Starting phenix.real_space_refine on Fri Mar 6 15:25:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n1w_9320/03_2026/6n1w_9320.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n1w_9320/03_2026/6n1w_9320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n1w_9320/03_2026/6n1w_9320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n1w_9320/03_2026/6n1w_9320.map" model { file = "/net/cci-nas-00/data/ceres_data/6n1w_9320/03_2026/6n1w_9320.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n1w_9320/03_2026/6n1w_9320.cif" } resolution = 4.2 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= 0.105 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 168 5.16 5 C 20007 2.51 5 N 5295 2.21 5 O 6435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31905 Number of models: 1 Model: "" Number of chains: 66 Chain: "2" 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: "3" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 980 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "4" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 787 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "5" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "6" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "7" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "8" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" 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: "C" 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: "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: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 980 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "L" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 787 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "Q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "R" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "c" 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: "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: "h" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 980 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "l" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 787 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "m" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "n" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "r" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} 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: "E" 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: "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: "G" 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: 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: "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: "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: 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: 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: "T" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 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: "W" 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: "X" 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: "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: 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: 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: "e" 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: "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: "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: "i" 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: "j" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: "o" 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: "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: "s" 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: "t" 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: "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: 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: "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: 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: "0" 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: "1" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "9" 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: "AA" 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: "2" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 8.08, per 1000 atoms: 0.25 Number of scatterers: 31905 At special positions: 0 Unit cell: (159.43, 155.15, 166.92, 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 168 16.00 O 6435 8.00 N 5295 7.00 C 20007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS 2 119 " - pdb=" SG CYS 2 205 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 131 " - pdb=" SG CYS 2 157 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 201 " - pdb=" SG CYS 2 433 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 218 " - pdb=" SG CYS 2 247 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 228 " - pdb=" SG CYS 2 239 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 296 " - pdb=" SG CYS 2 331 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 378 " - pdb=" SG CYS 2 445 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 385 " - pdb=" SG CYS 2 418 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 23 " - pdb=" SG CYS 4 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 22 " - pdb=" SG CYS 5 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 23 " - pdb=" SG CYS 6 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 22 " - pdb=" SG CYS 8 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 98 " - pdb=" SG CYS 8 100A" distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 98 " - pdb=" SG CYS Q 100A" distance=2.03 Simple disulfide: pdb=" SG CYS c 119 " - pdb=" SG CYS c 205 " distance=2.03 Simple disulfide: pdb=" SG CYS c 131 " - pdb=" SG CYS c 157 " distance=2.03 Simple disulfide: pdb=" SG CYS c 201 " - pdb=" SG CYS c 433 " distance=2.03 Simple disulfide: pdb=" SG CYS c 218 " - pdb=" SG CYS c 247 " distance=2.03 Simple disulfide: pdb=" SG CYS c 228 " - pdb=" SG CYS c 239 " distance=2.03 Simple disulfide: pdb=" SG CYS c 296 " - pdb=" SG CYS c 331 " distance=2.03 Simple disulfide: pdb=" SG CYS c 378 " - pdb=" SG CYS c 445 " distance=2.03 Simple disulfide: pdb=" SG CYS c 385 " - pdb=" SG CYS c 418 " distance=2.03 Simple disulfide: pdb=" SG CYS d 598 " - pdb=" SG CYS d 604 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS m 22 " - pdb=" SG CYS m 92 " distance=2.03 Simple disulfide: pdb=" SG CYS n 23 " - pdb=" SG CYS n 88 " distance=2.03 Simple disulfide: pdb=" SG CYS q 22 " - pdb=" SG CYS q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS q 98 " - pdb=" SG CYS q 100A" distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 1 4 " - " MAN 1 5 " " MAN 1 5 " - " MAN 1 6 " " MAN T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " " MAN j 4 " - " MAN j 5 " " MAN j 5 " - " MAN j 6 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA 1 3 " - " MAN 1 4 " " MAN 1 7 " - " MAN 1 8 " " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 8 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA b 3 " - " MAN b 4 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " " MAN j 7 " - " MAN j 8 " " BMA o 3 " - " MAN o 4 " " BMA s 3 " - " MAN s 4 " " BMA w 3 " - " MAN w 4 " " BMAAA 3 " - " MANAA 4 " ALPHA1-6 " BMA 1 3 " - " MAN 1 7 " " MAN 1 7 " - " MAN 1 9 " " BMA J 3 " - " MAN J 5 " " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 9 " " BMA b 3 " - " MAN b 5 " " BMA j 3 " - " MAN j 7 " " MAN j 7 " - " MAN j 9 " " BMA w 3 " - " MAN w 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 9 1 " - " NAG 9 2 " " NAG B 1 " - " NAG B 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 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 O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " 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 z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " NAG-ASN " NAG 0 1 " - " ASN c 386 " " NAG 1 1 " - " ASN c 332 " " NAG 2 611 " - " ASN 2 197 " " NAG 2 623 " - " ASN 2 355 " " NAG 2 631 " - " ASN 2 392 " " NAG B 1 " - " ASN 2 133 " " NAG C 611 " - " ASN C 197 " " NAG C 623 " - " ASN C 355 " " NAG C 631 " - " ASN C 392 " " NAG E 1 " - " ASN 2 137 " " NAG F 1 " - " ASN 2 156 " " NAG G 1 " - " ASN 2 160 " " NAG I 1 " - " ASN 2 234 " " NAG J 1 " - " ASN 2 262 " " NAG K 1 " - " ASN 2 295 " " NAG O 1 " - " ASN 2 301 " " NAG P 1 " - " ASN 2 363 " " NAG S 1 " - " ASN 2 386 " " NAG T 1 " - " ASN 2 332 " " NAG V 1 " - " ASN 2 276 " " NAG W 1 " - " ASN C 133 " " NAG X 1 " - " ASN C 137 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN C 234 " " NAG b 1 " - " ASN C 262 " " NAG c 611 " - " ASN c 197 " " NAG c 623 " - " ASN c 355 " " NAG c 631 " - " ASN c 392 " " NAG e 1 " - " ASN C 295 " " NAG f 1 " - " ASN C 301 " " NAG g 1 " - " ASN C 363 " " NAG i 1 " - " ASN C 386 " " NAG j 1 " - " ASN C 332 " " NAG o 1 " - " ASN C 276 " " NAG p 1 " - " ASN c 133 " " NAG s 1 " - " ASN c 137 " " NAG t 1 " - " ASN c 156 " " NAG u 1 " - " ASN c 160 " " NAG v 1 " - " ASN c 234 " " NAG w 1 " - " ASN c 262 " " NAG x 1 " - " ASN c 295 " " NAG y 1 " - " ASN c 301 " " NAG z 1 " - " ASN c 363 " " NAGAA 1 " - " ASN c 276 " Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.4 seconds 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7068 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 79 sheets defined 14.0% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain '2' and resid 58 through 63 removed outlier: 3.779A pdb=" N THR 2 63 " --> pdb=" O LYS 2 59 " (cutoff:3.500A) Processing helix chain '2' and resid 100 through 115 Processing helix chain '2' and resid 122 through 126 removed outlier: 3.992A pdb=" N CYS 2 126 " --> pdb=" O THR 2 123 " (cutoff:3.500A) Processing helix chain '2' and resid 195 through 198 removed outlier: 3.719A pdb=" N THR 2 198 " --> pdb=" O ASN 2 195 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 195 through 198' Processing helix chain '2' and resid 335 through 350 Processing helix chain '2' and resid 368 through 373 removed outlier: 3.974A pdb=" N THR 2 372 " --> pdb=" O ASP 2 368 " (cutoff:3.500A) Processing helix chain '2' and resid 425 through 429 removed outlier: 4.121A pdb=" N ARG 2 429 " --> pdb=" O MET 2 426 " (cutoff:3.500A) Processing helix chain '2' and resid 475 through 480 removed outlier: 3.617A pdb=" N TRP 2 479 " --> pdb=" O MET 2 475 " (cutoff:3.500A) Processing helix chain '3' and resid 61 through 64 Processing helix chain '3' and resid 83 through 87 Processing helix chain '4' and resid 79 through 83 removed outlier: 3.709A pdb=" N VAL 4 83 " --> pdb=" O PRO 4 80 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 87 removed outlier: 3.708A pdb=" N SER 5 87 " --> pdb=" O ALA 5 84 " (cutoff:3.500A) Processing helix chain '7' and resid 78 through 82 Processing helix chain '8' and resid 61 through 64 removed outlier: 3.578A pdb=" N GLN 8 64 " --> pdb=" O ARG 8 61 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 61 through 64' Processing helix chain '8' and resid 83 through 87 removed outlier: 3.748A pdb=" N THR 8 87 " --> pdb=" O PRO 8 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 543 removed outlier: 4.274A pdb=" N MET A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N THR A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL A 539 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 595 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.579A pdb=" N ILE A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'C' and resid 58 through 63 removed outlier: 3.786A pdb=" N THR C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 115 Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.907A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 removed outlier: 3.628A pdb=" N THR C 198 " --> pdb=" O ASN C 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 195 through 198' Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.912A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.103A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.593A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 543 removed outlier: 4.214A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL D 539 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.570A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.679A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.728A pdb=" N SER M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 64 removed outlier: 3.500A pdb=" N GLN Q 64 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 61 through 64' Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.836A pdb=" N THR Q 87 " --> pdb=" O PRO Q 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 82 removed outlier: 3.507A pdb=" N PHE R 82 " --> pdb=" O ARG R 79 " (cutoff:3.500A) Processing helix chain 'c' and resid 58 through 63 removed outlier: 3.803A pdb=" N THR c 63 " --> pdb=" O LYS c 59 " (cutoff:3.500A) Processing helix chain 'c' and resid 100 through 115 Processing helix chain 'c' and resid 122 through 126 removed outlier: 4.049A pdb=" N CYS c 126 " --> pdb=" O THR c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 195 through 198 removed outlier: 3.660A pdb=" N THR c 198 " --> pdb=" O ASN c 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 195 through 198' Processing helix chain 'c' and resid 335 through 350 Processing helix chain 'c' and resid 368 through 373 removed outlier: 3.865A pdb=" N THR c 372 " --> pdb=" O ASP c 368 " (cutoff:3.500A) Processing helix chain 'c' and resid 425 through 429 removed outlier: 4.151A pdb=" N ARG c 429 " --> pdb=" O MET c 426 " (cutoff:3.500A) Processing helix chain 'c' and resid 475 through 480 removed outlier: 3.617A pdb=" N TRP c 479 " --> pdb=" O MET c 475 " (cutoff:3.500A) Processing helix chain 'd' and resid 529 through 543 removed outlier: 4.287A pdb=" N MET d 535 " --> pdb=" O GLY d 531 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR d 536 " --> pdb=" O ALA d 532 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THR d 538 " --> pdb=" O SER d 534 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL d 539 " --> pdb=" O MET d 535 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN d 540 " --> pdb=" O THR d 536 " (cutoff:3.500A) Processing helix chain 'd' and resid 570 through 595 Processing helix chain 'd' and resid 618 through 625 removed outlier: 3.503A pdb=" N ILE d 622 " --> pdb=" O ASN d 618 " (cutoff:3.500A) Processing helix chain 'd' and resid 627 through 635 removed outlier: 3.600A pdb=" N ILE d 635 " --> pdb=" O TRP d 631 " (cutoff:3.500A) Processing helix chain 'd' and resid 638 through 661 Processing helix chain 'h' and resid 61 through 64 Processing helix chain 'h' and resid 83 through 87 Processing helix chain 'l' and resid 79 through 83 removed outlier: 3.699A pdb=" N VAL l 83 " --> pdb=" O PRO l 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 83 through 87 removed outlier: 3.659A pdb=" N SER m 87 " --> pdb=" O ALA m 84 " (cutoff:3.500A) Processing helix chain 'q' and resid 61 through 64 removed outlier: 3.632A pdb=" N GLN q 64 " --> pdb=" O ARG q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 61 through 64' Processing helix chain 'q' and resid 83 through 87 removed outlier: 3.710A pdb=" N THR q 87 " --> pdb=" O PRO q 84 " (cutoff:3.500A) Processing helix chain 'r' and resid 78 through 82 Processing sheet with id=AA1, first strand: chain '2' and resid 495 through 499 removed outlier: 5.927A pdb=" N VAL A 608 " --> pdb=" O VAL 2 36 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N VAL 2 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR A 606 " --> pdb=" O VAL 2 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 45 through 47 removed outlier: 3.602A pdb=" N ILE 2 225 " --> pdb=" O VAL 2 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain '2' and resid 91 through 94 removed outlier: 3.627A pdb=" N GLU 2 91 " --> pdb=" O CYS 2 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain '2' and resid 202 through 203 removed outlier: 6.669A pdb=" N THR 2 202 " --> pdb=" O TYR 2 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 271 through 273 removed outlier: 7.583A pdb=" N GLN 2 293 " --> pdb=" O SER 2 334 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER 2 334 " --> pdb=" O GLN 2 293 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS 2 421 " --> pdb=" O PHE 2 382 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE 2 382 " --> pdb=" O LYS 2 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 271 through 273 removed outlier: 11.252A pdb=" N VAL 2 286 " --> pdb=" O THR 2 455 " (cutoff:3.500A) removed outlier: 10.788A pdb=" N THR 2 455 " --> pdb=" O VAL 2 286 " (cutoff:3.500A) removed outlier: 12.358A pdb=" N PHE 2 288 " --> pdb=" O ILE 2 453 " (cutoff:3.500A) removed outlier: 11.916A pdb=" N ILE 2 453 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 11.143A pdb=" N THR 2 290 " --> pdb=" O GLY 2 451 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY 2 451 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE 2 358 " --> pdb=" O GLU 2 466 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N PHE 2 468 " --> pdb=" O ILE 2 358 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG 2 360 " --> pdb=" O PHE 2 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '2' and resid 304 through 312 removed outlier: 6.780A pdb=" N GLN 2 315 " --> pdb=" O ILE 2 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 6 through 7 Processing sheet with id=AB2, first strand: chain '3' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain '3' and resid 57 through 59 removed outlier: 6.456A pdb=" N TRP 3 36 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY 3 50 " --> pdb=" O TRP 3 34 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP 3 34 " --> pdb=" O GLY 3 50 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL A 518 " --> pdb=" O ARG 3 95 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LYS 3 97 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '4' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain '4' and resid 10 through 12 removed outlier: 6.962A pdb=" N LEU 4 33 " --> pdb=" O TYR 4 49 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TYR 4 49 " --> pdb=" O LEU 4 33 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TRP 4 35 " --> pdb=" O LEU 4 47 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR 4 49 " --> pdb=" O THR 4 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '5' and resid 5 through 7 removed outlier: 3.833A pdb=" N GLN 5 5 " --> pdb=" O ASN 5 23 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '5' and resid 11 through 12 removed outlier: 3.525A pdb=" N THR 5 105 " --> pdb=" O TYR 5 90 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR 5 90 " --> pdb=" O THR 5 105 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP 5 34 " --> pdb=" O TYR 5 50 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR 5 50 " --> pdb=" O TRP 5 34 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP 5 36 " --> pdb=" O ILE 5 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '5' and resid 95 through 96 Processing sheet with id=AB9, first strand: chain '5' and resid 99 through 100A Processing sheet with id=AC1, first strand: chain '6' and resid 9 through 12 removed outlier: 6.155A pdb=" N VAL 6 11 " --> pdb=" O ILE 6 105 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP 6 35 " --> pdb=" O ILE 6 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '6' and resid 18 through 23 removed outlier: 3.859A pdb=" N ALA 6 71 " --> pdb=" O CYS 6 23 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '7' and resid 4 through 6 Processing sheet with id=AC4, first strand: chain '7' and resid 10 through 13 removed outlier: 6.452A pdb=" N TRP 7 34 " --> pdb=" O LEU 7 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '7' and resid 10 through 13 removed outlier: 3.640A pdb=" N GLN 7 89 " --> pdb=" O PHE 7 92 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '8' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain '8' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain '8' and resid 10 through 11 removed outlier: 3.598A pdb=" N GLY 8 49 " --> pdb=" O TRP 8 36 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG 8 38 " --> pdb=" O TRP 8 47 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N TRP 8 47 " --> pdb=" O ARG 8 38 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE 8 40 " --> pdb=" O PHE 8 45 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N PHE 8 45 " --> pdb=" O ILE 8 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '8' and resid 10 through 11 Processing sheet with id=AD1, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.862A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.617A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AD4, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.651A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AD6, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.664A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.490A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.809A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.547A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.376A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.772A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 518 through 519 removed outlier: 3.936A pdb=" N TYR H 99 " --> pdb=" O VAL D 518 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AE3, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AE4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.949A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR L 49 " --> pdb=" O THR L 53 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 5 through 7 removed outlier: 3.997A pdb=" N GLN M 5 " --> pdb=" O ASN M 23 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.532A pdb=" N THR M 105 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR M 95 " --> pdb=" O TYR M 33 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR M 33 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 99 through 100A Processing sheet with id=AE9, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.123A pdb=" N VAL N 11 " --> pdb=" O ILE N 105 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP N 35 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 19 through 26 removed outlier: 3.925A pdb=" N ALA N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AF3, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'Q' and resid 10 through 11 removed outlier: 3.602A pdb=" N GLY Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE Q 40 " --> pdb=" O PHE Q 45 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N PHE Q 45 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 10 through 11 Processing sheet with id=AF6, first strand: chain 'R' and resid 4 through 6 Processing sheet with id=AF7, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.427A pdb=" N TRP R 34 " --> pdb=" O LEU R 46 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 10 through 13 removed outlier: 3.578A pdb=" N GLN R 89 " --> pdb=" O PHE R 92 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'c' and resid 495 through 499 removed outlier: 5.913A pdb=" N VAL d 608 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N VAL c 38 " --> pdb=" O THR d 606 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR d 606 " --> pdb=" O VAL c 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'c' and resid 45 through 47 removed outlier: 3.607A pdb=" N ILE c 225 " --> pdb=" O VAL c 245 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'c' and resid 53 through 56 Processing sheet with id=AG3, first strand: chain 'c' and resid 91 through 94 removed outlier: 3.675A pdb=" N GLU c 91 " --> pdb=" O CYS c 239 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'c' and resid 169 through 177 Processing sheet