Starting phenix.real_space_refine on Sun Jun 15 12:40:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g9x_29881/06_2025/8g9x_29881.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9x_29881/06_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_29881/06_2025/8g9x_29881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9x_29881/06_2025/8g9x_29881.map" model { file = "/net/cci-nas-00/data/ceres_data/8g9x_29881/06_2025/8g9x_29881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9x_29881/06_2025/8g9x_29881.cif" } resolution = 4.46 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 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.16, per 1000 atoms: 0.60 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: 5.07 Conformation dependent library (CDL) restraints added in 1.9 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: 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: 2.13 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: 5.03 Time building geometry restraints manager: 5.85 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: 1.480 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: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 38.280 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.670 ------------------------------------------------------------------------------- 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 : 9.75 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 (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: -4.84 (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 TRP 0.103 0.005 TRP G 427 HIS 0.012 0.003 HIS E 105 PHE 0.038 0.004 PHE P 288 TYR 0.034 0.003 TYR D 643 ARG 0.021 0.001 ARG G 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00954 ( 54) link_NAG-ASN : angle 3.88887 ( 162) link_BETA1-4 : bond 0.00842 ( 54) link_BETA1-4 : angle 2.54678 ( 162) link_ALPHA1-3 : bond 0.00393 ( 3) link_ALPHA1-3 : angle 1.79208 ( 9) hydrogen bonds : bond 0.15427 ( 458) hydrogen bonds : angle 8.37158 ( 1209) SS BOND : bond 0.00541 ( 38) SS BOND : angle 2.80276 ( 76) covalent geometry : bond 0.00814 (17352) covalent geometry : angle 1.32362 (23548) *********************** 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 : 1.791 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: 0.2511 time to fit residues: 24.2476 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 : 1.770 ------------------------------------------------------------------------------- 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: 20.0000 chunk 148 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 287 GLN E 289 ASN E 478 ASN G 103 GLN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.028272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.021827 restraints weight = 302750.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.022520 restraints weight = 177253.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.023012 restraints weight = 122082.401| |-----------------------------------------------------------------------------| r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17501 Z= 0.239 Angle : 0.864 15.410 23957 Z= 0.415 Chirality : 0.047 0.257 2975 Planarity : 0.005 0.038 2855 Dihedral : 14.397 75.011 4403 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % 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 (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: -3.50 (0.17), residues: 1949 helix: -2.33 (0.22), residues: 421 sheet: -2.61 (0.20), residues: 483 loop : -2.13 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP G 427 HIS 0.006 0.001 HIS E 216 PHE 0.016 0.002 PHE G 391 TYR 0.016 0.002 TYR O 638 ARG 0.005 0.001 ARG E 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 54) link_NAG-ASN : angle 2.54034 ( 162) link_BETA1-4 : bond 0.00516 ( 54) link_BETA1-4 : angle 2.27276 ( 162) link_ALPHA1-3 : bond 0.01093 ( 3) link_ALPHA1-3 : angle 2.35087 ( 9) hydrogen bonds : bond 0.04247 ( 458) hydrogen bonds : angle 6.21583 ( 1209) SS BOND : bond 0.00413 ( 38) SS BOND : angle 1.39343 ( 76) covalent geometry : bond 0.00474 (17352) covalent geometry : angle 0.81965 (23548) *********************** 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 : 1.864 Fit side-chains REVERT: D 530 MET cc_start: 0.8669 (mpp) cc_final: 0.8072 (mpp) REVERT: E 271 MET cc_start: 0.9410 (tpt) cc_final: 0.9194 (tpt) REVERT: P 271 MET cc_start: 0.9223 (tpt) cc_final: 0.8756 (tpt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2731 time to fit residues: 25.1790 Evaluate side-chains 46 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 84 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 93 optimal weight: 20.0000 chunk 128 optimal weight: 0.9990 chunk 168 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.028551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.022129 restraints weight = 299248.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.022823 restraints weight = 174815.