Starting phenix.real_space_refine on Sun May 18 20:07:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g9w_29880/05_2025/8g9w_29880.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9w_29880/05_2025/8g9w_29880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g9w_29880/05_2025/8g9w_29880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9w_29880/05_2025/8g9w_29880.map" model { file = "/net/cci-nas-00/data/ceres_data/8g9w_29880/05_2025/8g9w_29880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9w_29880/05_2025/8g9w_29880.cif" } resolution = 4.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 10664 2.51 5 N 2809 2.21 5 O 3547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17135 Number of models: 1 Model: "" Number of chains: 53 Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "E" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "G" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "H" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 933 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 100} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "P" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 12.07, per 1000 atoms: 0.70 Number of scatterers: 17135 At special positions: 0 Unit cell: (142.742, 138.449, 132.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 3547 8.00 N 2809 7.00 C 10664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS P 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS O 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.02 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.02 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS P 296 " - pdb=" SG CYS P 331 " distance=2.02 Simple disulfide: pdb=" SG CYS P 378 " - pdb=" SG CYS P 445 " distance=2.03 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 S 3 " - " MAN S 4 " " BMA a 3 " - " MAN a 4 " " BMA f 3 " - " MAN f 4 " " BMA n 3 " - " MAN n 4 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA f 3 " - " MAN f 5 " " BMA s 3 " - " MAN s 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " NAG-ASN " NAG A 1 " - " ASN E 88 " " NAG B 701 " - " ASN B 637 " " NAG C 1 " - " ASN E 156 " " NAG D 701 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 339 " " NAG E 603 " - " ASN E 355 " " NAG E 604 " - " ASN E 276 " " NAG F 1 " - " ASN E 160 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 339 " " NAG G 603 " - " ASN G 355 " " NAG G 604 " - " ASN G 276 " " NAG I 1 " - " ASN E 197 " " NAG J 1 " - " ASN E 234 " " NAG K 1 " - " ASN E 262 " " NAG M 1 " - " ASN E 295 " " NAG N 1 " - " ASN E 301 " " NAG O 701 " - " ASN O 637 " " NAG P 601 " - " ASN P 133 " " NAG P 602 " - " ASN P 339 " " NAG P 603 " - " ASN P 355 " " NAG P 604 " - " ASN P 276 " " NAG Q 1 " - " ASN E 332 " " NAG R 1 " - " ASN E 363 " " NAG S 1 " - " ASN E 386 " " NAG T 1 " - " ASN E 392 " " NAG U 1 " - " ASN E 448 " " NAG V 1 " - " ASN G 88 " " NAG W 1 " - " ASN G 156 " " NAG X 1 " - " ASN G 160 " " NAG Y 1 " - " ASN G 197 " " NAG Z 1 " - " ASN G 234 " " NAG a 1 " - " ASN G 262 " " NAG b 1 " - " ASN G 295 " " NAG c 1 " - " ASN G 301 " " NAG d 1 " - " ASN G 332 " " NAG e 1 " - " ASN G 363 " " NAG f 1 " - " ASN G 386 " " NAG g 1 " - " ASN G 392 " " NAG h 1 " - " ASN G 448 " " NAG i 1 " - " ASN P 88 " " NAG j 1 " - " ASN P 156 " " NAG k 1 " - " ASN P 160 " " NAG l 1 " - " ASN P 197 " " NAG m 1 " - " ASN P 234 " " NAG n 1 " - " ASN P 262 " " NAG o 1 " - " ASN P 295 " " NAG p 1 " - " ASN P 301 " " NAG q 1 " - " ASN P 332 " " NAG r 1 " - " ASN P 363 " " NAG s 1 " - " ASN P 386 " " NAG t 1 " - " ASN P 392 " " NAG u 1 " - " ASN P 448 " Time building additional restraints: 6.88 Conformation dependent library (CDL) restraints added in 2.0 seconds 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 42 sheets defined 20.8% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.865A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 595 removed outlier: 3.833A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 3.766A 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: 3.694A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.972A 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: 3.566A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 595 removed outlier: 3.946A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLU D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 616 removed outlier: 4.203A pdb=" N SER D 615 " --> pdb=" O ASN D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.542A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 664 removed outlier: 3.641A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 removed outlier: 3.748A pdb=" N GLU E 62 " --> pdb=" O LYS E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 115 removed outlier: 3.574A pdb=" N MET E 104 " --> pdb=" O MET E 100 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.915A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.614A pdb=" N LYS E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.279A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.830A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 removed outlier: 3.711A pdb=" N GLU G 62 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 115 removed outlier: 3.568A pdb=" N HIS G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.827A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 354 removed outlier: 3.801A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.294A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 3.776A 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 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.522A pdb=" N PHE L 83 " --> pdb=" O THR L 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 529 through 534 Processing helix chain 'O' and resid 537 through 