with id=AG5, first strand: chain 'c' and resid 202 through 203 removed outlier: 6.697A pdb=" N THR c 202 " --> pdb=" O TYR c 435 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'c' and resid 271 through 273 removed outlier: 7.410A pdb=" N GLN c 293 " --> pdb=" O SER c 334 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER c 334 " --> pdb=" O GLN c 293 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'c' and resid 271 through 273 removed outlier: 11.241A pdb=" N VAL c 286 " --> pdb=" O THR c 455 " (cutoff:3.500A) removed outlier: 10.741A pdb=" N THR c 455 " --> pdb=" O VAL c 286 " (cutoff:3.500A) removed outlier: 12.239A pdb=" N PHE c 288 " --> pdb=" O ILE c 453 " (cutoff:3.500A) removed outlier: 11.783A pdb=" N ILE c 453 " --> pdb=" O PHE c 288 " (cutoff:3.500A) removed outlier: 11.056A pdb=" N THR c 290 " --> pdb=" O GLY c 451 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLY c 451 " --> pdb=" O THR c 290 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE c 358 " --> pdb=" O GLU c 466 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE c 468 " --> pdb=" O ILE c 358 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG c 360 " --> pdb=" O PHE c 468 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'c' and resid 304 through 312 removed outlier: 6.743A pdb=" N GLN c 315 " --> pdb=" O ILE c 309 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'd' and resid 518 through 519 removed outlier: 3.969A pdb=" N TYR h 99 " --> pdb=" O VAL d 518 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TRP h 34 " --> pdb=" O GLY h 50 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY h 50 " --> pdb=" O TRP h 34 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP h 36 " --> pdb=" O ILE h 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'h' and resid 11 through 12 Processing sheet with id=AH2, first strand: chain 'h' and resid 6 through 7 Processing sheet with id=AH3, first strand: chain 'l' and resid 4 through 7 Processing sheet with id=AH4, first strand: chain 'l' and resid 10 through 12 removed outlier: 6.954A pdb=" N LEU l 33 " --> pdb=" O TYR l 49 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR l 49 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TRP l 35 " --> pdb=" O LEU l 47 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'm' and resid 5 through 7 removed outlier: 3.980A pdb=" N GLN m 5 " --> pdb=" O ASN m 23 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.518A pdb=" N THR m 105 " --> pdb=" O TYR m 90 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR m 90 " --> pdb=" O THR m 105 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TRP m 34 " --> pdb=" O TYR m 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR m 50 " --> pdb=" O TRP m 34 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP m 36 " --> pdb=" O ILE m 48 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'm' and resid 99 through 100A Processing sheet with id=AH8, first strand: chain 'n' and resid 9 through 12 removed outlier: 6.198A pdb=" N VAL n 11 " --> pdb=" O ILE n 105 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP n 35 " --> pdb=" O ILE n 47 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'n' and resid 18 through 26 removed outlier: 3.956A pdb=" N ALA n 71 " --> pdb=" O CYS n 23 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'q' and resid 3 through 6 Processing sheet with id=AI2, first strand: chain 'q' and resid 3 through 6 Processing sheet with id=AI3, first strand: chain 'q' and resid 10 through 11 removed outlier: 3.586A pdb=" N GLY q 49 " --> pdb=" O TRP q 36 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ARG q 38 " --> pdb=" O TRP q 47 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N TRP q 47 " --> pdb=" O ARG q 38 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE q 40 " --> pdb=" O PHE q 45 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N PHE q 45 " --> pdb=" O ILE q 40 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'q' and resid 10 through 11 Processing sheet with id=AI5, first strand: chain 'r' and resid 4 through 6 Processing sheet with id=AI6, first strand: chain 'r' and resid 10 through 13 removed outlier: 6.495A pdb=" N TRP r 34 " --> pdb=" O LEU r 46 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'r' and resid 10 through 13 removed outlier: 3.633A pdb=" N GLN r 89 " --> pdb=" O PHE r 92 " (cutoff:3.500A) 1124 hydrogen bonds defined for protein. 2832 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: 7.95 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9967 1.34 - 1.46: 8344 1.46 - 1.58: 14064 1.58 - 1.70: 1 1.70 - 1.82: 222 Bond restraints: 32598 Sorted by residual: bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.32e+00 bond pdb=" C1 MANAA 4 " pdb=" C2 MANAA 4 " ideal model delta sigma weight residual 1.526 1.583 -0.057 2.00e-02 2.50e+03 8.08e+00 bond pdb=" C1 MAN T 5 " pdb=" O5 MAN T 5 " ideal model delta sigma weight residual 1.399 1.456 -0.057 2.00e-02 2.50e+03 8.06e+00 bond pdb=" C1 NAG 0 2 " pdb=" O5 NAG 0 2 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" C1 NAG i 2 " pdb=" O5 NAG i 2 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.92e+00 ... (remaining 32593 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 42386 2.00 - 4.00: 1568 4.00 - 6.01: 229 6.01 - 8.01: 92 8.01 - 10.01: 17 Bond angle restraints: 44292 Sorted by residual: angle pdb=" N PHE 8 100D" pdb=" CA PHE 8 100D" pdb=" C PHE 8 100D" ideal model delta sigma weight residual 109.81 119.66 -9.85 2.21e+00 2.05e-01 1.99e+01 angle pdb=" N PHE Q 100D" pdb=" CA PHE Q 100D" pdb=" C PHE Q 100D" ideal model delta sigma weight residual 109.81 119.48 -9.67 2.21e+00 2.05e-01 1.92e+01 angle pdb=" N PHE q 100D" pdb=" CA PHE q 100D" pdb=" C PHE q 100D" ideal model delta sigma weight residual 109.81 118.81 -9.00 2.21e+00 2.05e-01 1.66e+01 angle pdb=" C ILE 4 29 " pdb=" N ASP 4 30 " pdb=" CA ASP 4 30 " ideal model delta sigma weight residual 121.54 129.10 -7.56 1.91e+00 2.74e-01 1.57e+01 angle pdb=" C ILE l 29 " pdb=" N ASP l 30 " pdb=" CA ASP l 30 " ideal model delta sigma weight residual 121.54 128.95 -7.41 1.91e+00 2.74e-01 1.51e+01 ... (remaining 44287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.91: 19597 21.91 - 43.82: 1033 43.82 - 65.74: 256 65.74 - 87.65: 115 87.65 - 109.56: 65 Dihedral angle restraints: 21066 sinusoidal: 10041 harmonic: 11025 Sorted by residual: dihedral pdb=" CA GLN 7 89 " pdb=" C GLN 7 89 " pdb=" N PHE 7 90 " pdb=" CA PHE 7 90 " ideal model delta harmonic sigma weight residual -180.00 -133.96 -46.04 0 5.00e+00 4.00e-02 8.48e+01 dihedral pdb=" CA GLN r 89 " pdb=" C GLN r 89 " pdb=" N PHE r 90 " pdb=" CA PHE r 90 " ideal model delta harmonic sigma weight residual -180.00 -134.52 -45.48 0 5.00e+00 4.00e-02 8.27e+01 dihedral pdb=" CA GLN R 89 " pdb=" C GLN R 89 " pdb=" N PHE R 90 " pdb=" CA PHE R 90 " ideal model delta harmonic sigma weight residual -180.00 -135.68 -44.32 0 5.00e+00 4.00e-02 7.86e+01 ... (remaining 21063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 4368 0.071 - 0.143: 864 0.143 - 0.214: 52 0.214 - 0.286: 20 0.286 - 0.357: 18 Chirality restraints: 5322 Sorted by residual: chirality pdb=" C1 NAG v 1 " pdb=" ND2 ASN c 234 " pdb=" C2 NAG v 1 " pdb=" O5 NAG v 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.60 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C5 BMA w 3 " pdb=" C4 BMA w 3 " pdb=" C6 BMA w 3 " pdb=" O5 BMA w 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.60 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 5319 not shown) Planarity restraints: 5499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE Q 100D" -0.048 5.00e-02 4.00e+02 7.27e-02 8.47e+00 pdb=" N PRO Q 100E" 0.126 5.00e-02 4.00e+02 pdb=" CA PRO Q 100E" -0.037 5.00e-02 4.00e+02 pdb=" CD PRO Q 100E" -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE q 100D" 0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO q 100E" -0.125 5.00e-02 4.00e+02 pdb=" CA PRO q 100E" 0.036 5.00e-02 4.00e+02 pdb=" CD PRO q 100E" 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE 8 100D" 0.046 5.00e-02 4.00e+02 6.91e-02 7.65e+00 pdb=" N PRO 8 100E" -0.120 5.00e-02 4.00e+02 pdb=" CA PRO 8 100E" 0.035 5.00e-02 4.00e+02 pdb=" CD PRO 8 100E" 0.039 5.00e-02 4.00e+02 ... (remaining 5496 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 10252 2.83 - 3.35: 26578 3.35 - 3.87: 53550 3.87 - 4.38: 58404 4.38 - 4.90: 100651 Nonbonded interactions: 249435 Sorted by model distance: nonbonded pdb=" O ASP 7 81 " pdb=" OH TYR 7 85 " model vdw 2.314 3.040 nonbonded pdb=" N ASN c 195 " pdb=" OD1 ASN c 195 " model vdw 2.317 3.120 nonbonded pdb=" OE1 GLN 7 6 " pdb=" OG SER 7 97 " model vdw 2.323 3.040 nonbonded pdb=" N ASP 8 76E" pdb=" OD1 ASP 8 76E" model vdw 2.325 3.120 nonbonded pdb=" OG SER m 7 " pdb=" OG1 THR m 21 " model vdw 2.333 3.040 ... (remaining 249430 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: 0.05 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'AA' selection = chain 'E' selection = chain 'S' selection = chain 'V' selection = chain 'X' selection = chain 'i' selection = chain 'o' selection = chain 's' } ncs_group { reference = chain '1' selection = chain 'T' selection = chain 'j' } ncs_group { reference = chain '2' selection = chain 'C' selection = chain 'c' } ncs_group { reference = chain '3' selection = chain 'H' selection = chain 'h' } ncs_group { reference = chain '4' selection = chain 'L' selection = chain 'l' } ncs_group { reference = chain '5' selection = chain 'M' selection = chain 'm' } ncs_group { reference = chain '6' selection = chain 'N' selection = chain 'n' } ncs_group { reference = chain '7' selection = chain 'R' selection = chain 'r' } ncs_group { reference = chain '8' selection = chain 'Q' selection = chain 'q' } ncs_group { reference = chain '9' selection = chain 'B' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'O' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'k' selection = chain 'p' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'J' selection = chain 'b' selection = chain 'w' } ncs_group { reference = chain 'P' selection = chain 'g' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 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: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 32.400 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.180 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 : 0.006 0.076 32778 Z= 0.300 Angle : 0.977 12.546 44787 Z= 0.484 Chirality : 0.058 0.357 5322 Planarity : 0.006 0.073 5454 Dihedral : 16.198 109.561 13863 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 7.06 % Allowed : 6.94 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.12), residues: 3786 helix: -1.82 (0.21), residues: 387 sheet: -1.65 (0.13), residues: 1317 loop : -2.34 (0.12), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG q 94 TYR 0.018 0.002 TYR 3 99 PHE 0.025 0.002 PHE 2 288 TRP 0.018 0.002 TRP D 571 HIS 0.011 0.002 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00617 (32598) covalent geometry : angle 0.92752 (44292) SS BOND : bond 0.00292 ( 45) SS BOND : angle 0.91375 ( 90) hydrogen bonds : bond 0.14912 ( 1043) hydrogen bonds : angle 7.26409 ( 2832) link_ALPHA1-2 : bond 0.00880 ( 6) link_ALPHA1-2 : angle 2.34970 ( 18) link_ALPHA1-3 : bond 0.00550 ( 18) link_ALPHA1-3 : angle 2.22686 ( 54) link_ALPHA1-6 : bond 0.00336 ( 9) link_ALPHA1-6 : angle 1.92008 ( 27) link_BETA1-4 : bond 0.00653 ( 57) link_BETA1-4 : angle 3.81074 ( 171) link_NAG-ASN : bond 0.00900 ( 45) link_NAG-ASN : angle 3.47795 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 898 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 83 GLU cc_start: 0.8793 (pt0) cc_final: 0.8560 (pm20) REVERT: 2 100 MET cc_start: 0.9182 (ptt) cc_final: 0.8916 (ptt) REVERT: 2 138 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8304 (mt) REVERT: 2 207 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8876 (tppt) REVERT: 2 260 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8031 (pp) REVERT: 2 321 ASP cc_start: 0.8596 (t0) cc_final: 0.8333 (t0) REVERT: 2 425 ASN cc_start: 0.8629 (t0) cc_final: 0.8117 (t0) REVERT: 2 443 ILE cc_start: 0.8809 (mm) cc_final: 0.8331 (tt) REVERT: 2 479 TRP cc_start: 0.9279 (m100) cc_final: 0.9009 (m100) REVERT: 2 492 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8450 (mp0) REVERT: 3 23 GLU cc_start: 0.9133 (tp30) cc_final: 0.8894 (tp30) REVERT: 3 53 ASN cc_start: 0.8554 (m-40) cc_final: 0.8240 (p0) REVERT: 3 55 GLU cc_start: 0.6060 (mm-30) cc_final: 0.5625 (mm-30) REVERT: 3 68 ILE cc_start: 0.8598 (mm) cc_final: 0.8361 (mm) REVERT: 3 95 ARG cc_start: 0.4762 (OUTLIER) cc_final: 0.4420 (ttp-170) REVERT: 6 78 VAL cc_start: 0.9085 (m) cc_final: 0.8760 (p) REVERT: 6 85 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8537 (t0) REVERT: 6 105 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6914 (tt) REVERT: 6 106 VAL cc_start: 0.7400 (OUTLIER) cc_final: 0.6666 (t) REVERT: 7 1 GLU cc_start: 0.7928 (pt0) cc_final: 0.7341 (pm20) REVERT: 7 33 THR cc_start: 0.9215 (m) cc_final: 0.8912 (m) REVERT: 7 48 TYR cc_start: 0.8717 (p90) cc_final: 0.8300 (p90) REVERT: 7 77 LEU cc_start: 0.9303 (mt) cc_final: 0.9066 (tp) REVERT: 7 78 ASP cc_start: 0.9284 (t70) cc_final: 0.9013 (t70) REVERT: 8 30 ARG cc_start: 0.9090 (mtt90) cc_final: 0.8741 (mtt90) REVERT: 8 47 TRP cc_start: 0.8940 (t60) cc_final: 0.8297 (t60) REVERT: 8 48 ILE cc_start: 0.8464 (mt) cc_final: 0.7127 (mp) REVERT: 8 72 GLN cc_start: 0.9521 (tt0) cc_final: 0.9010 (tm-30) REVERT: 8 89 GLU cc_start: 0.7624 (tt0) cc_final: 0.7351 (tt0) REVERT: 8 100 TYR cc_start: 0.8448 (m-80) cc_final: 0.8092 (m-10) REVERT: A 539 VAL cc_start: 0.9490 (OUTLIER) cc_final: 0.9268 (t) REVERT: A 588 ARG cc_start: 0.9100 (mtt180) cc_final: 0.8538 (ttm110) REVERT: A 589 ASP cc_start: 0.8728 (m-30) cc_final: 0.8500 (m-30) REVERT: A 592 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8766 (tt) REVERT: C 45 TRP cc_start: 0.8799 (p90) cc_final: 0.8596 (p90) REVERT: C 83 GLU cc_start: 0.8882 (pt0) cc_final: 0.8514 (pm20) REVERT: C 100 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8555 (ptt) REVERT: C 138 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8494 (tt) REVERT: C 207 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8847 (tptp) REVERT: C 279 ASN cc_start: 0.9273 (t0) cc_final: 0.8932 (t0) REVERT: C 492 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8634 (mp0) REVERT: D 592 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8665 (tp) REVERT: D 601 LYS cc_start: 0.8081 (mtpp) cc_final: 0.7801 (mtpt) REVERT: D 622 ILE cc_start: 0.9621 (pt) cc_final: 0.9384 (pt) REVERT: D 638 TYR cc_start: 0.8996 (OUTLIER) cc_final: 0.8506 (m-80) REVERT: H 23 GLU cc_start: 0.9142 (tp30) cc_final: 0.8935 (tp30) REVERT: H 53 ASN cc_start: 0.8562 (m-40) cc_final: 0.8200 (p0) REVERT: M 90 TYR cc_start: 0.8660 (m-10) cc_final: 0.8005 (m-10) REVERT: M 100 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7883 (mt-10) REVERT: M 105 THR cc_start: 0.7356 (m) cc_final: 0.7134 (p) REVERT: N 85 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8403 (t0) REVERT: N 106 VAL cc_start: 0.7466 (OUTLIER) cc_final: 0.6679 (p) REVERT: Q 5 VAL cc_start: 0.9241 (t) cc_final: 0.8855 (p) REVERT: Q 30 ARG cc_start: 0.9134 (mtt90) cc_final: 0.8788 (mtt90) REVERT: Q 72 GLN cc_start: 0.9397 (tt0) cc_final: 0.9004 (tm-30) REVERT: Q 73 LEU cc_start: 0.8308 (mt) cc_final: 0.7733 (mt) REVERT: Q 89 GLU cc_start: 0.7607 (tt0) cc_final: 0.7291 (tt0) REVERT: Q 108 VAL cc_start: 0.9623 (t) cc_final: 0.9360 (p) REVERT: R 33 THR cc_start: 0.9147 (m) cc_final: 0.8751 (m) REVERT: R 35 TYR cc_start: 0.8706 (m-10) cc_final: 0.8442 (m-80) REVERT: R 46 LEU cc_start: 0.9417 (mt) cc_final: 0.9074 (mt) REVERT: R 77 LEU cc_start: 0.9052 (mt) cc_final: 0.8720 (tp) REVERT: c 100 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8061 (ppp) REVERT: c 256 SER cc_start: 0.9264 (p) cc_final: 0.8966 (t) REVERT: c 321 ASP cc_start: 0.8716 (t0) cc_final: 0.8343 (t0) REVERT: c 334 SER cc_start: 0.8655 (OUTLIER) cc_final: 0.8126 (p) REVERT: c 425 ASN cc_start: 0.8732 (t0) cc_final: 0.8102 (t0) REVERT: c 475 MET cc_start: 0.8856 (mmm) cc_final: 0.8534 (mmm) REVERT: c 479 TRP cc_start: 0.9172 (m100) cc_final: 0.8799 (m100) REVERT: c 491 ILE cc_start: 0.9341 (mm) cc_final: 0.8893 (mp) REVERT: c 492 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8511 (mm-30) REVERT: d 539 VAL cc_start: 0.9517 (OUTLIER) cc_final: 0.9158 (t) REVERT: d 579 ARG cc_start: 0.8787 (ttp-170) cc_final: 0.8548 (ttp-170) REVERT: d 581 LEU cc_start: 0.9565 (tp) cc_final: 0.9364 (tt) REVERT: d 588 ARG cc_start: 0.9047 (mtt180) cc_final: 0.8755 (ttm-80) REVERT: d 592 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8766 (tt) REVERT: d 593 LEU cc_start: 0.9213 (tp) cc_final: 0.9008 (tp) REVERT: d 596 TRP cc_start: 0.8843 (m-10) cc_final: 0.8120 (m-10) REVERT: d 619 LEU cc_start: 0.9286 (tp) cc_final: 0.9083 (mm) REVERT: d 638 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8641 (m-80) REVERT: h 55 GLU cc_start: 0.5439 (mm-30) cc_final: 0.4997 (mm-30) REVERT: h 95 ARG cc_start: 0.4065 (OUTLIER) cc_final: 0.3816 (ttp-170) REVERT: m 90 TYR cc_start: 0.8555 (m-10) cc_final: 0.8043 (m-10) REVERT: m 100 LYS cc_start: 0.9085 (mptt) cc_final: 0.8795 (tmtt) REVERT: n 13 VAL cc_start: 0.8772 (OUTLIER) cc_final: 0.8541 (t) REVERT: n 78 VAL cc_start: 0.8752 (m) cc_final: 0.8432 (p) REVERT: n 85 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8050 (t0) REVERT: q 18 VAL cc_start: 0.9449 (OUTLIER) cc_final: 0.9129 (m) REVERT: q 28 ASN cc_start: 0.8589 (t0) cc_final: 0.8366 (t0) REVERT: q 42 ASP cc_start: 0.8456 (m-30) cc_final: 0.8135 (p0) REVERT: q 69 MET cc_start: 0.9302 (mtt) cc_final: 0.9080 (mtm) REVERT: q 72 GLN cc_start: 0.9430 (tt0) cc_final: 0.9137 (tm-30) REVERT: q 73 LEU cc_start: 0.8520 (mt) cc_final: 0.8157 (mt) REVERT: q 82 PHE cc_start: 0.8480 (t80) cc_final: 0.8146 (t80) REVERT: r 27 GLN cc_start: 0.8774 (mt0) cc_final: 0.8530 (mp10) REVERT: r 45 LEU cc_start: 0.9285 (tt) cc_final: 0.9003 (tt) REVERT: r 57 VAL cc_start: 0.8888 (t) cc_final: 0.8430 (t) REVERT: r 77 LEU cc_start: 0.9216 (mt) cc_final: 0.8935 (tp) outliers start: 236 outliers final: 65 residues processed: 1064 average time/residue: 0.2365 time to fit residues: 383.0610 Evaluate side-chains 561 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 471 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 298 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: 2 72 HIS ** 2 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 315 GLN ** 2 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 377 ASN 2 448 ASN 4 89 GLN ** 4 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 23 ASN 5 97 HIS 7 27 GLN 8 6 GLN 8 101 GLN A 611 ASN A 658 GLN C 72 HIS C 80 ASN C 293 GLN C 315 GLN ** C 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN D 577 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN L 89 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN Q 35 HIS Q 101 GLN R 27 GLN c 72 HIS c 80 ASN c 315 GLN ** c 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 377 ASN ** d 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 611 ASN d 658 GLN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 89 GLN l 90 GLN m 23 ASN q 6 GLN q 101 GLN r 30 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.092790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.066552 restraints weight = 121246.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.069018 restraints weight = 62061.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.070623 restraints weight = 39994.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.071659 restraints weight = 29787.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.072285 restraints weight = 24546.741| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 32778 Z= 0.186 Angle : 0.774 12.879 44787 Z= 0.377 Chirality : 0.049 0.285 5322 Planarity : 0.007 0.155 5454 Dihedral : 12.312 80.197 6945 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.27 % Allowed : 3.14 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -2.07 (0.13), residues: 3786 helix: -0.10 (0.25), residues: 393 sheet: -1.08 (0.13), residues: 1272 loop : -1.83 (0.12), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG 2 178 TYR 0.022 0.002 TYR Q 102 PHE 0.026 0.002 PHE Q 100D TRP 0.018 0.002 TRP Q 100F HIS 0.007 0.001 HIS c 374 Details of bonding type rmsd covalent geometry : bond 0.00410 (32598) covalent geometry : angle 0.73420 (44292) SS BOND : bond 0.00453 ( 45) SS BOND : angle 1.89873 ( 90) hydrogen bonds : bond 0.03992 ( 1043) hydrogen bonds : angle 6.09400 ( 2832) link_ALPHA1-2 : bond 0.01023 ( 6) link_ALPHA1-2 : angle 2.26083 ( 18) link_ALPHA1-3 : bond 0.00772 ( 18) link_ALPHA1-3 : angle 2.24418 ( 54) link_ALPHA1-6 : bond 0.00362 ( 9) link_ALPHA1-6 : angle 1.71108 ( 27) link_BETA1-4 : bond 0.00446 ( 57) link_BETA1-4 : angle 2.86357 ( 171) link_NAG-ASN : bond 0.00517 ( 45) link_NAG-ASN : angle 2.46387 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 627 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 83 GLU cc_start: 0.8781 (pt0) cc_final: 0.8295 (pm20) REVERT: 2 95 MET cc_start: 0.8633 (pmm) cc_final: 0.8250 (pmm) REVERT: 2 100 MET cc_start: 0.9162 (ptt) cc_final: 0.8855 (ptp) REVERT: 2 190 GLU cc_start: 0.8510 (pt0) cc_final: 0.8240 (pm20) REVERT: 2 321 ASP cc_start: 0.8123 (t0) cc_final: 0.7889 (t0) REVERT: 2 425 ASN cc_start: 0.8704 (t0) cc_final: 0.8305 (t0) REVERT: 2 492 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8540 (mm-30) REVERT: 3 23 GLU cc_start: 0.9123 (tp30) cc_final: 0.8866 (tp30) REVERT: 3 51 MET cc_start: 0.3145 (ttp) cc_final: 0.2073 (ttm) REVERT: 3 53 ASN cc_start: 0.8527 (m-40) cc_final: 0.8208 (p0) REVERT: 3 55 GLU cc_start: 0.6199 (mm-30) cc_final: 0.5573 (mm-30) REVERT: 3 71 LYS cc_start: 0.5867 (pttp) cc_final: 0.5637 (ptmm) REVERT: 3 81 ARG cc_start: 0.8752 (ttp-110) cc_final: 0.7996 (mtt90) REVERT: 4 4 MET cc_start: 0.2308 (mmt) cc_final: 0.1327 (mtp) REVERT: 7 33 THR cc_start: 0.9171 (m) cc_final: 0.8844 (p) REVERT: 7 48 TYR cc_start: 0.8699 (p90) cc_final: 0.8413 (p90) REVERT: 7 70 PHE cc_start: 0.8451 (m-10) cc_final: 0.8235 (m-10) REVERT: 7 77 LEU cc_start: 0.9327 (mt) cc_final: 0.9111 (tp) REVERT: 7 81 ASP cc_start: 0.9450 (m-30) cc_final: 0.8934 (m-30) REVERT: 8 27 TYR cc_start: 0.8422 (p90) cc_final: 0.8127 (p90) REVERT: 8 47 TRP cc_start: 0.8968 (t60) cc_final: 0.8318 (t60) REVERT: 8 48 ILE cc_start: 0.8437 (mt) cc_final: 0.7462 (mp) REVERT: 8 52 LYS cc_start: 0.9285 (mtmm) cc_final: 0.8558 (mtmm) REVERT: 8 72 GLN cc_start: 0.9379 (tt0) cc_final: 0.9089 (tp40) REVERT: 8 80 MET cc_start: 0.8359 (tmm) cc_final: 0.7942 (tmm) REVERT: 8 100 TYR cc_start: 0.8469 (m-80) cc_final: 0.8121 (m-10) REVERT: A 588 ARG cc_start: 0.9096 (mtt180) cc_final: 0.8633 (ttm110) REVERT: A 589 ASP cc_start: 0.8720 (m-30) cc_final: 0.8449 (m-30) REVERT: A 591 GLN cc_start: 0.9408 (tm-30) cc_final: 0.8916 (tm-30) REVERT: A 632 ASP cc_start: 0.8894 (t0) cc_final: 0.8630 (t70) REVERT: C 45 TRP cc_start: 0.9025 (p90) cc_final: 0.8459 (p90) REVERT: C 83 GLU cc_start: 0.8900 (pt0) cc_final: 0.8368 (pm20) REVERT: C 95 MET cc_start: 0.8784 (pmm) cc_final: 0.8364 (pmm) REVERT: C 492 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8489 (mp0) REVERT: D 601 LYS cc_start: 0.8050 (mtpp) cc_final: 0.7738 (mtpt) REVERT: D 647 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8324 (mt-10) REVERT: H 23 GLU cc_start: 0.9104 (tp30) cc_final: 0.8881 (tp30) REVERT: H 51 MET cc_start: 0.2750 (ttm) cc_final: 0.2071 (ttm) REVERT: H 53 ASN cc_start: 0.8444 (m-40) cc_final: 0.8081 (p0) REVERT: H 55 GLU cc_start: 0.5681 (mm-30) cc_final: 0.5428 (mm-30) REVERT: H 86 ASP cc_start: 0.3426 (m-30) cc_final: 0.3001 (m-30) REVERT: L 4 MET cc_start: 0.1924 (mmt) cc_final: 