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.023309 restraints weight = 119790.233| |-----------------------------------------------------------------------------| r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17501 Z= 0.165 Angle : 0.758 14.775 23957 Z= 0.363 Chirality : 0.046 0.270 2975 Planarity : 0.004 0.039 2855 Dihedral : 11.574 59.973 4403 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.01 (0.18), residues: 1949 helix: -1.39 (0.25), residues: 406 sheet: -2.33 (0.21), residues: 452 loop : -2.09 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 571 HIS 0.004 0.001 HIS G 374 PHE 0.020 0.002 PHE G 391 TYR 0.016 0.002 TYR E 318 ARG 0.003 0.000 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00561 ( 54) link_NAG-ASN : angle 2.35826 ( 162) link_BETA1-4 : bond 0.00470 ( 54) link_BETA1-4 : angle 2.00856 ( 162) link_ALPHA1-3 : bond 0.01190 ( 3) link_ALPHA1-3 : angle 1.82441 ( 9) hydrogen bonds : bond 0.03612 ( 458) hydrogen bonds : angle 5.74257 ( 1209) SS BOND : bond 0.00311 ( 38) SS BOND : angle 1.19582 ( 76) covalent geometry : bond 0.00332 (17352) covalent geometry : angle 0.71611 (23548) *********************** 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 52 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 2.199 Fit side-chains REVERT: D 530 MET cc_start: 0.8568 (mpp) cc_final: 0.7928 (mpp) REVERT: E 434 MET cc_start: 0.9303 (tpp) cc_final: 0.9089 (tpp) REVERT: P 161 MET cc_start: 0.8645 (tmm) cc_final: 0.8321 (tmm) REVERT: P 271 MET cc_start: 0.9188 (tpt) cc_final: 0.8853 (tpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2956 time to fit residues: 28.5446 Evaluate side-chains 46 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 54 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 0.2980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 432 GLN E 478 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.028401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.021969 restraints weight = 291166.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.022624 restraints weight = 172995.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.023116 restraints weight = 119682.999| |-----------------------------------------------------------------------------| r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2219 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= 0.158 Angle : 0.721 13.868 23957 Z= 0.346 Chirality : 0.045 0.262 2975 Planarity : 0.004 0.056 2855 Dihedral : 9.943 59.821 4403 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % 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: -2.73 (0.18), residues: 1949 helix: -1.10 (0.26), residues: 407 sheet: -2.17 (0.22), residues: 455 loop : -1.93 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 631 HIS 0.003 0.001 HIS L 34 PHE 0.013 0.002 PHE G 391 TYR 0.020 0.001 TYR D 643 ARG 0.003 0.000 ARG G 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 54) link_NAG-ASN : angle 2.18903 ( 162) link_BETA1-4 : bond 0.00419 ( 54) link_BETA1-4 : angle 1.85619 ( 162) link_ALPHA1-3 : bond 0.01061 ( 3) link_ALPHA1-3 : angle 2.21024 ( 9) hydrogen bonds : bond 0.03324 ( 458) hydrogen bonds : angle 5.53000 ( 1209) SS BOND : bond 0.00481 ( 38) SS BOND : angle 1.28951 ( 76) covalent geometry : bond 0.00320 (17352) covalent geometry : angle 0.68192 (23548) *********************** 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 52 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 1.819 Fit side-chains REVERT: D 530 MET cc_start: 0.8703 (mpp) cc_final: 0.8078 (mpp) REVERT: E 95 MET cc_start: 0.9516 (mmm) cc_final: 0.9287 (tpt) REVERT: E 271 MET cc_start: 0.9423 (tpt) cc_final: 0.9200 (tpt) REVERT: E 434 MET cc_start: 0.9316 (tpp) cc_final: 0.9102 (tpp) REVERT: P 100 MET cc_start: 0.9322 (ppp) cc_final: 0.9104 (ppp) REVERT: P 271 MET cc_start: 0.9141 (tpt) cc_final: 0.8834 (tpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2515 time to fit residues: 23.6200 Evaluate side-chains 46 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 49 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 43 optimal weight: 0.0570 chunk 31 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 overall best weight: 5.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 GLN G 478 ASN ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 315 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.027194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.020853 restraints weight = 304790.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.021450 restraints weight = 183085.