543 removed outlier: 3.535A pdb=" N ALA O 541 " --> pdb=" O LEU O 537 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN O 543 " --> pdb=" O VAL O 539 " (cutoff:3.500A) Processing helix chain 'O' and resid 572 through 595 removed outlier: 3.756A pdb=" N LEU O 581 " --> pdb=" O GLN O 577 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU O 584 " --> pdb=" O VAL O 580 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP O 589 " --> pdb=" O ARG O 585 " (cutoff:3.500A) Processing helix chain 'O' and resid 611 through 616 removed outlier: 4.381A pdb=" N SER O 615 " --> pdb=" O ASN O 611 " (cutoff:3.500A) Processing helix chain 'O' and resid 627 through 636 removed outlier: 3.515A pdb=" N LYS O 633 " --> pdb=" O LEU O 629 " (cutoff:3.500A) Processing helix chain 'O' and resid 641 through 664 removed outlier: 3.682A pdb=" N GLU O 647 " --> pdb=" O TYR O 643 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU O 648 " --> pdb=" O GLY O 644 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN O 653 " --> pdb=" O SER O 649 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU O 663 " --> pdb=" O ASP O 659 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP O 664 " --> pdb=" O LEU O 660 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 62 removed outlier: 3.658A pdb=" N GLU P 62 " --> pdb=" O LYS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 115 removed outlier: 3.645A pdb=" N MET P 104 " --> pdb=" O MET P 100 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS P 105 " --> pdb=" O VAL P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 126 removed outlier: 3.924A pdb=" N LEU P 125 " --> pdb=" O LEU P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 354 removed outlier: 3.577A pdb=" N LYS P 347 " --> pdb=" O GLY P 343 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG P 350 " --> pdb=" O VAL P 346 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS P 351 " --> pdb=" O LYS P 347 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS P 352 " --> pdb=" O GLN P 348 " (cutoff:3.500A) Processing helix chain 'P' and resid 425 through 429 removed outlier: 4.315A pdb=" N ARG P 429 " --> pdb=" O MET P 426 " (cutoff:3.500A) Processing helix chain 'P' and resid 475 through 480 removed outlier: 3.871A 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: 4.225A pdb=" N CYS B 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.825A 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: 3.760A pdb=" N CYS D 604 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 3.671A 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: 3.678A pdb=" N VAL E 38 " --> pdb=" O CYS O 604 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS O 604 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.817A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 3.568A 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 93 removed outlier: 3.832A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 154 through 155 Processing sheet with id=AA7, first strand: chain 'E' and resid 159 through 162 Processing sheet with id=AA8, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AA9, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.801A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.033A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.864A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.495A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.801A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (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: 6.592A 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: 4.793A 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 159 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: 7.091A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 11.106A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.442A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 12.062A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.695A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 260 through 261 removed outlier: 7.091A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 6.799A 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: 6.643A 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 11 through 12 removed outlier: 6.796A pdb=" N LEU H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.795A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.607A 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: 3.937A 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: 6.246A pdb=" N LEU L 33 " --> pdb=" O LYS L 49 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LYS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.975A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 45 through 47 removed outlier: 4.660A pdb=" N VAL P 242 " --> pdb=" O LEU P 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 91 through 92 Processing sheet with id=AD7, first strand: chain 'P' and resid 154 through 155 Processing sheet with id=AD8, first strand: chain 'P' and resid 159 through 162 Processing sheet with id=AD9, first strand: chain 'P' and resid 181 through 183 Processing sheet with id=AE1, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.806A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLY P 451 " --> pdb=" O THR P 290 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N THR P 290 " --> pdb=" O GLY P 451 " (cutoff:3.500A) removed outlier: 11.337A pdb=" N ILE P 453 " --> pdb=" O PHE P 288 " (cutoff:3.500A) removed outlier: 11.899A pdb=" N PHE P 288 " --> pdb=" O ILE P 453 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N THR P 455 " --> pdb=" O VAL P 286 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N VAL P 286 " --> pdb=" O THR P 455 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG P 273 " --> pdb=" O LEU P 285 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.806A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG P 360 " --> pdb=" O PHE P 468 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER P 393 " --> pdb=" O PHE P 361 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 297 through 298 Processing sheet with id=AE4, first strand: chain 'P' and resid 304 through 312 removed outlier: 6.745A pdb=" N GLN P 315 " --> pdb=" O ILE P 309 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 330 through 334 Processing sheet with id=AE6, first strand: chain 'P' and resid 375 through 378 475 hydrogen bonds defined for protein. 