Starting phenix.real_space_refine on Sun Aug 24 05:55:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g9y_29882/08_2025/8g9y_29882.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9y_29882/08_2025/8g9y_29882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g9y_29882/08_2025/8g9y_29882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9y_29882/08_2025/8g9y_29882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g9y_29882/08_2025/8g9y_29882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9y_29882/08_2025/8g9y_29882.map" } resolution = 4.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 10664 2.51 5 N 2809 2.21 5 O 3547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.47, per 1000 atoms: 0.32 Number of scatterers: 17135 At special positions: 0 Unit cell: (132.01, 129.863, 134.156, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 3547 8.00 N 2809 7.00 C 10664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS P 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.07 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS O 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.02 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.02 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS O 598 " - pdb=" SG CYS O 604 " distance=2.02 Simple disulfide: pdb=" SG CYS P 54 " - pdb=" SG CYS P 74 " distance=2.04 Simple disulfide: pdb=" SG CYS P 119 " - pdb=" SG CYS P 205 " distance=2.03 Simple disulfide: pdb=" SG CYS P 126 " - pdb=" SG CYS P 196 " distance=2.02 Simple disulfide: pdb=" SG CYS P 131 " - pdb=" SG CYS P 157 " distance=2.02 Simple disulfide: pdb=" SG CYS P 201 " - pdb=" SG CYS P 433 " distance=2.03 Simple disulfide: pdb=" SG CYS P 218 " - pdb=" SG CYS P 247 " distance=2.02 Simple disulfide: pdb=" SG CYS P 228 " - pdb=" SG CYS P 239 " distance=2.03 Simple disulfide: pdb=" SG CYS P 296 " - pdb=" SG CYS P 331 " distance=2.03 Simple disulfide: pdb=" SG CYS P 378 " - pdb=" SG CYS P 445 " distance=2.04 Simple disulfide: pdb=" SG CYS P 385 " - pdb=" SG CYS P 418 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA S 3 " - " MAN S 4 " " BMA a 3 " - " MAN a 4 " " BMA f 3 " - " MAN f 4 " " BMA n 3 " - " MAN n 4 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA f 3 " - " MAN f 5 " " BMA s 3 " - " MAN s 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " NAG-ASN " NAG A 1 " - " ASN E 88 " " NAG B 701 " - " ASN B 637 " " NAG C 1 " - " ASN E 156 " " NAG D 701 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 339 " " NAG E 603 " - " ASN E 355 " " NAG E 604 " - " ASN E 276 " " NAG F 1 " - " ASN E 160 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 339 " " NAG G 603 " - " ASN G 355 " " NAG G 604 " - " ASN G 276 " " NAG I 1 " - " ASN E 197 " " NAG J 1 " - " ASN E 234 " " NAG K 1 " - " ASN E 262 " " NAG M 1 " - " ASN E 295 " " NAG N 1 " - " ASN E 301 " " NAG O 701 " - " ASN O 637 " " NAG P 601 " - " ASN P 133 " " NAG P 602 " - " ASN P 339 " " NAG P 603 " - " ASN P 355 " " NAG P 604 " - " ASN P 276 " " NAG Q 1 " - " ASN E 332 " " NAG R 1 " - " ASN E 363 " " NAG S 1 " - " ASN E 386 " " NAG T 1 " - " ASN E 392 " " NAG U 1 " - " ASN E 448 " " NAG V 1 " - " ASN G 88 " " NAG W 1 " - " ASN G 156 " " NAG X 1 " - " ASN G 160 " " NAG Y 1 " - " ASN G 197 " " NAG Z 1 " - " ASN G 234 " " NAG a 1 " - " ASN G 262 " " NAG b 1 " - " ASN G 295 " " NAG c 1 " - " ASN G 301 " " NAG d 1 " - " ASN G 332 " " NAG e 1 " - " ASN G 363 " " NAG f 1 " - " ASN G 386 " " NAG g 1 " - " ASN G 392 " " NAG h 1 " - " ASN G 448 " " NAG i 1 " - " ASN P 88 " " NAG j 1 " - " ASN P 156 " " NAG k 1 " - " ASN P 160 " " NAG l 1 " - " ASN P 197 " " NAG m 1 " - " ASN P 234 " " NAG n 1 " - " ASN P 262 " " NAG o 1 " - " ASN P 295 " " NAG p 1 " - " ASN P 301 " " NAG q 1 " - " ASN P 332 " " NAG r 1 " - " ASN P 363 " " NAG s 1 " - " ASN P 386 " " NAG t 1 " - " ASN P 392 " " NAG u 1 " - " ASN P 448 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 800.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 42 sheets defined 20.6% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 4.065A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 595 removed outlier: 3.548A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 641 through 664 removed outlier: 3.659A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.854A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 595 removed outlier: 3.586A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 641 through 664 removed outlier: 3.689A pdb=" N GLN D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 removed outlier: 3.721A pdb=" N GLU E 62 " --> pdb=" O LYS E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 115 removed outlier: 3.531A pdb=" N MET E 104 " --> pdb=" O MET E 100 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.834A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.685A pdb=" N LYS E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG E 350 " --> pdb=" O VAL E 346 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.274A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.917A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 removed outlier: 3.658A pdb=" N GLU G 62 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 115 removed outlier: 3.594A pdb=" N HIS G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.873A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 354 removed outlier: 3.738A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG G 350 " --> pdb=" O VAL G 346 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.320A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 3.909A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 98 through 100B removed outlier: 4.248A pdb=" N