0.0583 (mtp) REVERT: L 92 PHE cc_start: 0.8057 (t80) cc_final: 0.7818 (t80) REVERT: M 100 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7696 (mt-10) REVERT: M 105 THR cc_start: 0.8001 (m) cc_final: 0.7655 (p) REVERT: Q 52 LYS cc_start: 0.9308 (mtmm) cc_final: 0.8671 (mtmm) REVERT: Q 80 MET cc_start: 0.8566 (tmm) cc_final: 0.8252 (tmm) REVERT: R 32 MET cc_start: 0.9124 (tpt) cc_final: 0.8893 (tpt) REVERT: R 45 LEU cc_start: 0.9075 (mt) cc_final: 0.8803 (mt) REVERT: R 53 ARG cc_start: 0.8462 (mtm-85) cc_final: 0.8088 (ttm110) REVERT: c 83 GLU cc_start: 0.8754 (pt0) cc_final: 0.8463 (pm20) REVERT: c 100 MET cc_start: 0.8952 (ptt) cc_final: 0.8575 (ptp) REVERT: c 321 ASP cc_start: 0.8330 (t0) cc_final: 0.7812 (t0) REVERT: c 425 ASN cc_start: 0.8731 (t0) cc_final: 0.8182 (t0) REVERT: c 491 ILE cc_start: 0.9331 (mm) cc_final: 0.8950 (mp) REVERT: c 492 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8339 (mp0) REVERT: d 542 ARG cc_start: 0.8826 (ttp-110) cc_final: 0.8492 (ptm160) REVERT: d 586 TYR cc_start: 0.9439 (t80) cc_final: 0.9200 (t80) REVERT: d 588 ARG cc_start: 0.9096 (mtt180) cc_final: 0.8813 (ttm-80) REVERT: d 589 ASP cc_start: 0.8816 (m-30) cc_final: 0.8574 (m-30) REVERT: d 591 GLN cc_start: 0.9327 (tm-30) cc_final: 0.9020 (tm-30) REVERT: d 655 LYS cc_start: 0.9586 (mmmm) cc_final: 0.9014 (pttp) REVERT: h 51 MET cc_start: 0.4058 (ttp) cc_final: 0.2782 (ttm) REVERT: h 55 GLU cc_start: 0.5454 (mm-30) cc_final: 0.4988 (mm-30) REVERT: h 97 LYS cc_start: 0.9070 (mtmt) cc_final: 0.8865 (mtpp) REVERT: l 4 MET cc_start: 0.2798 (mmt) cc_final: 0.1922 (mtp) REVERT: l 32 ASP cc_start: 0.5474 (p0) cc_final: 0.4547 (p0) REVERT: l 62 PHE cc_start: 0.2268 (m-80) cc_final: 0.2066 (m-80) REVERT: l 82 ASP cc_start: 0.5236 (p0) cc_final: 0.2944 (p0) REVERT: l 90 GLN cc_start: 0.5903 (OUTLIER) cc_final: 0.5555 (pp30) REVERT: m 90 TYR cc_start: 0.8414 (m-10) cc_final: 0.8140 (m-10) REVERT: m 100 LYS cc_start: 0.9083 (mptt) cc_final: 0.8782 (tmtt) REVERT: n 85 ASP cc_start: 0.8564 (m-30) cc_final: 0.8211 (t0) REVERT: q 28 ASN cc_start: 0.8848 (t0) cc_final: 0.8418 (t0) REVERT: q 52 LYS cc_start: 0.9258 (mtmm) cc_final: 0.8435 (mtmm) REVERT: q 69 MET cc_start: 0.9199 (mtt) cc_final: 0.8978 (mtm) REVERT: q 80 MET cc_start: 0.8085 (tmm) cc_final: 0.7810 (tmm) REVERT: q 105 GLN cc_start: 0.9029 (pp30) cc_final: 0.8768 (pp30) REVERT: r 33 THR cc_start: 0.9066 (m) cc_final: 0.8812 (p) REVERT: r 59 ASP cc_start: 0.8920 (t0) cc_final: 0.8614 (t0) REVERT: r 77 LEU cc_start: 0.9306 (mt) cc_final: 0.8998 (tp) outliers start: 9 outliers final: 2 residues processed: 635 average time/residue: 0.2293 time to fit residues: 225.0927 Evaluate side-chains 436 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 433 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 159 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 337 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 192 optimal weight: 20.0000 chunk 298 optimal weight: 10.0000 chunk 96 optimal weight: 0.0270 chunk 274 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 98 ASN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 103 GLN 2 293 GLN 2 352 HIS 4 90 GLN 6 42 GLN C 80 ASN C 85 HIS C 352 HIS ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN M 1 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 80 ASN ** c 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 575 GLN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 97 HIS q 6 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.092152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.065446 restraints weight = 122609.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.067828 restraints weight = 64561.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.069452 restraints weight = 42354.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.070472 restraints weight = 31864.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.071134 restraints weight = 26380.526| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 32778 Z= 0.163 Angle : 0.718 13.133 44787 Z= 0.350 Chirality : 0.047 0.243 5322 Planarity : 0.006 0.141 5454 Dihedral : 10.858 79.958 6945 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.12 % Allowed : 3.05 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: -1.71 (0.13), residues: 3786 helix: 0.58 (0.27), residues: 384 sheet: -1.03 (0.13), residues: 1290 loop : -1.52 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG l 61 TYR 0.017 0.001 TYR 6 87 PHE 0.018 0.002 PHE Q 91 TRP 0.023 0.001 TRP Q 100F HIS 0.004 0.001 HIS 2 374 Details of bonding type rmsd covalent geometry : bond 0.00359 (32598) covalent geometry : angle 0.68123 (44292) SS BOND : bond 0.00290 ( 45) SS BOND : angle 1.80763 ( 90) hydrogen bonds : bond 0.03773 ( 1043) hydrogen bonds : angle 5.75926 ( 2832) link_ALPHA1-2 : bond 0.00782 ( 6) link_ALPHA1-2 : angle 1.90938 ( 18) link_ALPHA1-3 : bond 0.00923 ( 18) link_ALPHA1-3 : angle 1.68611 ( 54) link_ALPHA1-6 : bond 0.00367 ( 9) link_ALPHA1-6 : angle 1.63352 ( 27) link_BETA1-4 : bond 0.00422 ( 57) link_BETA1-4 : angle 2.74380 ( 171) link_NAG-ASN : bond 0.00442 ( 45) link_NAG-ASN : angle 2.25239 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 575 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 45 TRP cc_start: 0.8994 (p90) cc_final: 0.8585 (p90) REVERT: 2 52 LEU cc_start: 0.9414 (mt) cc_final: 0.9168 (mm) REVERT: 2 83 GLU cc_start: 0.8812 (pt0) cc_final: 0.8188 (pm20) REVERT: 2 95 MET cc_start: 0.8869 (pmm) cc_final: 0.8397 (pmm) REVERT: 2 97 LYS cc_start: 0.9312 (mttt) cc_final: 0.8991 (mttt) REVERT: 2 100 MET cc_start: 0.9337 (ptt) cc_final: 0.8999 (ptp) REVERT: 2 119 CYS cc_start: 0.6653 (m) cc_final: 0.6305 (m) REVERT: 2 190 GLU cc_start: 0.8510 (pt0) cc_final: 0.8255 (pm20) REVERT: 2 321 ASP cc_start: 0.7942 (t0) cc_final: 0.7728 (t0) REVERT: 2 425 ASN cc_start: 0.8797 (t0) cc_final: 0.8252 (t0) REVERT: 2 492 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8523 (mm-30) REVERT: 3 23 GLU cc_start: 0.9212 (tp30) cc_final: 0.8966 (tp30) REVERT: 3 51 MET cc_start: 0.2929 (ttp) cc_final: 0.1864 (ttm) REVERT: 3 53 ASN cc_start: 0.8520 (m-40) cc_final: 0.8195 (p0) REVERT: 3 55 GLU cc_start: 0.6223 (mm-30) cc_final: 0.5590 (mm-30) REVERT: 3 71 LYS cc_start: 0.5877 (pttp) cc_final: 0.5514 (ptmm) REVERT: 4 4 MET cc_start: 0.3041 (mmt) cc_final: 0.1943 (mtp) REVERT: 5 100 LYS cc_start: 0.9463 (mmmm) cc_final: 0.8448 (tmtt) REVERT: 7 1 GLU cc_start: 0.8247 (pm20) cc_final: 0.8018 (pm20) REVERT: 7 48 TYR cc_start: 0.8752 (p90) cc_final: 0.8535 (p90) REVERT: 7 77 LEU cc_start: 0.9296 (mt) cc_final: 0.9073 (tp) REVERT: 7 78 ASP cc_start: 0.9254 (t70) cc_final: 0.8866 (t70) REVERT: 8 27 TYR cc_start: 0.8680 (p90) cc_final: 0.8406 (p90) REVERT: 8 47 TRP cc_start: 0.8950 (t60) cc_final: 0.8350 (t60) REVERT: 8 48 ILE cc_start: 0.8356 (mt) cc_final: 0.7267 (mp) REVERT: 8 52 LYS cc_start: 0.9294 (mtmm) cc_final: 0.8548 (mtmm) REVERT: 8 72 GLN cc_start: 0.9382 (tt0) cc_final: 0.9128 (tp40) REVERT: 8 76 ASP cc_start: 0.8060 (p0) cc_final: 0.7418 (p0) REVERT: 8 100 TYR cc_start: 0.8398 (m-80) cc_final: 0.8098 (m-10) REVERT: A 588 ARG cc_start: 0.9119 (mtt180) cc_final: 0.8619 (ttm110) REVERT: A 591 GLN cc_start: 0.9411 (tm-30) cc_final: 0.8925 (tm-30) REVERT: A 632 ASP cc_start: 0.8882 (t0) cc_final: 0.8661 (t70) REVERT: C 45 TRP cc_start: 0.9019 (p90) cc_final: 0.8344 (p90) REVERT: C 83 GLU cc_start: 0.8924 (pt0) cc_final: 0.8412 (pm20) REVERT: C 95 MET cc_start: 0.8945 (pmm) cc_final: 0.8653 (pmm) REVERT: C 161 MET cc_start: 0.9204 (tpp) cc_final: 0.8431 (tpp) REVERT: C 492 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8429 (mp0) REVERT: H 51 MET cc_start: 0.2999 (ttm) cc_final: 0.2732 (ttm) REVERT: H 53 ASN cc_start: 0.8417 (m-40) cc_final: 0.8071 (p0) REVERT: L 4 MET cc_start: 0.2565 (mmt) cc_final: 0.2298 (mtp) REVERT: L 32 ASP cc_start: 0.6799 (m-30) cc_final: 0.6550 (m-30) REVERT: L 90 GLN cc_start: 0.6495 (OUTLIER) cc_final: 0.4930 (pp30) REVERT: M 105 THR cc_start: 0.7996 (m) cc_final: 0.7656 (p) REVERT: Q 19 LYS cc_start: 0.8681 (tptm) cc_final: 0.8246 (tptm) REVERT: Q 52 LYS cc_start: 0.9299 (mtmm) cc_final: 0.8667 (mtmm) REVERT: Q 80 MET cc_start: 0.8457 (tmm) cc_final: 0.8130 (tmm) REVERT: R 45 LEU cc_start: 0.9035 (mt) cc_final: 0.8716 (mt) REVERT: R 53 ARG cc_start: 0.8631 (mtm-85) cc_final: 0.8067 (ttm110) REVERT: c 83 GLU cc_start: 0.8767 (pt0) cc_final: 0.8459 (pm20) REVERT: c 100 MET cc_start: 0.9110 (ptt) cc_final: 0.8856 (ptp) REVERT: c 104 MET cc_start: 0.9165 (tmm) cc_final: 0.8740 (tmm) REVERT: c 123 THR cc_start: 0.9091 (p) cc_final: 0.8767 (t) REVERT: c 425 ASN cc_start: 0.8757 (t0) cc_final: 0.8293 (t0) REVERT: c 491 ILE cc_start: 0.9358 (mm) cc_final: 0.9079 (mp) REVERT: c 492 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8462 (mm-30) REVERT: d 588 ARG cc_start: 0.9071 (mtt180) cc_final: 0.8801 (ttm-80) REVERT: d 589 ASP cc_start: 0.8853 (m-30) cc_final: 0.8575 (m-30) REVERT: d 591 GLN cc_start: 0.9333 (tm-30) cc_final: 0.9057 (tm-30) REVERT: d 633 LYS cc_start: 0.9282 (mmmm) cc_final: 0.9048 (mmmm) REVERT: d 655 LYS cc_start: 0.9428 (mmmm) cc_final: 0.9061 (pttp) REVERT: h 51 MET cc_start: 0.3059 (ttp) cc_final: 0.2517 (ttm) REVERT: h 55 GLU cc_start: 0.5132 (mm-30) cc_final: 0.4885 (mm-30) REVERT: m 100 LYS cc_start: 0.9103 (mptt) cc_final: 0.8778 (tmtt) REVERT: n 85 ASP cc_start: 0.8628 (m-30) cc_final: 0.8232 (t0) REVERT: q 28 ASN cc_start: 0.8879 (t0) cc_final: 0.8430 (t0) REVERT: q 52 LYS cc_start: 0.9241 (mtmm) cc_final: 0.8505 (mtmm) REVERT: q 69 MET cc_start: 0.9104 (mtt) cc_final: 0.8819 (mtm) REVERT: q 72 GLN cc_start: 0.9189 (tt0) cc_final: 0.8655 (tm-30) REVERT: q 73 LEU cc_start: 0.8980 (mt) cc_final: 0.8325 (mt) REVERT: q 80 MET cc_start: 0.8090 (tmm) cc_final: 0.7793 (tmm) REVERT: q 100 TYR cc_start: 0.8252 (m-80) cc_final: 0.7773 (m-10) REVERT: q 105 GLN cc_start: 0.9020 (pp30) cc_final: 0.8683 (pp30) REVERT: r 32 MET cc_start: 0.8970 (tpt) cc_final: 0.8723 (tpt) REVERT: r 33 THR cc_start: 0.9032 (m) cc_final: 0.8689 (p) REVERT: r 77 LEU cc_start: 0.9306 (mt) cc_final: 0.9020 (tp) REVERT: r 81 ASP cc_start: 0.9369 (m-30) cc_final: 0.9013 (m-30) outliers start: 4 outliers final: 0 residues processed: 578 average time/residue: 0.2222 time to fit residues: 198.6036 Evaluate side-chains 422 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 421 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 226 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 243 optimal weight: 0.9980 chunk 336 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 80 ASN 2 85 HIS 2 428 GLN 4 90 GLN 6 42 GLN 7 6 GLN 7 89 GLN C 80 ASN C 103 GLN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN L 89 GLN ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 HIS N 42 GLN Q 35 HIS R 6 GLN R 30 ASN c 80 ASN c 85 HIS c 98 ASN c 103 GLN ** c 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 377 ASN l 6 GLN m 68 HIS ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.090615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.063991 restraints weight = 124954.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.066309 restraints weight = 66311.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.067844 restraints weight = 43825.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.068853 restraints weight = 33328.