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.021952 restraints weight = 129468.824| |-----------------------------------------------------------------------------| r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17501 Z= 0.230 Angle : 0.787 12.811 23957 Z= 0.381 Chirality : 0.045 0.253 2975 Planarity : 0.004 0.040 2855 Dihedral : 9.518 59.575 4403 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.57 (0.18), residues: 1949 helix: -0.76 (0.26), residues: 389 sheet: -2.27 (0.21), residues: 480 loop : -1.77 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 96 HIS 0.005 0.001 HIS P 85 PHE 0.021 0.002 PHE G 391 TYR 0.016 0.002 TYR G 435 ARG 0.006 0.001 ARG G 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 54) link_NAG-ASN : angle 2.28147 ( 162) link_BETA1-4 : bond 0.00435 ( 54) link_BETA1-4 : angle 1.84504 ( 162) link_ALPHA1-3 : bond 0.01009 ( 3) link_ALPHA1-3 : angle 2.11863 ( 9) hydrogen bonds : bond 0.03582 ( 458) hydrogen bonds : angle 5.63614 ( 1209) SS BOND : bond 0.00451 ( 38) SS BOND : angle 1.22968 ( 76) covalent geometry : bond 0.00465 (17352) covalent geometry : angle 0.75153 (23548) *********************** 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 52 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 1.966 Fit side-chains REVERT: B 585 ARG cc_start: 0.9607 (ptm-80) cc_final: 0.9155 (ptm-80) REVERT: B 626 MET cc_start: 0.7786 (ppp) cc_final: 0.7547 (ppp) REVERT: D 530 MET cc_start: 0.8730 (mpp) cc_final: 0.8169 (mpp) REVERT: E 95 MET cc_start: 0.9596 (mmm) cc_final: 0.9294 (mmm) REVERT: E 271 MET cc_start: 0.9392 (tpt) cc_final: 0.9186 (tpt) REVERT: P 161 MET cc_start: 0.8709 (tmm) cc_final: 0.8455 (tmm) REVERT: P 271 MET cc_start: 0.9130 (tpt) cc_final: 0.8710 (tpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.3492 time to fit residues: 30.4179 Evaluate side-chains 46 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 142 optimal weight: 2.9990 chunk 168 optimal weight: 0.4980 chunk 177 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.027667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.021347 restraints weight = 297091.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.021992 restraints weight = 177684.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.022486 restraints weight = 123890.261| |-----------------------------------------------------------------------------| r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17501 Z= 0.166 Angle : 0.709 12.937 23957 Z= 0.342 Chirality : 0.045 0.262 2975 Planarity : 0.004 0.038 2855 Dihedral : 9.193 59.367 4403 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.33 (0.18), residues: 1949 helix: -0.56 (0.27), residues: 382 sheet: -1.92 (0.23), residues: 453 loop : -1.74 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 571 HIS 0.004 0.001 HIS E 374 PHE 0.012 0.002 PHE G 391 TYR 0.013 0.001 TYR L 50 ARG 0.004 0.000 ARG G 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 54) link_NAG-ASN : angle 2.11296 ( 162) link_BETA1-4 : bond 0.00442 ( 54) link_BETA1-4 : angle 1.65604 ( 162) link_ALPHA1-3 : bond 0.01112 ( 3) link_ALPHA1-3 : angle 2.00497 ( 9) hydrogen bonds : bond 0.03178 ( 458) hydrogen bonds : angle 5.45601 ( 1209) SS BOND : bond 0.00323 ( 38) SS BOND : angle 1.21173 ( 76) covalent geometry : bond 0.00339 (17352) covalent geometry : angle 0.67527 (23548) *********************** 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 51 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 1.992 Fit side-chains REVERT: B 585 ARG cc_start: 0.9610 (ptm-80) cc_final: 0.9163 (ptm-80) REVERT: D 530 MET cc_start: 0.8755 (mpp) cc_final: 0.8217 (mpp) REVERT: E 95 MET cc_start: 0.9584 (mmm) cc_final: 0.9345 (mmm) REVERT: E 271 MET cc_start: 0.9387 (tpt) cc_final: 0.9149 (tpt) REVERT: P 161 MET cc_start: 0.8690 (tmm) cc_final: 0.8274 (tmm) REVERT: P 271 MET cc_start: 0.9138 (tpt) cc_final: 0.8691 (tpp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.3010 time to fit residues: 26.8670 Evaluate side-chains 46 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 43 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 180 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 577 GLN E 67 ASN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.026952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.020653 restraints weight = 305548.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.021276 restraints weight = 182862.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.021753 restraints weight = 128194.456| |-----------------------------------------------------------------------------| r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3309 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= 0.213 Angle : 0.748 12.066 23957 Z= 0.361 Chirality : 0.045 0.255 2975 Planarity : 0.004 0.040 2855 Dihedral : 9.032 59.885 4403 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % 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 (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: -2.28 (0.18), residues: 1949 helix: -0.49 (0.27), residues: 380 sheet: -1.94 (0.23), residues: 453 loop : -1.70 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 571 HIS 0.004 0.001 HIS P 249 PHE 0.016 0.002 PHE G 391 TYR 0.021 