SER H 100B" --> pdb=" O LYS H 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.584A pdb=" N PHE L 83 " --> pdb=" O THR L 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 529 through 534 Processing helix chain 'O' and resid 537 through 543 removed outlier: 3.994A pdb=" N ASN O 543 " --> pdb=" O VAL O 539 " (cutoff:3.500A) Processing helix chain 'O' and resid 572 through 595 removed outlier: 3.526A pdb=" N ALA O 578 " --> pdb=" O LYS O 574 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU O 581 " --> pdb=" O GLN O 577 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU O 584 " --> pdb=" O VAL O 580 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP O 589 " --> pdb=" O ARG O 585 " (cutoff:3.500A) Processing helix chain 'O' and resid 627 through 636 Processing helix chain 'O' and resid 641 through 664 removed outlier: 3.602A pdb=" N GLU O 647 " --> pdb=" O TYR O 643 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU O 648 " --> pdb=" O GLY O 644 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN O 653 " --> pdb=" O SER O 649 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU O 663 " --> pdb=" O ASP O 659 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP O 664 " --> pdb=" O LEU O 660 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 62 removed outlier: 3.705A pdb=" N GLU P 62 " --> pdb=" O LYS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 115 removed outlier: 3.605A pdb=" N HIS P 105 " --> pdb=" O VAL P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 126 removed outlier: 3.879A pdb=" N LEU P 125 " --> pdb=" O LEU P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 354 removed outlier: 3.597A pdb=" N GLU P 340 " --> pdb=" O ALA P 336 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS P 347 " --> pdb=" O GLY P 343 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG P 350 " --> pdb=" O VAL P 346 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS P 351 " --> pdb=" O LYS P 347 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N HIS P 352 " --> pdb=" O GLN P 348 " (cutoff:3.500A) Processing helix chain 'P' and resid 425 through 429 removed outlier: 4.257A pdb=" N ARG P 429 " --> pdb=" O MET P 426 " (cutoff:3.500A) Processing helix chain 'P' and resid 475 through 480 removed outlier: 3.801A pdb=" N TRP P 479 " --> pdb=" O MET P 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 8.570A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL G 36 " --> pdb=" O VAL B 608 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 603 through 609 removed outlier: 7.989A pdb=" N THR D 606 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N VAL P 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL D 608 " --> pdb=" O VAL P 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 495 through 499 removed outlier: 3.805A pdb=" N VAL E 38 " --> pdb=" O CYS O 604 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N CYS O 604 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.547A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.553A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 154 through 155 Processing sheet with id=AA7, first strand: chain 'E' and resid 159 through 162 Processing sheet with id=AA8, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AA9, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.865A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.804A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.937A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.747A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG E 273 " --> pdb=" O LEU E 285 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET E 271 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.804A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 297 through 298 Processing sheet with id=AB4, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.715A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 330 through 334 Processing sheet with id=AB6, first strand: chain 'E' and resid 375 through 378 Processing sheet with id=AB7, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.587A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 91 through 92 removed outlier: 3.512A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AC1, first strand: chain 'G' and resid 158 through 162 Processing sheet with id=AC2, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AC3, first strand: chain 'G' and resid 260 through 261 removed outlier: 3.635A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.987A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.201A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 11.788A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.054A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU G 285 " --> pdb=" O ARG G 273 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG G 273 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN G 287 " --> pdb=" O MET G 271 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 260 through 261 removed outlier: 3.635A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 297 through 298 Processing sheet with id=AC6, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.810A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 330 through 334 Processing sheet with id=AC8, first strand: chain 'G' and resid 375 through 378 Processing sheet with id=AC9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.069A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.069A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG H 94 " --> pdb=" O ALA H 101 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.976A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.348A