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 70)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.069491 restraints weight = 27831.398| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 32778 Z= 0.190 Angle : 0.730 14.001 44787 Z= 0.355 Chirality : 0.046 0.253 5322 Planarity : 0.005 0.089 5454 Dihedral : 9.611 79.189 6945 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.18 % Allowed : 3.32 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: -1.56 (0.13), residues: 3786 helix: 0.83 (0.27), residues: 381 sheet: -0.88 (0.14), residues: 1281 loop : -1.48 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 3 81 TYR 0.017 0.002 TYR q 100 PHE 0.018 0.002 PHE 7 70 TRP 0.020 0.002 TRP d 631 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00416 (32598) covalent geometry : angle 0.69270 (44292) SS BOND : bond 0.00610 ( 45) SS BOND : angle 1.95258 ( 90) hydrogen bonds : bond 0.03684 ( 1043) hydrogen bonds : angle 5.66506 ( 2832) link_ALPHA1-2 : bond 0.00836 ( 6) link_ALPHA1-2 : angle 2.00672 ( 18) link_ALPHA1-3 : bond 0.00778 ( 18) link_ALPHA1-3 : angle 1.97170 ( 54) link_ALPHA1-6 : bond 0.00348 ( 9) link_ALPHA1-6 : angle 1.59647 ( 27) link_BETA1-4 : bond 0.00363 ( 57) link_BETA1-4 : angle 2.70016 ( 171) link_NAG-ASN : bond 0.00537 ( 45) link_NAG-ASN : angle 2.26516 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 530 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 45 TRP cc_start: 0.9099 (p90) cc_final: 0.8645 (p90) REVERT: 2 83 GLU cc_start: 0.8942 (pt0) cc_final: 0.8329 (pm20) REVERT: 2 97 LYS cc_start: 0.9374 (mttt) cc_final: 0.9132 (mttt) REVERT: 2 100 MET cc_start: 0.9398 (ptt) cc_final: 0.8918 (ptp) REVERT: 2 119 CYS cc_start: 0.6753 (m) cc_final: 0.6413 (m) REVERT: 2 190 GLU cc_start: 0.8598 (pt0) cc_final: 0.8305 (pm20) REVERT: 2 321 ASP cc_start: 0.8110 (t0) cc_final: 0.7906 (t0) REVERT: 2 425 ASN cc_start: 0.8904 (t0) cc_final: 0.8365 (t0) REVERT: 2 492 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8433 (mm-30) REVERT: 3 23 GLU cc_start: 0.9231 (tp30) cc_final: 0.9005 (tp30) REVERT: 3 51 MET cc_start: 0.2973 (ttp) cc_final: 0.1117 (ttm) REVERT: 3 53 ASN cc_start: 0.8511 (m-40) cc_final: 0.8111 (p0) REVERT: 3 55 GLU cc_start: 0.6290 (mm-30) cc_final: 0.5548 (mm-30) REVERT: 4 4 MET cc_start: 0.4288 (mmm) cc_final: 0.3975 (mtp) REVERT: 5 100 LYS cc_start: 0.9466 (mmmm) cc_final: 0.8554 (tmtt) REVERT: 5 103 LYS cc_start: 0.8933 (mmmt) cc_final: 0.8440 (mmtm) REVERT: 7 1 GLU cc_start: 0.8274 (pm20) cc_final: 0.8056 (pm20) REVERT: 7 48 TYR cc_start: 0.8705 (p90) cc_final: 0.8477 (p90) REVERT: 7 77 LEU cc_start: 0.9289 (mt) cc_final: 0.9088 (tp) REVERT: 8 27 TYR cc_start: 0.8732 (p90) cc_final: 0.8119 (p90) REVERT: 8 47 TRP cc_start: 0.8943 (t60) cc_final: 0.8270 (t60) REVERT: 8 48 ILE cc_start: 0.8252 (mt) cc_final: 0.7041 (mp) REVERT: 8 72 GLN cc_start: 0.9333 (tt0) cc_final: 0.9037 (tp40) REVERT: 8 100 TYR cc_start: 0.8417 (m-80) cc_final: 0.8160 (m-10) REVERT: A 542 ARG cc_start: 0.9022 (ttp-110) cc_final: 0.8773 (ttp-110) REVERT: A 588 ARG cc_start: 0.9154 (mtt180) cc_final: 0.8681 (ttm110) REVERT: A 591 GLN cc_start: 0.9446 (tm-30) cc_final: 0.8874 (tm-30) REVERT: A 632 ASP cc_start: 0.8971 (t0) cc_final: 0.8757 (t70) REVERT: C 45 TRP cc_start: 0.9030 (p90) cc_final: 0.8384 (p90) REVERT: C 83 GLU cc_start: 0.8985 (pt0) cc_final: 0.8556 (pm20) REVERT: C 161 MET cc_start: 0.9215 (tpp) cc_final: 0.8537 (tpp) REVERT: C 492 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8397 (mp0) REVERT: D 601 LYS cc_start: 0.8246 (mtpp) cc_final: 0.7928 (mtpt) REVERT: D 655 LYS cc_start: 0.9076 (pttp) cc_final: 0.8745 (mmmt) REVERT: H 51 MET cc_start: 0.2859 (ttm) cc_final: 0.2575 (ttm) REVERT: H 53 ASN cc_start: 0.8424 (m-40) cc_final: 0.8147 (p0) REVERT: H 55 GLU cc_start: 0.5631 (mm-30) cc_final: 0.5338 (mm-30) REVERT: M 105 THR cc_start: 0.7974 (m) cc_final: 0.7656 (p) REVERT: R 11 LEU cc_start: 0.8940 (mt) cc_final: 0.8721 (mp) REVERT: R 53 ARG cc_start: 0.8303 (mtm-85) cc_final: 0.7793 (mtm-85) REVERT: R 78 ASP cc_start: 0.9080 (t70) cc_final: 0.8857 (t70) REVERT: c 83 GLU cc_start: 0.8894 (pt0) cc_final: 0.8409 (pm20) REVERT: c 123 THR cc_start: 0.9228 (p) cc_final: 0.8830 (t) REVERT: c 321 ASP cc_start: 0.8349 (t0) cc_final: 0.8072 (t0) REVERT: c 425 ASN cc_start: 0.8932 (t0) cc_final: 0.8558 (t0) REVERT: c 492 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8297 (mp0) REVERT: d 588 ARG cc_start: 0.9087 (mtt180) cc_final: 0.8817 (ttm-80) REVERT: d 589 ASP cc_start: 0.8899 (m-30) cc_final: 0.8621 (m-30) REVERT: d 591 GLN cc_start: 0.9419 (tm-30) cc_final: 0.8884 (tm-30) REVERT: d 633 LYS cc_start: 0.9282 (mmmm) cc_final: 0.9071 (mmmm) REVERT: d 655 LYS cc_start: 0.9452 (mmmm) cc_final: 0.9036 (pttp) REVERT: h 51 MET cc_start: 0.1950 (ttp) cc_final: 0.1657 (ttm) REVERT: m 100 LYS cc_start: 0.9119 (mptt) cc_final: 0.8736 (tmtt) REVERT: n 85 ASP cc_start: 0.8642 (m-30) cc_final: 0.8326 (t0) REVERT: q 28 ASN cc_start: 0.8913 (t0) cc_final: 0.8442 (t0) REVERT: q 31 ASP cc_start: 0.8815 (m-30) cc_final: 0.8503 (p0) REVERT: q 52 LYS cc_start: 0.9251 (mtmm) cc_final: 0.8526 (mtmm) REVERT: q 72 GLN cc_start: 0.9225 (tt0) cc_final: 0.8659 (tm-30) REVERT: q 73 LEU cc_start: 0.8954 (mt) cc_final: 0.8239 (mt) REVERT: r 11 LEU cc_start: 0.9266 (tp) cc_final: 0.9050 (tt) REVERT: r 32 MET cc_start: 0.9015 (tpt) cc_final: 0.8813 (tpt) REVERT: r 33 THR cc_start: 0.9020 (m) cc_final: 0.8701 (p) REVERT: r 77 LEU cc_start: 0.9339 (mt) cc_final: 0.9040 (tt) outliers start: 6 outliers final: 1 residues processed: 536 average time/residue: 0.2090 time to fit residues: 176.1739 Evaluate side-chains 395 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 394 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 190 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 217 optimal weight: 6.9990 chunk 233 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 205 optimal weight: 9.9990 chunk 336 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 326 optimal weight: 5.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 42 GLN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN Q 6 GLN c 80 ASN ** c 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 577 GLN ** d 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 55 GLN n 37 GLN ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.090672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.063755 restraints weight = 124619.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.066101 restraints weight = 65978.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.067643 restraints weight = 43656.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.068663 restraints weight = 33103.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.069312 restraints weight = 27595.932| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 32778 Z= 0.155 Angle : 0.703 13.703 44787 Z= 0.341 Chirality : 0.046 0.232 5322 Planarity : 0.005 0.082 5454 Dihedral : 8.985 78.215 6945 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -1.36 (0.13), residues: 3786 helix: 0.83 (0.27), residues: 396 sheet: -0.68 (0.14), residues: 1254 loop : -1.38 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG h 31 TYR 0.028 0.001 TYR h 100 PHE 0.042 0.002 PHE d 519 TRP 0.014 0.001 TRP m 36 HIS 0.006 0.001 HIS Q 35 Details of bonding type rmsd covalent geometry : bond 0.00345 (32598) covalent geometry : angle 0.66812 (44292) SS BOND : bond 0.00267 ( 45) SS BOND : angle 1.80973 ( 90) hydrogen bonds : bond 0.03499 ( 1043) hydrogen bonds : angle 5.53578 ( 2832) link_ALPHA1-2 : bond 0.00715 ( 6) link_ALPHA1-2 : angle 1.87471 ( 18) link_ALPHA1-3 : bond 0.00911 ( 18) link_ALPHA1-3 : angle 1.75534 ( 54) link_ALPHA1-6 : bond 0.00398 ( 9) link_ALPHA1-6 : angle 1.56997 ( 27) link_BETA1-4 : bond 0.00361 ( 57) link_BETA1-4 : angle 2.64828 ( 171) link_NAG-ASN : bond 0.00415 ( 45) link_NAG-ASN : angle 2.10825 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 506 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 47 ASP cc_start: 0.8563 (t0) cc_final: 0.7881 (m-30) REVERT: 2 52 LEU cc_start: 0.9436 (mt) cc_final: 0.9203 (mm) REVERT: 2 83 GLU cc_start: 0.8861 (pt0) cc_final: 0.8252 (pm20) REVERT: 2 119 CYS cc_start: 0.6610 (m) cc_final: 0.6211 (m) REVERT: 2 190 GLU cc_start: 0.8557 (pt0) cc_final: 0.8264 (pm20) REVERT: 2 207 LYS cc_start: 0.9228 (tptt) cc_final: 0.8967 (tptt) REVERT: 2 370 GLU cc_start: 0.8055 (pm20) cc_final: 0.7751 (pm20) REVERT: 2 425 ASN cc_start: 0.8866 (t0) cc_final: 0.8315 (t0) REVERT: 2 443 ILE cc_start: 0.8652 (mm) cc_final: 0.8445 (tt) REVERT: 2 492 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8491 (mm-30) REVERT: 3 23 GLU cc_start: 0.9212 (tp30) cc_final: 0.8976 (tp30) REVERT: 3 51 MET cc_start: 0.2067 (ttp) cc_final: 0.1194 (ttm) REVERT: 3 53 ASN cc_start: 0.8451 (m-40) cc_final: 0.8099 (p0) REVERT: 3 55 GLU cc_start: 0.5736 (mm-30) cc_final: 0.5276 (mm-30) REVERT: 5 100 LYS cc_start: 0.9468 (mmmm) cc_final: 0.8555 (tmtt) REVERT: 7 1 GLU cc_start: 0.8226 (pm20) cc_final: 0.7982 (pm20) REVERT: 7 11 LEU cc_start: 0.9055 (tt) cc_final: 0.8705 (mt) REVERT: 7 48 TYR cc_start: 0.8640 (p90) cc_final: 0.8433 (p90) REVERT: 7 77 LEU cc_start: 0.9300 (mt) cc_final: 0.9088 (tp) REVERT: 8 27 TYR cc_start: 0.8734 (p90) cc_final: 0.8415 (p90) REVERT: 8 32 TYR cc_start: 0.8960 (m-80) cc_final: 0.7751 (m-10) REVERT: 8 47 TRP cc_start: 0.8961 (t60) cc_final: 0.8294 (t60) REVERT: 8 48 ILE cc_start: 0.8208 (mt) cc_final: 0.7059 (mp) REVERT: 8 72 GLN cc_start: 0.9315 (tt0) cc_final: 0.9064 (tp40) REVERT: 8 100 TYR cc_start: 0.8383 (m-80) cc_final: 0.8147 (m-10) REVERT: A 542 ARG cc_start: 0.8987 (ttp-110) cc_final: 0.8747 (ttp-110) REVERT: A 588 ARG cc_start: 0.9125 (mtt180) cc_final: 0.8596 (ttm110) REVERT: A 632 ASP cc_start: 0.8977 (t0) cc_final: 0.8732 (t70) REVERT: A 655 LYS cc_start: 0.8989 (pttp) cc_final: 0.8751 (pttm) REVERT: C 45 TRP cc_start: 0.8979 (p90) cc_final: 0.8358 (p90) REVERT: C 161 MET cc_start: 0.9242 (tpp) cc_final: 0.8564 (tpp) REVERT: C 492 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8380 (mp0) REVERT: D 601 LYS cc_start: 0.8161 (mtpp) cc_final: 0.7863 (mtpt) REVERT: H 51 MET cc_start: 0.2678 (ttm) cc_final: 0.1935 (ttm) REVERT: H 53 ASN cc_start: 0.8401 (m-40) cc_final: 0.8177 (p0) REVERT: H 55 GLU cc_start: 0.5626 (mm-30) cc_final: 0.5143 (mm-30) REVERT: L 4 MET cc_start: 0.1593 (mmt) cc_final: 0.1047 (mtp) REVERT: M 105 THR cc_start: 0.7959 (m) cc_final: 0.7653 (p) REVERT: Q 89 GLU cc_start: 0.6721 (tm-30) cc_final: 0.6278 (tm-30) REVERT: Q 105 GLN cc_start: 0.9212 (pp30) cc_final: 0.9000 (pp30) REVERT: R 45 LEU cc_start: 0.9134 (mt) cc_final: 0.8873 (mt) REVERT: c 83 GLU cc_start: 0.8848 (pt0) cc_final: 0.8314 (pm20) REVERT: c 104 MET cc_start: 0.9107 (tmm) cc_final: 0.8590 (tmm) REVERT: c 123 THR cc_start: 0.9222 (p) cc_final: 0.8807 (t) REVERT: c 321 ASP cc_start: 0.8332 (t0) cc_final: 0.8029 (t0) REVERT: c 425 ASN cc_start: 0.8933 (t0) cc_final: 0.8549 (t0) REVERT: c 492 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8471 (mm-30) REVERT: d 530 MET cc_start: 0.7872 (mmp) cc_final: 0.7324 (mmp) REVERT: d 588 ARG cc_start: 0.9029 (mtt180) cc_final: 0.8737 (ttm-80) REVERT: d 589 ASP cc_start: 0.8884 (m-30) cc_final: 0.8600 (m-30) REVERT: d 655 LYS cc_start: 0.9442 (mmmm) cc_final: 0.9009 (pttp) REVERT: h 51 MET cc_start: 0.2442 (ttp) cc_final: 0.1972 (ttm) REVERT: h 55 GLU cc_start: 0.5095 (mm-30) cc_final: 0.4871 (mm-30) REVERT: n 85 ASP cc_start: 0.8591 (m-30) cc_final: 0.8352 (t0) REVERT: q 28 ASN cc_start: 0.8900 (t0) cc_final: 0.8450 (t0) REVERT: q 52 LYS cc_start: 0.9245 (mtmm) cc_final: 0.8522 (mtmm) REVERT: q 80 MET cc_start: 0.7873 (tmm) cc_final: 0.7642 (tmm) REVERT: r 11 LEU cc_start: 0.9272 (tp) cc_final: 0.9023 (mt) REVERT: r 32 MET cc_start: 0.8994 (tpt) cc_final: 0.8566 (tpt) REVERT: r 33 THR cc_start: 0.8973 (m) cc_final: 0.8658 (p) REVERT: r 77 LEU cc_start: 0.9305 (mt) cc_final: 0.9022 (tt) outliers start: 0 outliers final: 0 residues processed: 506 average time/residue: 0.2074 time to fit residues: 165.7062 Evaluate side-chains 377 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 206 optimal weight: 3.9990 chunk 371 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 chunk 323 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 chunk 246 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 324 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 55 GLN ** 5 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 42 GLN 7 30 ASN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 99 ASN ** c 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 352 HIS c 377 ASN ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 30 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.085690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.059124 restraints weight = 128616.