1227 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: 5.63 Time building geometry restraints manager: 7.66 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: 5281 1.34 - 1.47: 4494 1.47 - 1.59: 7522 1.59 - 1.72: 0 1.72 - 1.84: 154 Bond restraints: 17451 Sorted by residual: bond pdb=" C1 BMA R 3 " pdb=" C2 BMA R 3 " ideal model delta sigma weight residual 1.519 1.573 -0.054 2.00e-02 2.50e+03 7.38e+00 bond pdb=" CG GLU D 584 " pdb=" CD GLU D 584 " ideal model delta sigma weight residual 1.516 1.455 0.061 2.50e-02 1.60e+03 5.99e+00 bond pdb=" CB GLN D 658 " pdb=" CG GLN D 658 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.85e+00 bond pdb=" CB ASN E 276 " pdb=" CG ASN E 276 " ideal model delta sigma weight residual 1.516 1.462 0.054 2.50e-02 1.60e+03 4.63e+00 bond pdb=" C1 MAN f 4 " pdb=" O5 MAN f 4 " ideal model delta sigma weight residual 1.399 1.440 -0.041 2.00e-02 2.50e+03 4.14e+00 ... (remaining 17446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.85: 23139 3.85 - 7.70: 495 7.70 - 11.56: 43 11.56 - 15.41: 4 15.41 - 19.26: 2 Bond angle restraints: 23683 Sorted by residual: angle pdb=" CB MET P 100 " pdb=" CG MET P 100 " pdb=" SD MET P 100 " ideal model delta sigma weight residual 112.70 131.96 -19.26 3.00e+00 1.11e-01 4.12e+01 angle pdb=" N GLU D 657 " pdb=" CA GLU D 657 " pdb=" CB GLU D 657 " ideal model delta sigma weight residual 110.28 120.07 -9.79 1.55e+00 4.16e-01 3.99e+01 angle pdb=" CB MET E 100 " pdb=" CG MET E 100 " pdb=" SD MET E 100 " ideal model delta sigma weight residual 112.70 131.37 -18.67 3.00e+00 1.11e-01 3.87e+01 angle pdb=" N GLY P 152 " pdb=" CA GLY P 152 " pdb=" C GLY P 152 " ideal model delta sigma weight residual 113.18 99.03 14.15 2.37e+00 1.78e-01 3.56e+01 angle pdb=" CA MET E 100 " pdb=" CB MET E 100 " pdb=" CG MET E 100 " ideal model delta sigma weight residual 114.10 124.85 -10.75 2.00e+00 2.50e-01 2.89e+01 ... (remaining 23678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 10822 21.92 - 43.85: 846 43.85 - 65.77: 154 65.77 - 87.70: 135 87.70 - 109.62: 73 Dihedral angle restraints: 12030 sinusoidal: 6329 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 -156.84 70.84 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CB CYS P 126 " pdb=" SG CYS P 126 " pdb=" SG CYS P 196 " pdb=" CB CYS P 196 " ideal model delta sinusoidal sigma weight residual 93.00 161.21 -68.21 1 1.00e+01 1.00e-02 6.04e+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 -154.11 68.11 1 1.00e+01 1.00e-02 6.02e+01 ... (remaining 12027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2688 0.108 - 0.216: 285 0.216 - 0.324: 42 0.324 - 0.432: 3 0.432 - 0.540: 2 Chirality restraints: 3020 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 2.10 0.54 2.00e-01 2.50e+01 7.29e+00 chirality pdb=" C1 NAG t 1 " pdb=" ND2 ASN P 392 " pdb=" C2 NAG t 1 " pdb=" O5 NAG t 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.17e+00 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 5.98e+00 ... (remaining 3017 not shown) Planarity restraints: 2909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 581 " 0.022 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C LEU D 581 " -0.078 2.00e-02 2.50e+03 pdb=" O LEU D 581 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA D 582 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 574 " 0.022 2.00e-02 2.50e+03 4.42e-02 1.96e+01 pdb=" C LYS D 574 " -0.077 2.00e-02 2.50e+03 pdb=" O LYS D 574 " 0.029 2.00e-02 2.50e+03 pdb=" N GLN D 575 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN P 99 " -0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C ASN P 99 " 0.073 2.00e-02 2.50e+03 pdb=" O ASN P 99 " -0.028 2.00e-02 2.50e+03 pdb=" N MET P 100 " -0.024 2.00e-02 2.50e+03 ... (remaining 2906 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1840 2.73 - 3.27: 17135 3.27 - 3.81: 28522 3.81 - 4.36: 32828 4.36 - 4.90: 55521 Nonbonded interactions: 135846 Sorted by model distance: nonbonded pdb=" O SER D 649 " pdb=" NE2 GLN D 653 " model vdw 2.186 3.120 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.210 3.040 nonbonded pdb=" OH TYR P 61 " pdb=" O CYS P 74 " model vdw 2.215 3.040 nonbonded pdb=" OG SER L 12 " pdb=" OE2 GLU L 105 " model vdw 2.215 3.040 nonbonded pdb=" OD1 ASN E 302 " pdb=" OG1 THR E 320 " model vdw 2.223 3.040 ... (remaining 135841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'u' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'W' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'j' selection = chain 'q' selection = chain 'r' selection = chain 't' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'P' } ncs_group { reference = chain 'K' selection = chain 'a' selection = chain 'n' } ncs_group { reference = chain 'S' selection = chain 'f' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 43.010 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 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 0.068 17609 Z= 0.403 Angle : 1.416 19.262 24119 Z= 0.713 Chirality : 0.073 0.540 3020 Planarity : 0.008 0.057 2855 Dihedral : 19.421 109.623 8236 