pdb=" N LEU L 33 " --> pdb=" O LYS L 49 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS L 49 " --> pdb=" O GLN L 53 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.599A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 45 through 47 removed outlier: 3.505A pdb=" N ILE P 225 " --> pdb=" O VAL P 245 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL P 242 " --> pdb=" O LEU P 86 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU P 86 " --> pdb=" O VAL P 242 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 154 through 155 Processing sheet with id=AD8, first strand: chain 'P' and resid 159 through 162 Processing sheet with id=AD9, first strand: chain 'P' and resid 181 through 184 removed outlier: 4.636A pdb=" N GLU P 190 " --> pdb=" O ILE P 184 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.899A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY P 451 " --> pdb=" O THR P 290 " (cutoff:3.500A) removed outlier: 11.072A pdb=" N THR P 290 " --> pdb=" O GLY P 451 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N ILE P 453 " --> pdb=" O PHE P 288 " (cutoff:3.500A) removed outlier: 11.854A pdb=" N PHE P 288 " --> pdb=" O ILE P 453 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N THR P 455 " --> pdb=" O VAL P 286 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N VAL P 286 " --> pdb=" O THR P 455 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG P 273 " --> pdb=" O LEU P 285 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.899A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG P 360 " --> pdb=" O PHE P 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 297 through 298 Processing sheet with id=AE4, first strand: chain 'P' and resid 304 through 312 removed outlier: 6.820A pdb=" N GLN P 315 " --> pdb=" O ILE P 309 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 330 through 334 Processing sheet with id=AE6, first strand: chain 'P' and resid 375 through 378 457 hydrogen bonds defined for protein. 1179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 5307 1.35 - 1.49: 4824 1.49 - 1.63: 7166 1.63 - 1.77: 17 1.77 - 1.91: 137 Bond restraints: 17451 Sorted by residual: bond pdb=" CB CYS E 205 " pdb=" SG CYS E 205 " ideal model delta sigma weight residual 1.808 1.700 0.108 3.30e-02 9.18e+02 1.08e+01 bond pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " ideal model delta sigma weight residual 1.808 1.909 -0.101 3.30e-02 9.18e+02 9.32e+00 bond pdb=" CG MET O 530 " pdb=" SD MET O 530 " ideal model delta sigma weight residual 1.803 1.739 0.064 2.50e-02 1.60e+03 6.57e+00 bond pdb=" CG LEU E 116 " pdb=" CD2 LEU E 116 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.80e+00 bond pdb=" C1 NAG s 2 " pdb=" O5 NAG s 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.42e+00 ... (remaining 17446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.12: 23209 4.12 - 8.24: 442 8.24 - 12.36: 28 12.36 - 16.47: 3 16.47 - 20.59: 1 Bond angle restraints: 23683 Sorted by residual: angle pdb=" CA LEU G 494 " pdb=" CB LEU G 494 " pdb=" CG LEU G 494 " ideal model delta sigma weight residual 116.30 136.89 -20.59 3.50e+00 8.16e-02 3.46e+01 angle pdb=" C ASN G 295 " pdb=" CA ASN G 295 " pdb=" CB ASN G 295 " ideal model delta sigma weight residual 111.97 123.50 -11.53 1.99e+00 2.53e-01 3.36e+01 angle pdb=" C ASN P 332 " pdb=" CA ASN P 332 " pdb=" CB ASN P 332 " ideal model delta sigma weight residual 109.35 120.81 -11.46 1.98e+00 2.55e-01 3.35e+01 angle pdb=" CA CYS E 433 " pdb=" CB CYS E 433 " pdb=" SG CYS E 433 " ideal model delta sigma weight residual 114.40 127.38 -12.98 2.30e+00 1.89e-01 3.18e+01 angle pdb=" N CYS E 433 " pdb=" CA CYS E 433 " pdb=" CB CYS E 433 " ideal model delta sigma weight residual 111.21 102.01 9.20 1.67e+00 3.59e-01 3.04e+01 ... (remaining 23678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.73: 10799 21.73 - 43.45: 872 43.45 - 65.17: 154 65.17 - 86.90: 128 86.90 - 108.62: 77 Dihedral angle restraints: 12030 sinusoidal: 6329 harmonic: 5701 Sorted by residual: dihedral pdb=" CB CYS E 201 " pdb=" SG CYS E 201 " pdb=" SG CYS E 433 " pdb=" CB CYS E 433 " ideal model delta sinusoidal sigma weight residual -86.00 3.17 -89.17 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS G 126 " pdb=" SG CYS G 126 " pdb=" SG CYS G 196 " pdb=" CB CYS G 196 " ideal model delta sinusoidal sigma weight residual 93.00 160.57 -67.57 1 1.00e+01 1.00e-02 5.94e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -152.85 66.85 1 1.00e+01 1.00e-02 5.83e+01 ... (remaining 12027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2333 0.079 - 0.158: 552 0.158 - 0.237: 92 0.237 - 0.316: 33 0.316 - 0.395: 10 Chirality restraints: 3020 Sorted by residual: chirality pdb=" CB ILE E 326 " pdb=" CA ILE E 326 " pdb=" CG1 ILE E 326 " pdb=" CG2 ILE E 326 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CA ASN G 295 " pdb=" N ASN G 295 " pdb=" C ASN G 295 " pdb=" CB ASN G 295 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN G 156 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 3017 not shown) Planarity restraints: 2909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 295 " -0.005 2.00e-02 2.50e+03 5.37e-02 3.61e+01 pdb=" CG ASN G 295 " 0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN G 295 " -0.062 2.00e-02 2.50e+03 pdb=" ND2 ASN G 295 " 0.063 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 427 " -0.025 2.00e-02 2.50e+03 2.83e-02 2.00e+01 pdb=" CG TRP G 427 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP G 427 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP G 427 " -0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP G 427 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP G 427 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP G 427 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 427 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 427 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP G 427 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 653 " -0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C GLN B 653 " 0.073 2.00e-02 2.50e+03 pdb=" O GLN B 653 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU B 654 " -0.025 2.00e-02 2.50e+03 ... (remaining 2906 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1913 2.73 - 3.28: 16983 3.28 - 3.82: 27716 3.82 - 4.36: 31756 4.36 - 4.90: 53916 Nonbonded interactions: 132284 Sorted by model distance: nonbonded pdb=" O SER L 43 " pdb=" NH1 ARG L 45 " model vdw 2.193 3.120 nonbonded pdb=" OD1 ASN P 302 " pdb=" OG1 THR P 320 " model vdw 2.231 3.040 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.245 3.040 nonbonded pdb=" OD1 ASN G 302 " pdb=" OG1 THR G 320 " model vdw 2.255 3.040 nonbonded pdb=" O LEU G 369 " pdb=" OG1 THR G 373 " model vdw 2.255 3.040 ... (remaining 132279 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'u' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'W' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'j' selection = chain 'q' selection = chain 'r' selection = chain 't' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'P' } ncs_group { reference = chain 'K' selection = chain 'a' selection = chain 'n' } ncs_group { reference = chain 'S' selection = chain 'f' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.260 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.108 17609 Z= 0.391 Angle : 1.397 21.636 24119 Z= 0.699 Chirality : 0.074 0.395 3020 Planarity : 0.008 0.058 2855 Dihedral : 19.158 108.624 8236 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.65 % Favored : 90.25 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.83 (0.15), residues: 1949 helix: -4.60 (0.10), residues: 414 sheet: -2.87 (0.20), residues: 448 loop : -2.79 (0.15), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 327 TYR 0.020 0.003 TYR L 36 PHE 0.025 0.003 PHE P 288 TRP 0.077 0.004 TRP G 427 HIS 0.013 0.002 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00810 (17451) covalent geometry : angle 1.33585 (23683) SS BOND : bond 0.00823 ( 38) SS BOND : angle 3.12481 ( 76) hydrogen bonds : bond 0.15381 ( 444) hydrogen bonds : angle 8.43165 ( 1179) link_ALPHA1-3 : bond 0.00629 ( 6) link_ALPHA1-3 : angle 1.88994 ( 18) link_ALPHA1-6 : bond 0.00568 ( 3) link_ALPHA1-6 : angle 1.59254 ( 9) link_BETA1-4 : bond 0.00889 ( 57) link_BETA1-4 : angle 2.27310 ( 171) link_NAG-ASN : bond 0.00802 ( 54) link_NAG-ASN : angle 4.39218 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9076 (mpp) cc_final: 0.8851 (mpp) REVERT: D 530 MET cc_start: 0.9175 (mmp) cc_final: 0.8492 (mmp) REVERT: D 535 MET cc_start: 0.9454 (mpp) cc_final: 0.9182 (mpp) REVERT: E 95 MET cc_start: 0.9143 (ppp) cc_final: 0.8791 (ppp) REVERT: G 104 MET cc_start: 0.9213 (ppp) cc_final: 0.8958 (ppp) REVERT: H 3 MET cc_start: 0.8684 (tmm) cc_final: 0.8462 (tmm) REVERT: O 530 MET cc_start: 0.9157 (mmp) cc_final: 0.8727 (mmp) REVERT: O 535 MET cc_start: 0.9495 (mmp) cc_final: 0.9260 (mmp) REVERT: O 632 ASP cc_start: 0.9108 (m-30) cc_final: 0.8896 (m-30) REVERT: P 95 MET cc_start: 0.9649 (ptm) cc_final: 0.8002 (ppp) REVERT: P 434 MET cc_start: 0.9084 (tmm) cc_final: 0.8518 (tmm) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1300 time to fit residues: 12.7929 Evaluate side-chains 48 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN G 289 ASN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 GLN ** P 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.027166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.020759 restraints weight = 241334.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.021356 restraints weight = 154714.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.021786 restraints weight = 114565.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.022079 restraints weight = 92876.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.022275 restraints weight = 80335.107| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17609 Z= 0.191 Angle : 0.825 13.965 24119 Z= 0.391 Chirality : 0.047 0.354 3020 Planarity : 0.005 0.034 2855 Dihedral : 14.630 73.445 4574 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.31 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.70 (0.17), residues: 1949 helix: -2.74 (0.20), residues: 403 sheet: -2.63 (0.20), residues: 507 loop : -2.19 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 298 TYR 0.013 0.001 TYR G 177 PHE 0.014 0.002 PHE G 288 TRP 0.024 0.002 TRP G 427 HIS 0.004 0.001 HIS P 374 Details of bonding type rmsd covalent geometry : bond 0.00390 (17451) covalent geometry : angle 0.77050 (23683) SS BOND : bond 0.00470 ( 38) SS BOND : angle 1.46280 ( 76) hydrogen bonds : bond 0.03992 ( 444) hydrogen bonds : angle 6.15771 ( 1179) link_ALPHA1-3 : bond 0.01049 ( 6) link_ALPHA1-3 : angle 2.63596 ( 18) link_ALPHA1-6 : bond 0.00230 ( 3) link_ALPHA1-6 : angle 2.16549 ( 9) link_BETA1-4 : bond 0.00531 ( 57) link_BETA1-4 : angle 2.01719 ( 171) link_NAG-ASN : bond 0.00412 ( 54) link_NAG-ASN : angle 2.87992 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: B 643 TYR cc_start: 0.9539 (m-80) cc_final: 0.9239 (m-80) REVERT: E 95 MET cc_start: 0.9100 (ppp) cc_final: 0.8801 (ppp) REVERT: E 475 MET cc_start: 0.9018 (tpt) cc_final: 0.8510 (mmm) REVERT: G 95 MET cc_start: 0.9410 (ppp) cc_final: 0.8424 (ppp) REVERT: G 104 MET cc_start: 0.9206 (ppp) cc_final: 0.9000 (ppp) REVERT: O 530 MET cc_start: 0.9068 (mmp) cc_final: 0.8230 (mmp) REVERT: O 643 TYR cc_start: 0.9363 (m-80) cc_final: 0.8843 (m-80) REVERT: P 95 MET cc_start: 0.9493 (ptm) cc_final: 0.7922 (ppp) REVERT: P 434 MET cc_start: 0.9152 (tmm) cc_final: 0.8664 (tmm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1005 time to fit residues: 9.1481 Evaluate side-chains 47 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 145 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 192 optimal weight: 0.0270 chunk 182 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 HIS ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 GLN L 32 ASN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN ** P 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 287 GLN P 289 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.026878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.020491 restraints weight = 245826.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.021081 restraints weight = 157084.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.021506 restraints weight = 116670.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.021786 restraints weight = 94498.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.021987 restraints weight = 81718.830| |-----------------------------------------------------------------------------| r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17609 Z= 0.195 Angle : 0.785 12.701 24119 Z= 0.372 Chirality : 0.046 0.336 3020 Planarity : 0.004 0.033 2855 Dihedral : 11.393 64.974 4574 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.67 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.00 (0.18), residues: 1949 helix: -1.52 (0.24), residues: 379 sheet: -2.54 (0.21), residues: 471 loop : -1.88 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 273 TYR 0.015 0.001 TYR G 318 PHE 0.014 0.002 PHE G 391 TRP 0.024 0.002 TRP D 571 HIS 0.004 0.001 HIS P 66 Details of bonding type rmsd covalent geometry : bond 0.00403 (17451) covalent geometry : angle 0.73476 (23683) SS BOND : bond 0.00343 ( 38) SS BOND : angle 1.30969 ( 76) hydrogen bonds : bond 0.03550 ( 444) hydrogen bonds : angle 5.61363 ( 1179) link_ALPHA1-3 : bond 0.01063 ( 6) link_ALPHA1-3 : angle 1.77664 ( 18) link_ALPHA1-6 : bond 0.00422 ( 3) link_ALPHA1-6 : angle 2.13019 ( 9) link_BETA1-4 : bond 0.00539 ( 57) link_BETA1-4 : angle 1.82246 ( 171) link_NAG-ASN : bond 0.00425 ( 54) link_NAG-ASN : angle 2.81170 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: B 643 TYR cc_start: 0.9546 (m-80) cc_final: 0.9235 (m-80) REVERT: D 535 MET cc_start: 0.9495 (mpp) cc_final: 0.9246 (mpp) REVERT: E 95 MET cc_start: 0.9206 (ppp) cc_final: 0.8926 (ppp) REVERT: E 475 MET cc_start: 0.9085 (tpt) cc_final: 0.8646 (mmm) REVERT: G 95 MET cc_start: 0.9461 (ppp) cc_final: 0.8436 (ppp) REVERT: H 3 MET cc_start: 0.9073 (tmm) cc_final: 0.8789 (tmm) REVERT: O 530 MET cc_start: 0.9049 (mmp) cc_final: 0.8453 (mmp) REVERT: O 643 TYR cc_start: 0.9411 (m-80) cc_final: 0.8995 (m-80) REVERT: P 95 MET cc_start: 0.9460 (ptm) cc_final: 0.7942 (ppp) REVERT: P 434 MET cc_start: 0.9226 (tmm) cc_final: 0.8754 (tmm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1342 time to fit residues: 11.8564 Evaluate side-chains 47 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 154 optimal weight: 20.0000 chunk 93 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 186 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.027190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.020749 restraints weight = 241228.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.021359 restraints weight = 154689.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.021778 restraints weight = 114463.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.022067 restraints weight = 93078.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.022272 restraints weight = 80465.704| |-----------------------------------------------------------------------------| r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17609 Z= 0.125 Angle : 0.715 13.217 24119 Z= 0.335 Chirality : 0.046 0.336 3020 Planarity : 0.004 0.040 2855 Dihedral : 10.258 59.705 4574 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.26 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.75 (0.18), residues: 1949 helix: -1.08 (0.26), residues: 379 sheet: -2.25 (0.21), residues: 474 loop : -1.90 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 273 TYR 0.011 0.001 TYR D 638 PHE 0.012 0.001 PHE G 288 TRP 0.018 0.001 TRP D 571 HIS 0.007 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00257 (17451) covalent geometry : angle 0.66547 (23683) SS BOND : bond 0.00288 ( 38) SS BOND : angle 1.35336 ( 76) hydrogen bonds : bond 0.03024 ( 444) hydrogen bonds : angle 5.39052 ( 1179) link_ALPHA1-3 : bond 0.01176 ( 6) link_ALPHA1-3 : angle 2.02500 ( 18) link_ALPHA1-6 : bond 0.00537 ( 3) link_ALPHA1-6 : angle 2.12107 ( 9) link_BETA1-4 : bond 0.00489 ( 57) link_BETA1-4 : angle 1.67099 ( 171) link_NAG-ASN : bond 0.00319 ( 54) link_NAG-ASN : angle 2.61344 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: B 643 TYR cc_start: 0.9520 (m-80) cc_final: 0.9244 (m-80) REVERT: E 95 MET cc_start: 0.9189 (ppp) cc_final: 0.8734 (ppp) REVERT: E 475 MET cc_start: 0.9072 (tpt) cc_final: 0.8821 (tpt) REVERT: G 95 MET cc_start: 0.9431 (ppp) cc_final: 0.8353 (ppp) REVERT: H 3 MET cc_start: 0.9077 (tmm) cc_final: 0.8837 (tmm) REVERT: O 643 TYR cc_start: 0.9416 (m-80) cc_final: 0.9021 (m-80) REVERT: P 95 MET cc_start: 0.9388 (ptm) cc_final: 0.7974 (ppp) REVERT: P 434 MET cc_start: 0.9283 (tmm) cc_final: 0.8830 (tmm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1432 time to fit residues: 13.1783 Evaluate side-chains 48 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 178 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.028398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.022865 restraints weight = 262779.