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.061220 restraints weight = 70696.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.062566 restraints weight = 47995.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.063477 restraints weight = 37210.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.063897 restraints weight = 31517.087| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 32778 Z= 0.392 Angle : 0.938 12.902 44787 Z= 0.452 Chirality : 0.051 0.308 5322 Planarity : 0.006 0.095 5454 Dihedral : 9.543 77.637 6945 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -1.82 (0.13), residues: 3786 helix: -0.11 (0.25), residues: 417 sheet: -0.92 (0.14), residues: 1269 loop : -1.62 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG R 53 TYR 0.031 0.002 TYR A 643 PHE 0.030 0.003 PHE 8 100D TRP 0.028 0.003 TRP M 36 HIS 0.015 0.002 HIS 2 374 Details of bonding type rmsd covalent geometry : bond 0.00847 (32598) covalent geometry : angle 0.89891 (44292) SS BOND : bond 0.00999 ( 45) SS BOND : angle 2.16487 ( 90) hydrogen bonds : bond 0.04431 ( 1043) hydrogen bonds : angle 6.20478 ( 2832) link_ALPHA1-2 : bond 0.01041 ( 6) link_ALPHA1-2 : angle 2.49720 ( 18) link_ALPHA1-3 : bond 0.00621 ( 18) link_ALPHA1-3 : angle 2.63293 ( 54) link_ALPHA1-6 : bond 0.00388 ( 9) link_ALPHA1-6 : angle 1.63835 ( 27) link_BETA1-4 : bond 0.00517 ( 57) link_BETA1-4 : angle 2.96732 ( 171) link_NAG-ASN : bond 0.01187 ( 45) link_NAG-ASN : angle 2.90650 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 449 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 52 LEU cc_start: 0.9475 (mt) cc_final: 0.9251 (mm) REVERT: 2 83 GLU cc_start: 0.8870 (pt0) cc_final: 0.8349 (pm20) REVERT: 2 119 CYS cc_start: 0.6583 (m) cc_final: 0.6193 (m) REVERT: 2 140 ASP cc_start: 0.7909 (m-30) cc_final: 0.7360 (t0) REVERT: 2 492 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8529 (mp0) REVERT: 3 23 GLU cc_start: 0.9235 (tp30) cc_final: 0.9030 (tp30) REVERT: 3 53 ASN cc_start: 0.8532 (m-40) cc_final: 0.8126 (p0) REVERT: 3 55 GLU cc_start: 0.5569 (mm-30) cc_final: 0.5298 (mm-30) REVERT: 7 1 GLU cc_start: 0.8260 (pm20) cc_final: 0.8032 (pm20) REVERT: 7 46 LEU cc_start: 0.9640 (mp) cc_final: 0.9413 (mp) REVERT: 7 48 TYR cc_start: 0.8688 (p90) cc_final: 0.8459 (p90) REVERT: 7 77 LEU cc_start: 0.9469 (mt) cc_final: 0.9252 (tp) REVERT: 8 72 GLN cc_start: 0.9372 (tt0) cc_final: 0.8986 (tp40) REVERT: 8 80 MET cc_start: 0.7763 (tmm) cc_final: 0.7173 (tmm) REVERT: A 588 ARG cc_start: 0.9098 (mtt180) cc_final: 0.8582 (ttm110) REVERT: C 45 TRP cc_start: 0.9085 (p90) cc_final: 0.8263 (p90) REVERT: C 140 ASP cc_start: 0.8147 (m-30) cc_final: 0.7620 (t0) REVERT: C 161 MET cc_start: 0.9335 (tpp) cc_final: 0.8640 (tpp) REVERT: C 492 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8581 (mp0) REVERT: D 530 MET cc_start: 0.8345 (mmm) cc_final: 0.8009 (mmm) REVERT: D 601 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7847 (mtpt) REVERT: H 51 MET cc_start: 0.3082 (ttm) cc_final: 0.2106 (ttm) REVERT: H 53 ASN cc_start: 0.8169 (m-40) cc_final: 0.7842 (p0) REVERT: H 55 GLU cc_start: 0.5513 (mm-30) cc_final: 0.5124 (mm-30) REVERT: H 73 THR cc_start: 0.8960 (p) cc_final: 0.8750 (p) REVERT: L 32 ASP cc_start: 0.6790 (m-30) cc_final: 0.6561 (m-30) REVERT: Q 76 ASP cc_start: 0.6375 (p0) cc_final: 0.5567 (p0) REVERT: R 46 LEU cc_start: 0.9351 (mp) cc_final: 0.9133 (mp) REVERT: R 78 ASP cc_start: 0.9101 (t70) cc_final: 0.8738 (t70) REVERT: c 83 GLU cc_start: 0.8910 (pt0) cc_final: 0.8390 (pm20) REVERT: c 104 MET cc_start: 0.9191 (tmm) cc_final: 0.8885 (tmm) REVERT: c 123 THR cc_start: 0.9393 (p) cc_final: 0.9047 (t) REVERT: c 140 ASP cc_start: 0.7723 (m-30) cc_final: 0.7225 (t70) REVERT: c 492 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8466 (mp0) REVERT: d 530 MET cc_start: 0.8081 (mmp) cc_final: 0.7857 (mmp) REVERT: d 588 ARG cc_start: 0.8970 (mtt180) cc_final: 0.8701 (ttm-80) REVERT: d 589 ASP cc_start: 0.8942 (m-30) cc_final: 0.8679 (m-30) REVERT: d 647 GLU cc_start: 0.8791 (mp0) cc_final: 0.8438 (mp0) REVERT: d 655 LYS cc_start: 0.9482 (mmmm) cc_final: 0.9043 (pttp) REVERT: h 51 MET cc_start: 0.3505 (ttp) cc_final: 0.3230 (ttm) REVERT: q 28 ASN cc_start: 0.9015 (t0) cc_final: 0.8579 (t0) REVERT: q 52 LYS cc_start: 0.9337 (mtmm) cc_final: 0.8668 (mtmm) REVERT: q 72 GLN cc_start: 0.9350 (tt0) cc_final: 0.8939 (tm-30) REVERT: q 73 LEU cc_start: 0.8937 (mt) cc_final: 0.8303 (mt) REVERT: q 76 ASP cc_start: 0.8706 (m-30) cc_final: 0.8387 (m-30) REVERT: q 80 MET cc_start: 0.7862 (tmm) cc_final: 0.7400 (tmm) REVERT: r 11 LEU cc_start: 0.9343 (tp) cc_final: 0.9018 (tt) REVERT: r 77 LEU cc_start: 0.9384 (mt) cc_final: 0.8987 (tt) outliers start: 1 outliers final: 0 residues processed: 450 average time/residue: 0.2156 time to fit residues: 153.5259 Evaluate side-chains 341 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 249 optimal weight: 0.7980 chunk 188 optimal weight: 6.9990 chunk 322 optimal weight: 30.0000 chunk 151 optimal weight: 2.9990 chunk 343 optimal weight: 0.2980 chunk 71 optimal weight: 3.9990 chunk 236 optimal weight: 0.6980 chunk 224 optimal weight: 1.9990 chunk 312 optimal weight: 10.0000 chunk 369 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 98 ASN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 1 GLN 6 42 GLN 7 89 GLN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 1 GLN ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN ** Q 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 105 GLN ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.090165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.063055 restraints weight = 124323.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.065353 restraints weight = 66190.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.066884 restraints weight = 44038.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.067866 restraints weight = 33615.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.068464 restraints weight = 28169.471| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32778 Z= 0.134 Angle : 0.740 20.488 44787 Z= 0.359 Chirality : 0.046 0.229 5322 Planarity : 0.005 0.088 5454 Dihedral : 8.734 78.153 6945 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.03 % Allowed : 1.71 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -1.43 (0.13), residues: 3786 helix: 0.57 (0.26), residues: 417 sheet: -0.87 (0.14), residues: 1290 loop : -1.29 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 3 81 TYR 0.021 0.002 TYR H 99 PHE 0.040 0.002 PHE A 519 TRP 0.020 0.002 TRP d 631 HIS 0.008 0.001 HIS N 89 Details of bonding type rmsd covalent geometry : bond 0.00299 (32598) covalent geometry : angle 0.70823 (44292) SS BOND : bond 0.00225 ( 45) SS BOND : angle 1.69944 ( 90) hydrogen bonds : bond 0.03501 ( 1043) hydrogen bonds : angle 5.67375 ( 2832) link_ALPHA1-2 : bond 0.00736 ( 6) link_ALPHA1-2 : angle 1.97737 ( 18) link_ALPHA1-3 : bond 0.00947 ( 18) link_ALPHA1-3 : angle 1.56573 ( 54) link_ALPHA1-6 : bond 0.00504 ( 9) link_ALPHA1-6 : angle 1.57327 ( 27) link_BETA1-4 : bond 0.00420 ( 57) link_BETA1-4 : angle 2.66969 ( 171) link_NAG-ASN : bond 0.00335 ( 45) link_NAG-ASN : angle 2.01783 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 500 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 45 TRP cc_start: 0.9010 (p90) cc_final: 0.8467 (p90) REVERT: 2 52 LEU cc_start: 0.9406 (mt) cc_final: 0.9122 (mm) REVERT: 2 83 GLU cc_start: 0.8820 (pt0) cc_final: 0.8270 (pm20) REVERT: 2 119 CYS cc_start: 0.6233 (m) cc_final: 0.5784 (m) REVERT: 2 207 LYS cc_start: 0.9149 (tptt) cc_final: 0.8896 (tptt) REVERT: 2 492 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8505 (mm-30) REVERT: 3 23 GLU cc_start: 0.9225 (tp30) cc_final: 0.9023 (tp30) REVERT: 3 51 MET cc_start: 0.1940 (ttp) cc_final: 0.1359 (ttm) REVERT: 3 55 GLU cc_start: 0.5767 (mm-30) cc_final: 0.5320 (mm-30) REVERT: 3 81 ARG cc_start: 0.8611 (ttp-110) cc_final: 0.7994 (ptp90) REVERT: 5 34 TRP cc_start: 0.6612 (m100) cc_final: 0.6276 (m100) REVERT: 5 100 LYS cc_start: 0.9464 (mmmm) cc_final: 0.8623 (tmtt) REVERT: 5 103 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8446 (mmtm) REVERT: 7 46 LEU cc_start: 0.9596 (mp) cc_final: 0.9358 (mp) REVERT: 7 77 LEU cc_start: 0.9310 (mt) cc_final: 0.9087 (tp) REVERT: 8 80 MET cc_start: 0.7859 (tmm) cc_final: 0.7241 (tmm) REVERT: A 530 MET cc_start: 0.7722 (mmp) cc_final: 0.7439 (mmp) REVERT: A 588 ARG cc_start: 0.9019 (mtt180) cc_final: 0.8522 (ttm110) REVERT: A 632 ASP cc_start: 0.8864 (t70) cc_final: 0.8545 (t70) REVERT: A 655 LYS cc_start: 0.9104 (pttp) cc_final: 0.8846 (pttm) REVERT: C 45 TRP cc_start: 0.8906 (p90) cc_final: 0.8339 (p90) REVERT: C 104 MET cc_start: 0.9153 (tmm) cc_final: 0.8855 (tmm) REVERT: C 140 ASP cc_start: 0.8113 (m-30) cc_final: 0.7468 (t0) REVERT: C 161 MET cc_start: 0.9306 (tpp) cc_final: 0.8732 (tpp) REVERT: C 370 GLU cc_start: 0.8167 (pm20) cc_final: 0.7889 (pm20) REVERT: C 479 TRP cc_start: 0.9420 (m100) cc_final: 0.9136 (m100) REVERT: C 492 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8339 (mp0) REVERT: D 580 VAL cc_start: 0.9612 (m) cc_final: 0.9381 (m) REVERT: H 51 MET cc_start: 0.2094 (ttm) cc_final: 0.1629 (ttm) REVERT: H 53 ASN cc_start: 0.8282 (m-40) cc_final: 0.8057 (p0) REVERT: H 55 GLU cc_start: 0.5351 (mm-30) cc_final: 0.5047 (mm-30) REVERT: M 105 THR cc_start: 0.7990 (m) cc_final: 0.7693 (p) REVERT: R 33 THR cc_start: 0.8983 (m) cc_final: 0.8762 (m) REVERT: R 45 LEU cc_start: 0.9165 (mt) cc_final: 0.8807 (mp) REVERT: R 46 LEU cc_start: 0.9220 (mp) cc_final: 0.8891 (mp) REVERT: R 53 ARG cc_start: 0.8842 (mpp80) cc_final: 0.7749 (mtm-85) REVERT: c 45 TRP cc_start: 0.8897 (p90) cc_final: 0.8573 (p90) REVERT: c 83 GLU cc_start: 0.8855 (pt0) cc_final: 0.8352 (pm20) REVERT: c 95 MET cc_start: 0.8982 (ptp) cc_final: 0.8417 (ptp) REVERT: c 123 THR cc_start: 0.9240 (p) cc_final: 0.8839 (t) REVERT: c 321 ASP cc_start: 0.8250 (t0) cc_final: 0.8049 (t0) REVERT: c 425 ASN cc_start: 0.9006 (t0) cc_final: 0.8462 (t0) REVERT: c 466 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7988 (mp0) REVERT: c 492 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8432 (mp0) REVERT: d 530 MET cc_start: 0.7828 (mmp) cc_final: 0.7456 (mmp) REVERT: d 588 ARG cc_start: 0.8930 (mtt180) cc_final: 0.8636 (ttm-80) REVERT: d 589 ASP cc_start: 0.8856 (m-30) cc_final: 0.8563 (m-30) REVERT: d 632 ASP cc_start: 0.8852 (t0) cc_final: 0.8639 (t70) REVERT: d 655 LYS cc_start: 0.9470 (mmmm) cc_final: 0.9014 (pttp) REVERT: h 51 MET cc_start: 0.0983 (ttp) cc_final: 0.0593 (ttm) REVERT: h 55 GLU cc_start: 0.5158 (mm-30) cc_final: 0.4923 (mm-30) REVERT: q 28 ASN cc_start: 0.8919 (t0) cc_final: 0.8657 (t0) REVERT: q 52 LYS cc_start: 0.9312 (mtmm) cc_final: 0.8648 (mtmm) REVERT: q 76 ASP cc_start: 0.8691 (m-30) cc_final: 0.8405 (m-30) REVERT: r 11 LEU cc_start: 0.9328 (tp) cc_final: 0.9126 (mt) REVERT: r 33 THR cc_start: 0.8957 (m) cc_final: 0.8587 (p) REVERT: r 77 LEU cc_start: 0.9233 (mt) cc_final: 0.8985 (tt) outliers start: 1 outliers final: 0 residues processed: 501 average time/residue: 0.2169 time to fit residues: 172.0740 Evaluate side-chains 367 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 280 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 284 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 91 optimal weight: 0.0030 chunk 179 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 197 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 231 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 overall best weight: 2.