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.83 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.16 % 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: -4.89 (0.15), residues: 1949 helix: -4.60 (0.10), residues: 432 sheet: -2.91 (0.19), residues: 547 loop : -2.69 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.005 TRP E 427 HIS 0.012 0.003 HIS G 105 PHE 0.033 0.004 PHE P 176 TYR 0.027 0.003 TYR D 638 ARG 0.021 0.001 ARG G 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00893 ( 54) link_NAG-ASN : angle 4.28632 ( 162) link_ALPHA1-6 : bond 0.00432 ( 3) link_ALPHA1-6 : angle 1.56214 ( 9) link_BETA1-4 : bond 0.00906 ( 57) link_BETA1-4 : angle 2.64136 ( 171) link_ALPHA1-3 : bond 0.00352 ( 6) link_ALPHA1-3 : angle 1.88665 ( 18) hydrogen bonds : bond 0.15487 ( 461) hydrogen bonds : angle 8.83581 ( 1227) SS BOND : bond 0.00589 ( 38) SS BOND : angle 2.62946 ( 76) covalent geometry : bond 0.00808 (17451) covalent geometry : angle 1.35617 (23683) *********************** 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 66 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.775 Fit side-chains revert: symmetry clash REVERT: B 530 MET cc_start: 0.9138 (mpp) cc_final: 0.8395 (mpp) REVERT: G 45 TRP cc_start: 0.9545 (p90) cc_final: 0.9181 (p90) REVERT: P 95 MET cc_start: 0.9482 (pmm) cc_final: 0.9226 (pmm) REVERT: P 161 MET cc_start: 0.9255 (tpt) cc_final: 0.8548 (tpt) REVERT: P 475 MET cc_start: 0.8644 (pmm) cc_final: 0.8245 (pmm) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2678 time to fit residues: 29.5385 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 : 2.021 ------------------------------------------------------------------------------- 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: 10.0000 chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 607 ASN D 656 ASN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN ** O 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 658 GLN P 103 GLN P 289 ASN ** P 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.026790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.021772 restraints weight = 310530.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.022429 restraints weight = 171137.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.022865 restraints weight = 112867.075| |-----------------------------------------------------------------------------| r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17609 Z= 0.275 Angle : 0.912 9.778 24119 Z= 0.439 Chirality : 0.047 0.274 3020 Planarity : 0.005 0.036 2855 Dihedral : 14.818 80.823 4574 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.06 % Allowed : 7.02 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.17), residues: 1949 helix: -2.46 (0.21), residues: 444 sheet: -2.89 (0.19), residues: 555 loop : -1.94 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP P 479 HIS 0.008 0.002 HIS P 216 PHE 0.024 0.003 PHE P 176 TYR 0.019 0.002 TYR H 100 ARG 0.006 0.001 ARG O 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00720 ( 54) link_NAG-ASN : angle 2.91687 ( 162) link_ALPHA1-6 : bond 0.00512 ( 3) link_ALPHA1-6 : angle 1.79853 ( 9) link_BETA1-4 : bond 0.00614 ( 57) link_BETA1-4 : angle 2.36784 ( 171) link_ALPHA1-3 : bond 0.00960 ( 6) link_ALPHA1-3 : angle 3.00732 ( 18) hydrogen bonds : bond 0.04529 ( 461) hydrogen bonds : angle 6.69621 ( 1227) SS BOND : bond 0.00582 ( 38) SS BOND : angle 1.42773 ( 76) covalent geometry : bond 0.00539 (17451) covalent geometry : angle 0.85638 (23683) *********************** 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 63 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 1.720 Fit side-chains REVERT: B 530 MET cc_start: 0.8923 (mpp) cc_final: 0.8365 (mpp) REVERT: D 530 MET cc_start: 0.9359 (mpp) cc_final: 0.8584 (mmt) REVERT: D 626 MET cc_start: 0.8403 (tmm) cc_final: 0.8175 (tmm) REVERT: G 161 MET cc_start: 0.9198 (tmm) cc_final: 0.8787 (tmm) REVERT: L 85 MET cc_start: 0.9523 (tpt) cc_final: 0.9297 (tpp) REVERT: O 584 GLU cc_start: 0.9224 (tt0) cc_final: 0.8433 (tt0) REVERT: P 45 TRP cc_start: 0.9491 (p90) cc_final: 0.9082 (p90) REVERT: P 95 MET cc_start: 0.9492 (pmm) cc_final: 0.9137 (pmm) REVERT: P 100 MET cc_start: 0.9084 (pmm) cc_final: 0.8882 (pmm) REVERT: P 161 MET cc_start: 0.9155 (tpt) cc_final: 0.8477 (tpt) REVERT: P 271 MET cc_start: 0.9712 (mmp) cc_final: 0.9314 (mmt) REVERT: P 475 MET cc_start: 0.8708 (pmm) cc_final: 0.8127 (pmm) outliers start: 1 outliers final: 1 residues processed: 63 average time/residue: 0.2713 time to fit residues: 28.7290 Evaluate side-chains 51 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 20 optimal weight: 0.0870 chunk 135 optimal weight: 50.0000 chunk 173 optimal weight: 7.9990 chunk 122 optimal weight: 0.3980 chunk 64 optimal weight: 10.0000 chunk 174 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 87 optimal weight: 20.0000 chunk 168 optimal weight: 5.9990 overall best weight: 4.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 GLN P 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.026705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.021714 restraints weight = 313225.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.022378 restraints weight = 169817.