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.023558 restraints weight = 153705.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.024026 restraints weight = 106285.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.024323 restraints weight = 82199.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.024557 restraints weight = 69257.252| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17609 Z= 0.172 Angle : 0.725 12.177 24119 Z= 0.342 Chirality : 0.045 0.331 3020 Planarity : 0.004 0.034 2855 Dihedral : 9.645 59.942 4574 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.93 % Favored : 93.02 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.18), residues: 1949 helix: -0.73 (0.26), residues: 380 sheet: -2.02 (0.24), residues: 402 loop : -1.71 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 298 TYR 0.011 0.001 TYR G 318 PHE 0.010 0.001 PHE G 288 TRP 0.019 0.002 TRP D 631 HIS 0.004 0.001 HIS P 66 Details of bonding type rmsd covalent geometry : bond 0.00354 (17451) covalent geometry : angle 0.67761 (23683) SS BOND : bond 0.00367 ( 38) SS BOND : angle 1.28489 ( 76) hydrogen bonds : bond 0.03015 ( 444) hydrogen bonds : angle 5.29068 ( 1179) link_ALPHA1-3 : bond 0.01117 ( 6) link_ALPHA1-3 : angle 1.97433 ( 18) link_ALPHA1-6 : bond 0.00531 ( 3) link_ALPHA1-6 : angle 2.19677 ( 9) link_BETA1-4 : bond 0.00441 ( 57) link_BETA1-4 : angle 1.61584 ( 171) link_NAG-ASN : bond 0.00381 ( 54) link_NAG-ASN : angle 2.64394 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 643 TYR cc_start: 0.9446 (m-80) cc_final: 0.9188 (m-80) REVERT: E 95 MET cc_start: 0.9264 (ppp) cc_final: 0.8919 (ppp) REVERT: E 475 MET cc_start: 0.9099 (tpt) cc_final: 0.8687 (mmm) REVERT: G 95 MET cc_start: 0.9264 (ppp) cc_final: 0.8616 (ppp) REVERT: H 3 MET cc_start: 0.9089 (tmm) cc_final: 0.8886 (tmm) REVERT: L 76 ASN cc_start: 0.9238 (m110) cc_final: 0.8884 (p0) REVERT: O 530 MET cc_start: 0.8952 (mmp) cc_final: 0.8152 (mmp) REVERT: O 643 TYR cc_start: 0.9418 (m-80) cc_final: 0.9042 (m-80) REVERT: P 95 MET cc_start: 0.9424 (ptm) cc_final: 0.8600 (tmm) REVERT: P 271 MET cc_start: 0.9213 (tpt) cc_final: 0.8666 (tmm) REVERT: P 434 MET cc_start: 0.9287 (tmm) cc_final: 0.8877 (tmm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1222 time to fit residues: 11.0392 Evaluate side-chains 49 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 3 optimal weight: 0.6980 chunk 144 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN E 287 GLN ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 ASN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 85 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 = 0.2938 r_free = 0.2938 target = 0.027270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.021746 restraints weight = 269644.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.022394 restraints weight = 158278.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.022828 restraints weight = 111000.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.023132 restraints weight = 86999.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.023320 restraints weight = 73608.209| |-----------------------------------------------------------------------------| r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17609 Z= 0.233 Angle : 0.800 11.307 24119 Z= 0.379 Chirality : 0.045 0.311 3020 Planarity : 0.004 0.036 2855 Dihedral : 9.459 59.864 4574 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.95 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.18), residues: 1949 helix: -0.77 (0.26), residues: 390 sheet: -2.13 (0.23), residues: 465 loop : -1.57 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 192 TYR 0.013 0.002 TYR E 191 PHE 0.015 0.002 PHE G 176 TRP 0.025 0.002 TRP D 571 HIS 0.007 0.001 HIS P 66 Details of bonding type rmsd covalent geometry : bond 0.00476 (17451) covalent geometry : angle 0.75370 (23683) SS BOND : bond 0.00460 ( 38) SS BOND : angle 1.56113 ( 76) hydrogen bonds : bond 0.03257 ( 444) hydrogen bonds : angle 5.47739 ( 1179) link_ALPHA1-3 : bond 0.01087 ( 6) link_ALPHA1-3 : angle 1.89669 ( 18) link_ALPHA1-6 : bond 0.00546 ( 3) link_ALPHA1-6 : angle 2.22127 ( 9) link_BETA1-4 : bond 0.00440 ( 57) link_BETA1-4 : angle 1.65099 ( 171) link_NAG-ASN : bond 0.00529 ( 54) link_NAG-ASN : angle 2.73525 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 643 TYR cc_start: 0.9490 (m-80) cc_final: 0.9219 (m-80) REVERT: E 95 MET cc_start: 0.9410 (ppp) cc_final: 0.9023 (ppp) REVERT: G 95 MET cc_start: 0.9364 (ppp) cc_final: 0.8729 (ppp) REVERT: G 161 MET cc_start: 0.9122 (tpt) cc_final: 0.8880 (tpp) REVERT: L 76 ASN cc_start: 0.9298 (m110) cc_final: 0.8967 (p0) REVERT: O 530 MET cc_start: 0.9009 (mmp) cc_final: 0.8181 (mmp) REVERT: P 95 MET cc_start: 0.9479 (ptm) cc_final: 0.8757 (tmm) REVERT: P 434 MET cc_start: 0.9299 (tmm) cc_final: 0.8947 (tmm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1149 time to fit residues: 9.7630 Evaluate side-chains 48 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 113 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.026485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.020303 restraints weight = 246625.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.020890 restraints weight = 157661.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.021297 restraints weight = 116558.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.021585 restraints weight = 94927.