0.002 TYR D 643 ARG 0.005 0.001 ARG G 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00557 ( 54) link_NAG-ASN : angle 2.20374 ( 162) link_BETA1-4 : bond 0.00425 ( 54) link_BETA1-4 : angle 1.73822 ( 162) link_ALPHA1-3 : bond 0.00965 ( 3) link_ALPHA1-3 : angle 1.95440 ( 9) hydrogen bonds : bond 0.03337 ( 458) hydrogen bonds : angle 5.56777 ( 1209) SS BOND : bond 0.00419 ( 38) SS BOND : angle 1.20681 ( 76) covalent geometry : bond 0.00431 (17352) covalent geometry : angle 0.71288 (23548) *********************** 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 49 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.974 Fit side-chains REVERT: B 585 ARG cc_start: 0.9614 (ptm-80) cc_final: 0.9187 (ptm-80) REVERT: B 626 MET cc_start: 0.7888 (ppp) cc_final: 0.7390 (ppp) REVERT: D 530 MET cc_start: 0.8829 (mpp) cc_final: 0.8287 (mpp) REVERT: E 95 MET cc_start: 0.9716 (mmm) cc_final: 0.9408 (mmm) REVERT: E 271 MET cc_start: 0.9396 (tpt) cc_final: 0.9110 (tpt) REVERT: E 434 MET cc_start: 0.9350 (tpp) cc_final: 0.9073 (tpp) REVERT: P 271 MET cc_start: 0.9181 (tpt) cc_final: 0.8686 (tpp) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.3155 time to fit residues: 26.4354 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 : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 111 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 129 optimal weight: 0.0670 chunk 163 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 overall best weight: 4.0126 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.025167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.017826 restraints weight = 274068.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.018309 restraints weight = 190045.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.018667 restraints weight = 147452.935| |-----------------------------------------------------------------------------| r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17501 Z= 0.182 Angle : 0.716 14.608 23957 Z= 0.344 Chirality : 0.044 0.259 2975 Planarity : 0.004 0.039 2855 Dihedral : 8.810 59.276 4403 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.16 (0.18), residues: 1949 helix: -0.30 (0.27), residues: 380 sheet: -2.01 (0.23), residues: 446 loop : -1.58 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 571 HIS 0.003 0.001 HIS P 249 PHE 0.013 0.002 PHE P 288 TYR 0.016 0.001 TYR O 638 ARG 0.004 0.000 ARG G 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 54) link_NAG-ASN : angle 2.05745 ( 162) link_BETA1-4 : bond 0.00417 ( 54) link_BETA1-4 : angle 1.61654 ( 162) link_ALPHA1-3 : bond 0.00803 ( 3) link_ALPHA1-3 : angle 1.72487 ( 9) hydrogen bonds : bond 0.03189 ( 458) hydrogen bonds : angle 5.44406 ( 1209) SS BOND : bond 0.00385 ( 38) SS BOND : angle 1.21353 ( 76) covalent geometry : bond 0.00371 (17352) covalent geometry : angle 0.68419 (23548) *********************** 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 : 1.943 Fit side-chains revert: symmetry clash REVERT: B 585 ARG cc_start: 0.9671 (ptm-80) cc_final: 0.9252 (ptm-80) REVERT: B 626 MET cc_start: 0.8023 (ppp) cc_final: 0.7547 (ppp) REVERT: E 95 MET cc_start: 0.9702 (mmm) cc_final: 0.9455 (mmm) REVERT: E 271 MET cc_start: 0.9373 (tpt) cc_final: 0.8854 (tmm) REVERT: E 434 MET cc_start: 0.9368 (tpp) cc_final: 0.9067 (tpp) REVERT: P 271 MET cc_start: 0.9116 (tpt) cc_final: 0.8596 (tpp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2851 time to fit residues: 24.5127 Evaluate side-chains 46 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 144 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 112 optimal weight: 0.0470 chunk 126 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 175 optimal weight: 20.0000 overall best weight: 3.0084 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.027162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.020867 restraints weight = 304723.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.021530 restraints weight = 181707.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.021973 restraints weight = 126883.208| |-----------------------------------------------------------------------------| r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17501 Z= 0.150 Angle : 0.701 13.714 23957 Z= 0.335 Chirality : 0.044 0.260 2975 Planarity : 0.004 0.039 2855 Dihedral : 8.654 59.437 4403 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: -2.09 (0.18), residues: 1949 helix: -0.26 (0.27), residues: 398 sheet: -1.97 (0.23), residues: 446 loop : -1.55 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 571 HIS 0.004 0.001 HIS L 34 PHE 0.011 0.001 PHE P 288 TYR 0.016 0.001 TYR O 638 ARG 0.005 0.000 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 54) link_NAG-ASN : angle 2.00888 ( 162) link_BETA1-4 : bond 0.00402 ( 54) link_BETA1-4 : angle 1.58955 ( 162) link_ALPHA1-3 : bond 0.00816 ( 3) link_ALPHA1-3 : angle 1.59990 ( 9) hydrogen bonds : bond 0.02999 ( 