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.022823 restraints weight = 111958.144| |-----------------------------------------------------------------------------| r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17609 Z= 0.212 Angle : 0.806 9.402 24119 Z= 0.386 Chirality : 0.047 0.287 3020 Planarity : 0.004 0.043 2855 Dihedral : 12.334 72.225 4574 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % 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: -3.11 (0.18), residues: 1949 helix: -1.61 (0.24), residues: 434 sheet: -2.65 (0.19), residues: 534 loop : -1.83 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP P 479 HIS 0.007 0.002 HIS L 34 PHE 0.018 0.002 PHE P 176 TYR 0.018 0.002 TYR D 638 ARG 0.005 0.001 ARG P 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 54) link_NAG-ASN : angle 2.69523 ( 162) link_ALPHA1-6 : bond 0.00498 ( 3) link_ALPHA1-6 : angle 2.08612 ( 9) link_BETA1-4 : bond 0.00492 ( 57) link_BETA1-4 : angle 2.02999 ( 171) link_ALPHA1-3 : bond 0.01078 ( 6) link_ALPHA1-3 : angle 2.10620 ( 18) hydrogen bonds : bond 0.03925 ( 461) hydrogen bonds : angle 6.36180 ( 1227) SS BOND : bond 0.00344 ( 38) SS BOND : angle 1.17081 ( 76) covalent geometry : bond 0.00414 (17451) covalent geometry : angle 0.75676 (23683) *********************** 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 62 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8941 (mpp) cc_final: 0.8237 (mpp) REVERT: D 530 MET cc_start: 0.9203 (mpp) cc_final: 0.8683 (mmt) REVERT: E 100 MET cc_start: 0.9336 (pmm) cc_final: 0.9075 (pmm) REVERT: L 85 MET cc_start: 0.9542 (tpt) cc_final: 0.9318 (tpp) REVERT: O 530 MET cc_start: 0.8357 (mmp) cc_final: 0.8089 (mmp) REVERT: P 95 MET cc_start: 0.9499 (pmm) cc_final: 0.9140 (pmm) REVERT: P 161 MET cc_start: 0.9087 (tpt) cc_final: 0.8591 (tpp) REVERT: P 271 MET cc_start: 0.9639 (mmp) cc_final: 0.9202 (mmm) REVERT: P 426 MET cc_start: 0.9627 (pmm) cc_final: 0.9415 (pmm) REVERT: P 434 MET cc_start: 0.9704 (tpp) cc_final: 0.9485 (tpp) REVERT: P 475 MET cc_start: 0.8829 (pmm) cc_final: 0.8159 (pmm) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2757 time to fit residues: 28.2824 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 : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 96 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 640 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.025935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.020999 restraints weight = 317655.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.021642 restraints weight = 174900.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.022082 restraints weight = 116550.766| |-----------------------------------------------------------------------------| r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17609 Z= 0.229 Angle : 0.800 9.372 24119 Z= 0.383 Chirality : 0.046 0.286 3020 Planarity : 0.004 0.035 2855 Dihedral : 10.718 64.777 4574 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % 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: -2.80 (0.18), residues: 1949 helix: -1.45 (0.24), residues: 442 sheet: -2.47 (0.20), residues: 492 loop : -1.63 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP P 479 HIS 0.007 0.001 HIS L 34 PHE 0.019 0.002 PHE P 176 TYR 0.020 0.002 TYR D 638 ARG 0.005 0.001 ARG P 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 54) link_NAG-ASN : angle 2.62182 ( 162) link_ALPHA1-6 : bond 0.00634 ( 3) link_ALPHA1-6 : angle 2.16804 ( 9) link_BETA1-4 : bond 0.00455 ( 57) link_BETA1-4 : angle 1.90333 ( 171) link_ALPHA1-3 : bond 0.00910 ( 6) link_ALPHA1-3 : angle 2.40834 ( 18) hydrogen bonds : bond 0.03732 ( 461) hydrogen bonds : angle 6.24645 ( 1227) SS BOND : bond 0.00485 ( 38) SS BOND : angle 1.30236 ( 76) covalent geometry : bond 0.00457 (17451) covalent geometry : angle 0.75302 (23683) *********************** 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 56 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.759 Fit side-chains revert: symmetry clash REVERT: D 530 MET cc_start: 0.9082 (mpp) cc_final: 0.8506 (mmt) REVERT: E 100 MET cc_start: 0.9388 (pmm) cc_final: 0.9176 (pmm) REVERT: L 85 MET cc_start: 0.9521 (tpt) cc_final: 0.9282 (tpp) REVERT: O 530 MET cc_start: 0.8508 (mmp) cc_final: 0.8238 (mmp) REVERT: O 584 GLU cc_start: 0.9119 (tt0) cc_final: 0.8891 (mt-10) REVERT: P 95 MET cc_start: 0.9537 (pmm) cc_final: 0.9195 (pmm) REVERT: P 161 MET cc_start: 0.9112 (tpt) cc_final: 0.8663 (tpp) REVERT: P 271 MET cc_start: 0.9562 (mmp) cc_final: 0.9068 (mmm) REVERT: P 426 MET cc_start: 0.9661 (pmm) cc_final: 0.9402 (pmm) REVERT: P 475 MET cc_start: 0.8867 (pmm) cc_final: 0.8547 (pmm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2723 time to fit residues: 25.5931 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 : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 127 optimal weight: 8.9990 chunk 75 optimal weight: 30.0000 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 315 GLN G 114 GLN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 GLN P 302 ASN ** P 374 HIS ** 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 = 0.2732 r_free = 0.2732 target = 0.024975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.020095 restraints weight = 330363.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.020714 restraints weight = 185167.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.021133 restraints weight = 124102.468| |-----------------------------------------------------------------------------| r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 17609 Z= 0.277 Angle : 0.866 9.862 24119 Z= 0.414 Chirality : 0.047 0.287 3020 Planarity : 0.004 0.043 2855 Dihedral : 10.479 61.313 4574 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.06 % Allowed : 3.74 % Favored : 96.20 % 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: -2.81 (0.18), residues: 1949 helix: -1.50 (0.23), residues: 452 sheet: -2.43 (0.21), residues: 474 loop : -1.67 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP P 96 HIS 0.008 0.002 HIS L 34 PHE 0.025 0.003 PHE P 176 TYR 0.027 0.002 TYR D 638 ARG 0.005 0.001 ARG G 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00693 ( 54) link_NAG-ASN : angle 2.76378 ( 162) link_ALPHA1-6 : bond 0.00746 ( 3) link_ALPHA1-6 : angle 2.19724 ( 9) link_BETA1-4 : bond 0.00462 ( 57) link_BETA1-4 : angle 1.91371 ( 171) link_ALPHA1-3 : bond 0.01013 ( 6) link_ALPHA1-3 : angle 2.34394 ( 18) hydrogen bonds : bond 0.03979 ( 461) hydrogen bonds : angle 6.44382 ( 1227) SS BOND : bond 0.00477 ( 38) SS BOND : angle 1.46160 ( 76) covalent geometry : bond 0.00550 (17451) covalent geometry : angle 0.81971 (23683) *********************** 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 56 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 1.720 Fit side-chains revert: symmetry clash REVERT: D 530 MET cc_start: 0.9111 (mpp) cc_final: 0.8599 (mmt) REVERT: E 100 MET cc_start: 0.9351 (pmm) cc_final: 0.9019 (pmm) REVERT: L 85 MET cc_start: 0.9541 (tpt) cc_final: 0.9304 (tpp) REVERT: O 584 GLU cc_start: 0.9139 (tt0) cc_final: 0.8581 (mt-10) REVERT: P 95 MET cc_start: 0.9540 (pmm) cc_final: 0.9251 (pmm) REVERT: P 161 MET cc_start: 0.9118 (tpt) cc_final: 0.8640 (tpp) REVERT: P 271 MET cc_start: 0.9453 (mmp) cc_final: 0.8973 (mmm) REVERT: P 426 MET cc_start: 0.9671 (pmm) cc_final: 0.9394 (pmm) REVERT: P 475 MET cc_start: 0.8891 (pmm) cc_final: 0.8388 (pmm) outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 0.2775 time to fit residues: 25.7296 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 : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 130 optimal weight: 40.0000 chunk 72 optimal weight: 9.9990 chunk 173 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 182 optimal weight: 0.5980 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN D 543 ASN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 543 ASN ** O 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 315 GLN ** P 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.025355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.020403 restraints weight = 324272.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.021039 restraints weight = 181758.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.021473 restraints weight = 121190.862| |-----------------------------------------------------------------------------| r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17609 Z= 0.215 Angle : 0.780 9.413 24119 Z= 0.372 Chirality : 0.046 0.293 3020 Planarity : 0.004 0.036 2855 Dihedral : 9.921 59.963 4574 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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: -2.67 (0.18), residues: 1949 helix: -1.28 (0.23), residues: 452 sheet: -2.36 (0.21), residues: 480 loop : -1.62 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P 96 HIS 0.007 0.001 HIS L 34 PHE 0.020 0.002 PHE H 67 TYR 0.027 0.002 TYR D 638 ARG 0.005 0.001 ARG G 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 54) link_NAG-ASN : angle 2.54665 ( 162) link_ALPHA1-6 : bond 0.00843 ( 3) link_ALPHA1-6 : angle 1.98540 ( 9) link_BETA1-4 : bond 0.00438 ( 57) link_BETA1-4 : angle 1.73332 ( 171) link_ALPHA1-3 : bond 0.01085 ( 6) link_ALPHA1-3 : angle 2.09525 ( 18) hydrogen bonds : bond 0.03570 ( 461) hydrogen bonds : angle 6.25848 ( 1227) SS BOND : bond 0.00403 ( 38) SS BOND : angle 1.35859 ( 76) covalent geometry : bond 0.00431 (17451) covalent geometry : angle 0.73647 (23683) *********************** 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 56 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.728 Fit side-chains revert: symmetry clash REVERT: B 530 MET cc_start: 0.9060 (mpp) cc_final: 0.8301 (mpp) REVERT: B 626 MET cc_start: 0.9382 (pmm) cc_final: 0.9065 (pmm) REVERT: E 100 MET cc_start: 0.9403 (pmm) cc_final: 0.9183 (pmm) REVERT: G 475 MET cc_start: 0.9220 (pmm) cc_final: 0.8977 (pmm) REVERT: L 85 MET cc_start: 0.9547 (tpt) cc_final: 0.9302 (tpp) REVERT: O 530 MET cc_start: 0.8616 (mmp) cc_final: 0.8412 (mmp) REVERT: O 584 GLU cc_start: 0.9151 (tt0) cc_final: 0.8636 (mt-10) REVERT: P 95 MET cc_start: 0.9503 (pmm) cc_final: 0.9195 (pmm) REVERT: P 161 MET cc_start: 0.9173 (tpt) cc_final: 0.8693 (tpp) REVERT: P 271 MET cc_start: 0.9377 (mmp) cc_final: 0.8905 (mmm) REVERT: P 426 MET cc_start: 0.9656 (pmm) cc_final: 0.9388 (pmm) REVERT: P 475 MET cc_start: 0.8979 (pmm) cc_final: 0.8416 (pmm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2852 time to fit residues: 26.5648 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 : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 184 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 135 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN B 658 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 577 GLN ** P 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.024746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.019837 restraints weight = 327763.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.020444 restraints weight = 187334.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.020867 restraints weight = 127042.926| |-----------------------------------------------------------------------------| r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17609 Z= 0.237 Angle : 0.815 10.224 24119 Z= 0.389 Chirality : 0.046 0.302 3020 Planarity : 0.004 0.046 2855 Dihedral : 9.683 59.876 4574 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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: -2.65 (0.18), residues: 1949 helix: -1.15 (0.24), residues: 428 sheet: -2.29 (0.22), residues: 474 loop : -1.70 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP P 96 HIS 0.008 0.002 HIS L 34 PHE 0.019 0.002 PHE P 176 TYR 0.031 0.002 TYR D 638 ARG 0.005 0.001 ARG G 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 54) link_NAG-ASN : angle 2.58156 ( 162) link_ALPHA1-6 : bond 0.00709 ( 3) link_ALPHA1-6 : angle 1.92860 ( 9) link_BETA1-4 : bond 0.00451 ( 57) link_BETA1-4 : angle 1.79876 ( 171) link_ALPHA1-3 : bond 0.01062 ( 