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.021775 restraints weight = 82077.336| |-----------------------------------------------------------------------------| r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17609 Z= 0.113 Angle : 0.693 13.670 24119 Z= 0.323 Chirality : 0.045 0.328 3020 Planarity : 0.003 0.036 2855 Dihedral : 9.034 59.617 4574 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.18), residues: 1949 helix: -0.31 (0.27), residues: 381 sheet: -1.77 (0.25), residues: 402 loop : -1.57 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 273 TYR 0.010 0.001 TYR E 191 PHE 0.014 0.001 PHE G 93 TRP 0.017 0.001 TRP D 571 HIS 0.006 0.001 HIS G 66 Details of bonding type rmsd covalent geometry : bond 0.00236 (17451) covalent geometry : angle 0.65103 (23683) SS BOND : bond 0.00278 ( 38) SS BOND : angle 1.28655 ( 76) hydrogen bonds : bond 0.02751 ( 444) hydrogen bonds : angle 5.11549 ( 1179) link_ALPHA1-3 : bond 0.01052 ( 6) link_ALPHA1-3 : angle 1.56552 ( 18) link_ALPHA1-6 : bond 0.00681 ( 3) link_ALPHA1-6 : angle 1.97959 ( 9) link_BETA1-4 : bond 0.00510 ( 57) link_BETA1-4 : angle 1.38431 ( 171) link_NAG-ASN : bond 0.00314 ( 54) link_NAG-ASN : angle 2.48772 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.7800 (ppp) cc_final: 0.7575 (ppp) REVERT: B 643 TYR cc_start: 0.9514 (m-80) cc_final: 0.9256 (m-80) REVERT: E 95 MET cc_start: 0.9329 (ppp) cc_final: 0.8932 (ppp) REVERT: E 475 MET cc_start: 0.8994 (tpt) cc_final: 0.8595 (mmm) REVERT: G 95 MET cc_start: 0.9344 (ppp) cc_final: 0.8628 (ppp) REVERT: H 3 MET cc_start: 0.9244 (tmm) cc_final: 0.8928 (tmm) REVERT: L 76 ASN cc_start: 0.9294 (m110) cc_final: 0.9002 (p0) REVERT: O 530 MET cc_start: 0.8991 (mmp) cc_final: 0.8528 (mmp) REVERT: O 643 TYR cc_start: 0.9509 (m-80) cc_final: 0.9191 (m-80) REVERT: P 95 MET cc_start: 0.9283 (ptm) cc_final: 0.8545 (tmm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1387 time to fit residues: 12.0537 Evaluate side-chains 51 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 24 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 6 optimal weight: 0.0870 chunk 1 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 195 optimal weight: 20.0000 overall best weight: 2.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.027938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.022483 restraints weight = 266157.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.023148 restraints weight = 154378.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.023595 restraints weight = 107298.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.023907 restraints weight = 83552.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.024105 restraints weight = 70312.653| |-----------------------------------------------------------------------------| r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17609 Z= 0.146 Angle : 0.693 12.651 24119 Z= 0.324 Chirality : 0.044 0.326 3020 Planarity : 0.004 0.037 2855 Dihedral : 8.745 59.981 4574 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.18), residues: 1949 helix: -0.23 (0.27), residues: 381 sheet: -1.41 (0.27), residues: 369 loop : -1.64 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 273 TYR 0.009 0.001 TYR G 318 PHE 0.010 0.001 PHE G 93 TRP 0.019 0.002 TRP P 96 HIS 0.005 0.001 HIS P 66 Details of bonding type rmsd covalent geometry : bond 0.00306 (17451) covalent geometry : angle 0.64905 (23683) SS BOND : bond 0.00254 ( 38) SS BOND : angle 1.25100 ( 76) hydrogen bonds : bond 0.02818 ( 444) hydrogen bonds : angle 5.10536 ( 1179) link_ALPHA1-3 : bond 0.01012 ( 6) link_ALPHA1-3 : angle 1.52882 ( 18) link_ALPHA1-6 : bond 0.00634 ( 3) link_ALPHA1-6 : angle 1.96325 ( 9) link_BETA1-4 : bond 0.00439 ( 57) link_BETA1-4 : angle 1.47647 ( 171) link_NAG-ASN : bond 0.00353 ( 54) link_NAG-ASN : angle 2.51663 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.7898 (ppp) cc_final: 0.7530 (ppp) REVERT: B 643 TYR cc_start: 0.9422 (m-80) cc_final: 0.9193 (m-80) REVERT: E 95 MET cc_start: 0.9386 (ppp) cc_final: 0.9014 (ppp) REVERT: G 95 MET cc_start: 0.9348 (ppp) cc_final: 0.8655 (ppp) REVERT: H 3 MET cc_start: 0.9225 (tmm) cc_final: 0.8914 (tmm) REVERT: H 100 TYR cc_start: 0.8873 (m-80) cc_final: 0.8474 (m-80) REVERT: L 76 ASN cc_start: 0.9259 (m110) cc_final: 0.8948 (p0) REVERT: O 530 MET cc_start: 0.8961 (mmp) cc_final: 0.8360 (mmp) REVERT: O 643 TYR cc_start: 0.9483 (m-80) cc_final: 0.9175 (m-80) REVERT: P 95 MET cc_start: 0.9579 (ptm) cc_final: 0.9352 (ptm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1563 time to fit residues: 13.1137 Evaluate side-chains 50 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 0 optimal weight: 50.0000 chunk 67 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.027165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.021691 restraints weight = 272039.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.022338 restraints weight = 158433.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.022784 restraints weight = 110701.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.023077 restraints weight = 86543.