********************** 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 53 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.903 Fit side-chains revert: symmetry clash REVERT: B 643 TYR cc_start: 0.9562 (m-80) cc_final: 0.9260 (m-80) REVERT: D 535 MET cc_start: 0.9432 (mpp) cc_final: 0.9224 (mpp) REVERT: E 95 MET cc_start: 0.9113 (ppp) cc_final: 0.8814 (ppp) REVERT: E 475 MET cc_start: 0.9048 (tpt) cc_final: 0.8541 (mmm) REVERT: G 95 MET cc_start: 0.9425 (ppp) cc_final: 0.8439 (ppp) REVERT: G 104 MET cc_start: 0.9233 (ppp) cc_final: 0.9020 (ppp) REVERT: O 530 MET cc_start: 0.9086 (mmp) cc_final: 0.8253 (mmp) REVERT: O 643 TYR cc_start: 0.9387 (m-80) cc_final: 0.8868 (m-80) REVERT: P 95 MET cc_start: 0.9501 (ptm) cc_final: 0.7931 (ppp) REVERT: P 434 MET cc_start: 0.9178 (tmm) cc_final: 0.8689 (tmm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2764 time to fit residues: 25.0685 Evaluate side-chains 47 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.3196 > 50: distance: 82 - 87: 3.782 distance: 87 - 88: 9.762 distance: 88 - 89: 7.565 distance: 88 - 91: 5.702 distance: 89 - 93: 6.317 distance: 91 - 92: 20.192 distance: 93 - 94: 5.320 distance: 94 - 97: 5.265 distance: 95 - 96: 16.235 distance: 95 - 104: 8.214 distance: 97 - 98: 11.508 distance: 98 - 99: 6.440 distance: 98 - 100: 11.883 distance: 99 - 101: 9.304 distance: 100 - 102: 9.092 distance: 101 - 103: 7.486 distance: 102 - 103: 8.194 distance: 104 - 105: 12.186 distance: 105 - 106: 14.483 distance: 105 - 108: 5.001 distance: 106 - 107: 18.116 distance: 106 - 113: 8.954 distance: 108 - 109: 11.453 distance: 109 - 110: 4.590 distance: 110 - 111: 5.723 distance: 110 - 112: 3.091 distance: 113 - 114: 10.734 distance: 113 - 119: 3.040 distance: 114 - 115: 6.704 distance: 114 - 117: 5.790 distance: 115 - 116: 20.215 distance: 115 - 120: 8.690 distance: 117 - 118: 10.518 distance: 118 - 119: 5.110 distance: 120 - 121: 6.255 distance: 121 - 122: 8.118 distance: 121 - 124: 6.044 distance: 122 - 123: 13.709 distance: 122 - 128: 14.077 distance: 124 - 125: 10.502 distance: 124 - 126: 5.787 distance: 125 - 127: 20.111 distance: 128 - 129: 6.087 distance: 128 - 134: 8.461 distance: 129 - 130: 20.157 distance: 129 - 132: 13.354 distance: 130 - 131: 37.315 distance: 130 - 135: 23.478 distance: 132 - 133: 8.996 distance: 133 - 134: 10.440 distance: 135 - 136: 4.770 distance: 136 - 137: 5.580 distance: 136 - 139: 3.076 distance: 137 - 138: 10.005 distance: 137 - 143: 4.620 distance: 139 - 140: 8.355 distance: 139 - 141: 27.832 distance: 140 - 142: 13.816 distance: 143 - 144: 15.588 distance: 144 - 145: 11.863 distance: 144 - 147: 14.634 distance: 145 - 146: 17.353 distance: 145 - 153: 12.038 distance: 147 - 148: 10.098 distance: 148 - 149: 8.274 distance: 148 - 150: 16.210 distance: 149 - 151: 13.195 distance: 150 - 152: 7.261 distance: 151 - 152: 12.410 distance: 153 - 154: 8.775 distance: 154 - 155: 3.871 distance: 154 - 157: 6.314 distance: 155 - 156: 9.864 distance: 155 - 165: 8.735 distance: 163 - 164: 5.879 distance: 166 - 167: 4.473 distance: 166 - 169: 3.355 distance: 167 - 168: 8.304 distance: 167 - 171: 8.602 distance: 170 - 186: 7.299