6) link_ALPHA1-3 : angle 2.07610 ( 18) hydrogen bonds : bond 0.03650 ( 461) hydrogen bonds : angle 6.40428 ( 1227) SS BOND : bond 0.00386 ( 38) SS BOND : angle 1.23790 ( 76) covalent geometry : bond 0.00473 (17451) covalent geometry : angle 0.77341 (23683) *********************** 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 56 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.753 Fit side-chains REVERT: B 530 MET cc_start: 0.9089 (mpp) cc_final: 0.8317 (mpp) REVERT: B 626 MET cc_start: 0.9462 (pmm) cc_final: 0.9025 (pmm) REVERT: E 100 MET cc_start: 0.9432 (pmm) cc_final: 0.9144 (pmm) REVERT: G 150 MET cc_start: -0.0395 (ptp) cc_final: -0.0888 (ptt) REVERT: G 475 MET cc_start: 0.9148 (pmm) cc_final: 0.8880 (pmm) REVERT: H 82 MET cc_start: 0.6172 (ptp) cc_final: 0.5940 (ptp) REVERT: L 85 MET cc_start: 0.9547 (tpt) cc_final: 0.9323 (tpp) REVERT: O 530 MET cc_start: 0.8653 (mmp) cc_final: 0.8429 (mmp) REVERT: O 584 GLU cc_start: 0.9170 (tt0) cc_final: 0.8922 (mt-10) REVERT: P 95 MET cc_start: 0.9519 (pmm) cc_final: 0.9202 (pmm) REVERT: P 100 MET cc_start: 0.8946 (pmm) cc_final: 0.8705 (pmm) REVERT: P 161 MET cc_start: 0.9223 (tpt) cc_final: 0.8742 (tpp) REVERT: P 271 MET cc_start: 0.9276 (mmp) cc_final: 0.8801 (mmm) REVERT: P 426 MET cc_start: 0.9639 (pmm) cc_final: 0.9380 (pmm) REVERT: P 475 MET cc_start: 0.8997 (pmm) cc_final: 0.8335 (pmm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2771 time to fit residues: 25.8145 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN D 658 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 GLN O 577 GLN O 656 ASN ** P 374 HIS ** 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 = 0.2759 r_free = 0.2759 target = 0.025568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.020632 restraints weight = 319064.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.021277 restraints weight = 176976.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.021714 restraints weight = 118330.900| |-----------------------------------------------------------------------------| r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17609 Z= 0.153 Angle : 0.728 9.505 24119 Z= 0.345 Chirality : 0.045 0.301 3020 Planarity : 0.004 0.036 2855 Dihedral : 9.393 59.854 4574 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: -2.47 (0.18), residues: 1949 helix: -0.86 (0.25), residues: 428 sheet: -2.20 (0.22), residues: 480 loop : -1.65 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 69 HIS 0.007 0.001 HIS L 34 PHE 0.016 0.002 PHE H 67 TYR 0.022 0.002 TYR D 638 ARG 0.006 0.001 ARG G 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 54) link_NAG-ASN : angle 2.37817 ( 162) link_ALPHA1-6 : bond 0.00690 ( 3) link_ALPHA1-6 : angle 1.91159 ( 9) link_BETA1-4 : bond 0.00447 ( 57) link_BETA1-4 : angle 1.64166 ( 171) link_ALPHA1-3 : bond 0.01057 ( 6) link_ALPHA1-3 : angle 1.71976 ( 18) hydrogen bonds : bond 0.03115 ( 461) hydrogen bonds : angle 6.08767 ( 1227) SS BOND : bond 0.00422 ( 38) SS BOND : angle 1.24162 ( 76) covalent geometry : bond 0.00318 (17451) covalent geometry : angle 0.68734 (23683) *********************** 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 56 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9008 (mpp) cc_final: 0.8226 (mpp) REVERT: B 626 MET cc_start: 0.9469 (pmm) cc_final: 0.9003 (pmm) REVERT: E 100 MET cc_start: 0.9399 (pmm) cc_final: 0.9140 (pmm) REVERT: G 475 MET cc_start: 0.9090 (pmm) cc_final: 0.8829 (pmm) REVERT: L 85 MET cc_start: 0.9552 (tpt) cc_final: 0.9322 (tpp) REVERT: P 95 MET cc_start: 0.9446 (pmm) cc_final: 0.9128 (pmm) REVERT: P 161 MET cc_start: 0.9185 (tpt) cc_final: 0.8683 (tpp) REVERT: P 271 MET cc_start: 0.9248 (mmp) cc_final: 0.8810 (mmm) REVERT: P 426 MET cc_start: 0.9645 (pmm) cc_final: 0.9377 (pmm) REVERT: P 475 MET cc_start: 0.8834 (pmm) cc_final: 0.8226 (pmm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.3084 time to fit residues: 28.0355 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 : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 92 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 136 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 87 optimal weight: 0.0020 chunk 8 optimal weight: 0.0010 chunk 195 optimal weight: 6.9990 overall best weight: 2.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN B 577 GLN D 640 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 577 GLN ** P 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.025863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.020946 restraints weight = 318226.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.021604 restraints weight = 174967.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.022044 restraints weight = 116374.700| |-----------------------------------------------------------------------------| r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17609 Z= 0.132 Angle : 0.709 10.188 24119 Z= 0.332 Chirality : 0.045 0.296 3020 Planarity : 0.004 0.041 2855 Dihedral : 9.059 59.952 4574 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.25 (0.18), residues: 1949 helix: -0.58 (0.26), residues: 398 sheet: -1.89 (0.23), residues: 456 loop : -1.65 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 571 HIS 0.006 0.001 HIS L 34 PHE 0.012 0.001 PHE H 67 TYR 0.017 0.001 TYR D 638 ARG 0.010 0.000 ARG G 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 54) link_NAG-ASN : angle 2.25653 ( 162) link_ALPHA1-6 : bond 0.00679 ( 3) link_ALPHA1-6 : angle 1.85310 ( 9) link_BETA1-4 : bond 0.00444 ( 57) link_BETA1-4 : angle 1.58074 ( 171) link_ALPHA1-3 : bond 0.01056 ( 6) link_ALPHA1-3 : angle 1.58872 ( 18) hydrogen bonds : bond 0.02928 ( 461) hydrogen bonds : angle 5.84891 ( 1227) SS BOND : bond 0.00455 ( 38) SS BOND : angle 1.29963 ( 