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.023271 restraints weight = 73176.779| |-----------------------------------------------------------------------------| r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3682 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= 0.206 Angle : 0.752 12.036 24119 Z= 0.357 Chirality : 0.044 0.318 3020 Planarity : 0.004 0.036 2855 Dihedral : 8.755 59.522 4574 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.18), residues: 1949 helix: -0.37 (0.27), residues: 385 sheet: -1.34 (0.26), residues: 405 loop : -1.69 (0.17), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 273 TYR 0.012 0.001 TYR G 318 PHE 0.015 0.002 PHE G 223 TRP 0.025 0.002 TRP P 96 HIS 0.010 0.002 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00425 (17451) covalent geometry : angle 0.70981 (23683) SS BOND : bond 0.00328 ( 38) SS BOND : angle 1.29370 ( 76) hydrogen bonds : bond 0.03176 ( 444) hydrogen bonds : angle 5.29104 ( 1179) link_ALPHA1-3 : bond 0.00895 ( 6) link_ALPHA1-3 : angle 1.51175 ( 18) link_ALPHA1-6 : bond 0.00520 ( 3) link_ALPHA1-6 : angle 1.94706 ( 9) link_BETA1-4 : bond 0.00427 ( 57) link_BETA1-4 : angle 1.53628 ( 171) link_NAG-ASN : bond 0.00451 ( 54) link_NAG-ASN : angle 2.60026 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.8012 (ppp) cc_final: 0.7705 (ppp) REVERT: B 643 TYR cc_start: 0.9476 (m-80) cc_final: 0.9249 (m-80) REVERT: E 95 MET cc_start: 0.9444 (ppp) cc_final: 0.9062 (ppp) REVERT: G 95 MET cc_start: 0.9421 (ppp) cc_final: 0.8749 (ppp) REVERT: H 3 MET cc_start: 0.9228 (tmm) cc_final: 0.8943 (tmm) REVERT: L 76 ASN cc_start: 0.9298 (m110) cc_final: 0.9007 (p0) REVERT: O 530 MET cc_start: 0.9017 (mmp) cc_final: 0.8388 (mmp) REVERT: O 626 MET cc_start: 0.8354 (pmm) cc_final: 0.7872 (pmm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1353 time to fit residues: 12.7418 Evaluate side-chains 49 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 188 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 175 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.027539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.022136 restraints weight = 267362.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.022801 restraints weight = 155125.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.023253 restraints weight = 107881.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.023560 restraints weight = 83890.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.023765 restraints weight = 70369.512| |-----------------------------------------------------------------------------| r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17609 Z= 0.156 Angle : 0.702 12.283 24119 Z= 0.331 Chirality : 0.044 0.315 3020 Planarity : 0.004 0.036 2855 Dihedral : 8.642 59.817 4574 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.19), residues: 1949 helix: -0.09 (0.27), residues: 366 sheet: -1.33 (0.24), residues: 441 loop : -1.48 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 273 TYR 0.009 0.001 TYR E 61 PHE 0.009 0.001 PHE G 223 TRP 0.019 0.002 TRP D 571 HIS 0.005 0.001 HIS P 66 Details of bonding type rmsd covalent geometry : bond 0.00324 (17451) covalent geometry : angle 0.66093 (23683) SS BOND : bond 0.00277 ( 38) SS BOND : angle 1.29992 ( 76) hydrogen bonds : bond 0.02907 ( 444) hydrogen bonds : angle 5.21393 ( 1179) link_ALPHA1-3 : bond 0.00895 ( 6) link_ALPHA1-3 : angle 1.39291 ( 18) link_ALPHA1-6 : bond 0.00534 ( 3) link_ALPHA1-6 : angle 1.85768 ( 9) link_BETA1-4 : bond 0.00442 ( 57) link_BETA1-4 : angle 1.43191 ( 171) link_NAG-ASN : bond 0.00356 ( 54) link_NAG-ASN : angle 2.49686 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.8238 (ppp) cc_final: 0.7868 (ppp) REVERT: B 643 TYR cc_start: 0.9565 (m-80) cc_final: 0.9309 (m-80) REVERT: E 95 MET cc_start: 0.9472 (ppp) cc_final: 0.9063 (ppp) REVERT: G 95 MET cc_start: 0.9448 (ppp) cc_final: 0.8745 (ppp) REVERT: H 3 MET cc_start: 0.9193 (tmm) cc_final: 0.8908 (tmm) REVERT: L 76 ASN cc_start: 0.9292 (m110) cc_final: 0.9006 (p0) REVERT: O 530 MET cc_start: 0.9178 (mmp) cc_final: 0.8614 (mmp) REVERT: O 626 MET cc_start: 0.8556 (pmm) cc_final: 0.8066 (pmm) REVERT: O 643 TYR cc_start: 0.9569 (m-80) cc_final: 0.9224 (m-80) REVERT: P 95 MET cc_start: 0.9595 (ptm) cc_final: 0.8510 (tmm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1451 time to fit residues: 12.9787 Evaluate side-chains 51 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 114 optimal weight: 0.7980 chunk 178 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 155 optimal weight: 0.0470 chunk 77 optimal weight: 0.4980 chunk 142 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.028364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.022961 restraints weight = 263547.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.023649 restraints weight = 150904.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.024124 restraints weight = 104083.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.024441 restraints weight = 80235.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.024642 restraints weight = 66925.527| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17609 Z= 0.106 Angle : 0.663 12.751 24119 Z= 0.309 Chirality : 0.044 0.311 3020 Planarity : 0.003 0.038 2855 Dihedral : 8.357 59.731 4574 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.19), residues: 1949 helix: -0.15 (0.27), residues: 383 sheet: -1.13 (0.24), residues: 456 loop : -1.60 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 298 TYR 0.007 0.001 TYR E 61 PHE 0.011 0.001 PHE O 519 TRP 0.013 0.001 TRP P 96 HIS 0.004 0.001 HIS P 66 Details of bonding type rmsd covalent geometry : bond 0.00221 (17451) covalent geometry : angle 0.62512 (23683) SS BOND : bond 0.00242 ( 38) SS BOND : angle 1.10703 ( 76) hydrogen bonds : bond 0.02683 ( 444) hydrogen bonds : angle 4.93716 ( 1179) link_ALPHA1-3 : bond 0.00928 ( 6) link_ALPHA1-3 : angle 1.28861 ( 18) link_ALPHA1-6 : bond 0.00600 ( 3) link_ALPHA1-6 : angle 1.70477 ( 9) link_BETA1-4 : bond 0.00504 ( 57) link_BETA1-4 : angle 1.34303 ( 171) link_NAG-ASN : bond 0.00303 ( 54) link_NAG-ASN : angle 2.34395 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2158.85 seconds wall clock time: 38 minutes 53.41 seconds (2333.41 seconds total)