458) hydrogen bonds : angle 5.33652 ( 1209) SS BOND : bond 0.00353 ( 38) SS BOND : angle 1.23859 ( 76) covalent geometry : bond 0.00310 (17352) covalent geometry : angle 0.66958 (23548) *********************** 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 52 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 1.986 Fit side-chains REVERT: B 585 ARG cc_start: 0.9589 (ptm-80) cc_final: 0.9172 (ptm-80) REVERT: B 626 MET cc_start: 0.8024 (ppp) cc_final: 0.7601 (ppp) REVERT: D 530 MET cc_start: 0.8935 (mpp) cc_final: 0.8607 (mpp) REVERT: E 95 MET cc_start: 0.9690 (mmm) cc_final: 0.9457 (mmm) REVERT: E 271 MET cc_start: 0.9340 (tpt) cc_final: 0.8887 (tmm) REVERT: E 434 MET cc_start: 0.9306 (tpp) cc_final: 0.9000 (tpp) REVERT: P 271 MET cc_start: 0.9129 (tpt) cc_final: 0.8667 (tpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2975 time to fit residues: 26.1120 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 : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 90 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 86 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 chunk 179 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 577 GLN ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.027353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.021065 restraints weight = 299976.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.021725 restraints weight = 179131.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.022186 restraints weight = 124750.504| |-----------------------------------------------------------------------------| r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17501 Z= 0.133 Angle : 0.684 14.381 23957 Z= 0.326 Chirality : 0.044 0.260 2975 Planarity : 0.004 0.038 2855 Dihedral : 8.479 59.589 4403 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -1.97 (0.18), residues: 1949 helix: -0.02 (0.27), residues: 380 sheet: -1.92 (0.23), residues: 446 loop : -1.50 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 112 HIS 0.003 0.001 HIS E 374 PHE 0.010 0.001 PHE P 288 TYR 0.016 0.001 TYR L 50 ARG 0.004 0.000 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 54) link_NAG-ASN : angle 1.93916 ( 162) link_BETA1-4 : bond 0.00421 ( 54) link_BETA1-4 : angle 1.54126 ( 162) link_ALPHA1-3 : bond 0.00692 ( 3) link_ALPHA1-3 : angle 1.49414 ( 9) hydrogen bonds : bond 0.02878 ( 458) hydrogen bonds : angle 5.21953 ( 1209) SS BOND : bond 0.00270 ( 38) SS BOND : angle 1.19687 ( 76) covalent geometry : bond 0.00279 (17352) covalent geometry : angle 0.65482 (23548) ********************** 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 53 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 4.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 585 ARG cc_start: 0.9584 (ptm-80) cc_final: 0.9164 (ptm-80) REVERT: B 626 MET cc_start: 0.8108 (ppp) cc_final: 0.7855 (ppp) REVERT: E 271 MET cc_start: 0.9336 (tpt) cc_final: 0.8898 (tmm) REVERT: E 434 MET cc_start: 0.9279 (tpp) cc_final: 0.9021 (tpp) REVERT: P 271 MET cc_start: 0.9119 (tpt) cc_final: 0.8669 (tpp) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.3701 time to fit residues: 32.8764 Evaluate side-chains 46 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 11 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 188 optimal weight: 0.5980 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN D 577 GLN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.026801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.020522 restraints weight = 306123.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.021152 restraints weight = 184169.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.021621 restraints weight = 129181.725| |-----------------------------------------------------------------------------| r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3945 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= 0.172 Angle : 0.714 13.148 23957 Z= 0.341 Chirality : 0.044 0.257 2975 Planarity : 0.004 0.038 2855 Dihedral : 8.480 59.667 4403 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -1.98 (0.19), residues: 1949 helix: -0.04 (0.27), residues: 387 sheet: -2.05 (0.22), residues: 467 loop : -1.41 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 96 HIS 0.004 0.001 HIS G 66 PHE 0.013 0.002 PHE P 288 TYR 0.016 0.001 TYR L 50 ARG 0.005 0.000 ARG G 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 54) link_NAG-ASN : angle 2.02784 ( 162) link_BETA1-4 : bond 0.00398 ( 54) link_BETA1-4 : angle 1.62469 ( 162) link_ALPHA1-3 : bond 0.00655 ( 3) link_ALPHA1-3 : angle 1.52857 ( 9) hydrogen bonds : bond 0.03059 ( 458) hydrogen bonds : angle 5.30105 ( 1209) SS BOND : bond 0.00303 ( 38) SS BOND : angle 1.37646 ( 76) covalent geometry : bond 0.00354 (17352) covalent geometry : angle 0.68206 (23548) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4662.03 seconds wall clock time: 84 minutes 38.16 seconds (5078.16 seconds total)