76) covalent geometry : bond 0.00275 (17451) covalent geometry : angle 0.67081 (23683) *********************** 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 57 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9017 (mpp) cc_final: 0.8318 (mpp) REVERT: B 626 MET cc_start: 0.9511 (pmm) cc_final: 0.9016 (pmm) REVERT: D 530 MET cc_start: 0.9123 (mpp) cc_final: 0.8560 (mpp) REVERT: D 583 VAL cc_start: 0.9902 (p) cc_final: 0.9687 (m) REVERT: E 100 MET cc_start: 0.9357 (pmm) cc_final: 0.9093 (pmm) REVERT: G 475 MET cc_start: 0.9054 (pmm) cc_final: 0.8818 (pmm) REVERT: H 82 MET cc_start: 0.6068 (ptp) cc_final: 0.5842 (ptp) REVERT: P 95 MET cc_start: 0.9433 (pmm) cc_final: 0.9097 (pmm) REVERT: P 161 MET cc_start: 0.9202 (tpt) cc_final: 0.8685 (tpp) REVERT: P 271 MET cc_start: 0.9220 (mmp) cc_final: 0.8796 (mmm) REVERT: P 475 MET cc_start: 0.8800 (pmm) cc_final: 0.8192 (pmm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.2784 time to fit residues: 25.9830 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 : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 146 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 134 optimal weight: 30.0000 chunk 4 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 543 ASN ** O 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 80 ASN P 246 GLN ** P 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.024152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.019334 restraints weight = 333058.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.019938 restraints weight = 191044.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.020349 restraints weight = 130325.445| |-----------------------------------------------------------------------------| r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17609 Z= 0.283 Angle : 0.881 11.095 24119 Z= 0.422 Chirality : 0.047 0.306 3020 Planarity : 0.005 0.082 2855 Dihedral : 9.396 59.550 4574 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 24.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 0.06 % Allowed : 0.35 % Favored : 99.60 % 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: -2.38 (0.18), residues: 1949 helix: -0.90 (0.25), residues: 392 sheet: -2.12 (0.22), residues: 462 loop : -1.56 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 571 HIS 0.012 0.002 HIS P 216 PHE 0.029 0.003 PHE H 67 TYR 0.028 0.002 TYR D 638 ARG 0.013 0.001 ARG G 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00747 ( 54) link_NAG-ASN : angle 2.60529 ( 162) link_ALPHA1-6 : bond 0.00564 ( 3) link_ALPHA1-6 : angle 1.75418 ( 9) link_BETA1-4 : bond 0.00458 ( 57) link_BETA1-4 : angle 1.88494 ( 171) link_ALPHA1-3 : bond 0.00822 ( 6) link_ALPHA1-3 : angle 1.91020 ( 18) hydrogen bonds : bond 0.03889 ( 461) hydrogen bonds : angle 6.43807 ( 1227) SS BOND : bond 0.00449 ( 38) SS BOND : angle 1.53358 ( 76) covalent geometry : bond 0.00563 (17451) covalent geometry : angle 0.84118 (23683) ********************** 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 57 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 1.768 Fit side-chains REVERT: B 530 MET cc_start: 0.9067 (mpp) cc_final: 0.8242 (mpp) REVERT: B 626 MET cc_start: 0.9478 (pmm) cc_final: 0.9019 (pmm) REVERT: E 100 MET cc_start: 0.9431 (pmm) cc_final: 0.9126 (pmm) REVERT: G 104 MET cc_start: 0.9406 (ppp) cc_final: 0.9195 (ppp) REVERT: G 150 MET cc_start: -0.0560 (ptt) cc_final: -0.1245 (ppp) REVERT: G 475 MET cc_start: 0.9106 (pmm) cc_final: 0.8851 (pmm) REVERT: H 82 MET cc_start: 0.6150 (ptp) cc_final: 0.5861 (ptp) REVERT: O 530 MET cc_start: 0.8502 (mmp) cc_final: 0.8062 (mmp) REVERT: P 95 MET cc_start: 0.9500 (pmm) cc_final: 0.9149 (pmm) REVERT: P 161 MET cc_start: 0.9250 (tpt) cc_final: 0.8733 (tpp) REVERT: P 271 MET cc_start: 0.9171 (mmp) cc_final: 0.8756 (mmm) REVERT: P 475 MET cc_start: 0.8943 (pmm) cc_final: 0.8270 (pmm) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.2947 time to fit residues: 28.3678 Evaluate side-chains 48 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 24 optimal weight: 5.9990 chunk 193 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 577 GLN P 246 GLN ** P 374 HIS ** 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 = 0.2774 r_free = 0.2774 target = 0.025956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.021072 restraints weight = 314478.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.021726 restraints weight = 172214.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.022167 restraints weight = 114250.137| |-----------------------------------------------------------------------------| r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17609 Z= 0.121 Angle : 0.711 10.163 24119 Z= 0.334 Chirality : 0.046 0.310 3020 Planarity : 0.004 0.048 2855 Dihedral : 9.019 59.845 4574 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -2.17 (0.18), residues: 1949 helix: -0.57 (0.26), residues: 398 sheet: -1.92 (0.23), residues: 450 loop : -1.53 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 571 HIS 0.005 0.001 HIS L 34 PHE 0.014 0.001 PHE H 67 TYR 0.020 0.002 TYR D 643 ARG 0.007 0.000 ARG G 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 54) link_NAG-ASN : angle 2.20531 ( 162) link_ALPHA1-6 : bond 0.00630 ( 3) link_ALPHA1-6 : angle 1.76690 ( 9) link_BETA1-4 : bond 0.00491 ( 57) link_BETA1-4 : angle 1.53834 ( 171) link_ALPHA1-3 : bond 0.01039 ( 6) link_ALPHA1-3 : angle 1.38474 ( 18) hydrogen bonds : bond 0.02937 ( 461) hydrogen bonds : angle 5.84114 ( 1227) SS BOND : bond 0.00294 ( 38) SS BOND : angle 1.30477 ( 76) covalent geometry : bond 0.00259 (17451) covalent geometry : angle 0.67582 (23683) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3867.75 seconds wall clock time: 70 minutes 14.30 seconds (4214.30 seconds total)