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN ** Q 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 105 GLN ** c 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.088177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.061422 restraints weight = 126815.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.063633 restraints weight = 68328.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.065106 restraints weight = 45732.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.066046 restraints weight = 35114.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.066545 restraints weight = 29514.623| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 32778 Z= 0.211 Angle : 0.776 15.454 44787 Z= 0.377 Chirality : 0.047 0.247 5322 Planarity : 0.006 0.185 5454 Dihedral : 8.701 76.524 6945 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.03 % Allowed : 0.96 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.13), residues: 3786 helix: 0.64 (0.26), residues: 414 sheet: -0.85 (0.14), residues: 1275 loop : -1.33 (0.14), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 6 31 TYR 0.036 0.002 TYR D 643 PHE 0.025 0.002 PHE d 519 TRP 0.033 0.002 TRP A 571 HIS 0.006 0.001 HIS 2 374 Details of bonding type rmsd covalent geometry : bond 0.00470 (32598) covalent geometry : angle 0.73682 (44292) SS BOND : bond 0.00373 ( 45) SS BOND : angle 2.60660 ( 90) hydrogen bonds : bond 0.03759 ( 1043) hydrogen bonds : angle 5.76158 ( 2832) link_ALPHA1-2 : bond 0.00762 ( 6) link_ALPHA1-2 : angle 2.07796 ( 18) link_ALPHA1-3 : bond 0.00750 ( 18) link_ALPHA1-3 : angle 1.93792 ( 54) link_ALPHA1-6 : bond 0.00471 ( 9) link_ALPHA1-6 : angle 1.52748 ( 27) link_BETA1-4 : bond 0.00360 ( 57) link_BETA1-4 : angle 2.74157 ( 171) link_NAG-ASN : bond 0.00577 ( 45) link_NAG-ASN : angle 2.25436 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 462 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 52 LEU cc_start: 0.9411 (mt) cc_final: 0.9173 (mm) REVERT: 2 83 GLU cc_start: 0.8842 (pt0) cc_final: 0.8287 (pm20) REVERT: 2 119 CYS cc_start: 0.6295 (m) cc_final: 0.5899 (m) REVERT: 2 140 ASP cc_start: 0.7666 (m-30) cc_final: 0.7098 (t0) REVERT: 2 492 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8497 (mm-30) REVERT: 3 23 GLU cc_start: 0.9168 (tp30) cc_final: 0.8951 (tp30) REVERT: 3 51 MET cc_start: 0.1660 (ttp) cc_final: 0.1423 (ttm) REVERT: 3 55 GLU cc_start: 0.5809 (mm-30) cc_final: 0.5481 (mm-30) REVERT: 5 34 TRP cc_start: 0.6644 (m100) cc_final: 0.6291 (m100) REVERT: 5 100 LYS cc_start: 0.9491 (mmmm) cc_final: 0.8548 (tmtt) REVERT: 5 103 LYS cc_start: 0.8993 (mmmt) cc_final: 0.8472 (mmtm) REVERT: 7 48 TYR cc_start: 0.8754 (p90) cc_final: 0.8501 (p90) REVERT: 7 59 ASP cc_start: 0.9236 (t70) cc_final: 0.9012 (t0) REVERT: 7 77 LEU cc_start: 0.9391 (mt) cc_final: 0.9180 (tp) REVERT: 8 72 GLN cc_start: 0.9333 (tt0) cc_final: 0.9018 (tp40) REVERT: 8 80 MET cc_start: 0.7894 (tmm) cc_final: 0.7417 (tmm) REVERT: A 530 MET cc_start: 0.7649 (mmp) cc_final: 0.7289 (mmp) REVERT: A 574 LYS cc_start: 0.9411 (ptpt) cc_final: 0.9145 (pttt) REVERT: A 588 ARG cc_start: 0.9071 (mtt180) cc_final: 0.8566 (ttm110) REVERT: A 622 ILE cc_start: 0.9592 (pt) cc_final: 0.9348 (pt) REVERT: A 632 ASP cc_start: 0.8935 (t70) cc_final: 0.8631 (t70) REVERT: C 45 TRP cc_start: 0.9020 (p90) cc_final: 0.8365 (p90) REVERT: C 140 ASP cc_start: 0.8054 (m-30) cc_final: 0.7453 (t0) REVERT: C 161 MET cc_start: 0.9353 (tpp) cc_final: 0.8774 (tpp) REVERT: C 425 ASN cc_start: 0.8981 (t0) cc_final: 0.8670 (t0) REVERT: C 426 MET cc_start: 0.9176 (tmm) cc_final: 0.8895 (tmm) REVERT: C 492 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8369 (mp0) REVERT: D 542 ARG cc_start: 0.9223 (ttp-110) cc_final: 0.9013 (ttp-110) REVERT: H 51 MET cc_start: 0.1813 (ttm) cc_final: 0.1519 (ttm) REVERT: H 53 ASN cc_start: 0.8282 (m-40) cc_final: 0.8026 (p0) REVERT: H 55 GLU cc_start: 0.5602 (mm-30) cc_final: 0.5326 (mm-30) REVERT: L 4 MET cc_start: 0.5557 (mtm) cc_final: 0.5342 (mpp) REVERT: L 32 ASP cc_start: 0.7419 (m-30) cc_final: 0.7215 (m-30) REVERT: M 100 MET cc_start: 0.7436 (mmm) cc_final: 0.6910 (mmm) REVERT: M 105 THR cc_start: 0.8227 (m) cc_final: 0.7933 (p) REVERT: R 33 THR cc_start: 0.9012 (m) cc_final: 0.8783 (m) REVERT: R 46 LEU cc_start: 0.9296 (mp) cc_final: 0.8968 (mp) REVERT: R 77 LEU cc_start: 0.9195 (mt) cc_final: 0.8900 (tp) REVERT: R 81 ASP cc_start: 0.9290 (m-30) cc_final: 0.9060 (m-30) REVERT: c 83 GLU cc_start: 0.8851 (pt0) cc_final: 0.8373 (pm20) REVERT: c 95 MET cc_start: 0.9029 (ptp) cc_final: 0.8397 (ptp) REVERT: c 123 THR cc_start: 0.9299 (p) cc_final: 0.8890 (t) REVERT: c 140 ASP cc_start: 0.7595 (m-30) cc_final: 0.7009 (t70) REVERT: c 321 ASP cc_start: 0.8314 (t0) cc_final: 0.8091 (t0) REVERT: c 370 GLU cc_start: 0.7900 (pm20) cc_final: 0.7552 (pm20) REVERT: c 492 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8474 (mp0) REVERT: d 530 MET cc_start: 0.7864 (mmp) cc_final: 0.7540 (mmp) REVERT: d 588 ARG cc_start: 0.8957 (mtt180) cc_final: 0.8663 (ttm-80) REVERT: d 589 ASP cc_start: 0.8900 (m-30) cc_final: 0.8612 (m-30) REVERT: d 655 LYS cc_start: 0.9460 (mmmm) cc_final: 0.8989 (pttp) REVERT: q 28 ASN cc_start: 0.8927 (t0) cc_final: 0.8666 (t0) REVERT: q 52 LYS cc_start: 0.9317 (mtmm) cc_final: 0.8651 (mtmm) REVERT: q 76 ASP cc_start: 0.8651 (m-30) cc_final: 0.8347 (m-30) REVERT: q 80 MET cc_start: 0.7497 (tmm) cc_final: 0.7110 (tmm) REVERT: r 11 LEU cc_start: 0.9337 (tp) cc_final: 0.9129 (mt) REVERT: r 46 LEU cc_start: 0.9452 (mp) cc_final: 0.9225 (mp) outliers start: 1 outliers final: 0 residues processed: 463 average time/residue: 0.2043 time to fit residues: 149.9599 Evaluate side-chains 352 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 361 optimal weight: 3.9990 chunk 307 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 363 optimal weight: 0.7980 chunk 293 optimal weight: 2.9990 chunk 116 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 42 GLN ** 7 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 HIS Q 105 GLN c 80 ASN c 98 ASN d 591 GLN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.090283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.063417 restraints weight = 124173.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.065713 restraints weight = 66092.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.067262 restraints weight = 43863.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.068239 restraints weight = 33416.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.068864 restraints weight = 27947.651| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32778 Z= 0.131 Angle : 0.728 14.187 44787 Z= 0.356 Chirality : 0.046 0.228 5322 Planarity : 0.005 0.099 5454 Dihedral : 8.304 76.229 6945 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.06 % Allowed : 0.63 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.14), residues: 3786 helix: 0.70 (0.27), residues: 414 sheet: -0.75 (0.14), residues: 1269 loop : -1.22 (0.14), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG 3 31 TYR 0.021 0.001 TYR D 586 PHE 0.022 0.002 PHE d 519 TRP 0.026 0.002 TRP 2 45 HIS 0.006 0.001 HIS c 374 Details of bonding type rmsd covalent geometry : bond 0.00291 (32598) covalent geometry : angle 0.69479 (44292) SS BOND : bond 0.00414 ( 45) SS BOND : angle 2.25212 ( 90) hydrogen bonds : bond 0.03395 ( 1043) hydrogen bonds : angle 5.49125 ( 2832) link_ALPHA1-2 : bond 0.00633 ( 6) link_ALPHA1-2 : angle 1.75034 ( 18) link_ALPHA1-3 : bond 0.00828 ( 18) link_ALPHA1-3 : angle 1.56623 ( 54) link_ALPHA1-6 : bond 0.00563 ( 9) link_ALPHA1-6 : angle 1.53504 ( 27) link_BETA1-4 : bond 0.00421 ( 57) link_BETA1-4 : angle 2.61883 ( 171) link_NAG-ASN : bond 0.00313 ( 45) link_NAG-ASN : angle 1.92561 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 491 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 45 TRP cc_start: 0.9019 (p90) cc_final: 0.8511 (p90) REVERT: 2 52 LEU cc_start: 0.9412 (mt) cc_final: 0.9124 (mm) REVERT: 2 83 GLU cc_start: 0.8851 (pt0) cc_final: 0.8299 (pm20) REVERT: 2 100 MET cc_start: 0.9154 (ptp) cc_final: 0.8820 (ptp) REVERT: 2 119 CYS cc_start: 0.6396 (m) cc_final: 0.6024 (m) REVERT: 2 140 ASP cc_start: 0.7610 (m-30) cc_final: 0.7058 (t0) REVERT: 2 492 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8475 (mm-30) REVERT: 3 51 MET cc_start: 0.1642 (ttp) cc_final: 0.1175 (ttm) REVERT: 5 34 TRP cc_start: 0.6662 (m100) cc_final: 0.6249 (m100) REVERT: 5 100 LYS cc_start: 0.9477 (mmmm) cc_final: 0.8636 (tmtt) REVERT: 5 103 LYS cc_start: 0.9024 (mmmt) cc_final: 0.8533 (mmtm) REVERT: 7 59 ASP cc_start: 0.9232 (t70) cc_final: 0.9020 (t0) REVERT: 7 77 LEU cc_start: 0.9270 (mt) cc_final: 0.9045 (tp) REVERT: 8 80 MET cc_start: 0.7775 (tmm) cc_final: 0.7189 (tmm) REVERT: 8 89 GLU cc_start: 0.7629 (tt0) cc_final: 0.7424 (tt0) REVERT: A 530 MET cc_start: 0.7460 (mmp) cc_final: 0.7096 (mmp) REVERT: A 588 ARG cc_start: 0.9129 (mtt180) cc_final: 0.8705 (ttm110) REVERT: A 632 ASP cc_start: 0.8895 (t70) cc_final: 0.8611 (t70) REVERT: A 655 LYS cc_start: 0.9087 (pttp) cc_final: 0.8831 (pttm) REVERT: C 45 TRP cc_start: 0.8995 (p90) cc_final: 0.8575 (p90) REVERT: C 140 ASP cc_start: 0.8027 (m-30) cc_final: 0.7397 (t0) REVERT: C 161 MET cc_start: 0.9334 (tpp) cc_final: 0.8785 (tpp) REVERT: C 425 ASN cc_start: 0.8878 (t0) cc_final: 0.8557 (t0) REVERT: C 479 TRP cc_start: 0.9404 (m100) cc_final: 0.9109 (m100) REVERT: C 492 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8456 (mm-30) REVERT: D 542 ARG cc_start: 0.9250 (ttp-110) cc_final: 0.8991 (ttp-110) REVERT: D 632 ASP cc_start: 0.8854 (t70) cc_final: 0.8625 (t70) REVERT: D 633 LYS cc_start: 0.9396 (mmmm) cc_final: 0.8967 (mmtm) REVERT: H 51 MET cc_start: 0.1535 (ttm) cc_final: 0.1186 (ttm) REVERT: H 55 GLU cc_start: 0.5515 (mm-30) cc_final: 0.4960 (mm-30) REVERT: M 100 LYS cc_start: 0.9462 (mmmm) cc_final: 0.8780 (tmtt) REVERT: M 100 MET cc_start: 0.7235 (mmm) cc_final: 0.6692 (mmm) REVERT: M 103 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8458 (mmtm) REVERT: M 105 THR cc_start: 0.8126 (m) cc_final: 0.7821 (p) REVERT: Q 82 PHE cc_start: 0.8613 (t80) cc_final: 0.8324 (t80) REVERT: R 46 LEU cc_start: 0.9227 (mp) cc_final: 0.8790 (mp) REVERT: c 83 GLU cc_start: 0.8839 (pt0) cc_final: 0.8375 (pm20) REVERT: c 123 THR cc_start: 0.9229 (p) cc_final: 0.8787 (t) REVERT: c 259 LEU cc_start: 0.8854 (mp) cc_final: 0.8546 (pp) REVERT: c 280 ASN cc_start: 0.9230 (p0) cc_final: 0.9013 (p0) REVERT: c 425 ASN cc_start: 0.8965 (t0) cc_final: 0.8406 (t0) REVERT: c 466 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8102 (mp0) REVERT: c 492 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8403 (mp0) REVERT: d 530 MET cc_start: 0.7692 (mmp) cc_final: 0.7303 (mmp) REVERT: d 589 ASP cc_start: 0.8901 (m-30) cc_final: 0.8566 (m-30) REVERT: d 591 GLN cc_start: 0.9441 (OUTLIER) cc_final: 0.9160 (tm-30) REVERT: d 632 ASP cc_start: 0.8767 (t70) cc_final: 0.8477 (t70) REVERT: d 655 LYS cc_start: 0.9410 (mmmm) cc_final: 0.8977 (pttp) REVERT: n 30 SER cc_start: 0.9387 (m) cc_final: 0.8876 (p) REVERT: q 23 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7248 (ttp80) REVERT: q 28 ASN cc_start: 0.8934 (t0) cc_final: 0.8559 (t0) REVERT: q 52 LYS cc_start: 0.9293 (mtmm) cc_final: 0.8643 (mtmm) REVERT: q 73 LEU cc_start: 0.8786 (mt) cc_final: 0.8522 (mt) REVERT: q 76 ASP cc_start: 0.8647 (m-30) cc_final: 0.8356 (m-30) REVERT: r 46 LEU cc_start: 0.9437 (mp) cc_final: 0.9187 (mp) outliers start: 2 outliers final: 0 residues processed: 493 average time/residue: 0.2104 time to fit residues: 163.4163 Evaluate side-chains 369 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 368 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 166 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 237 optimal weight: 0.4980 chunk 79 optimal weight: 9.9990 chunk 324 optimal weight: 10.0000 chunk 312 optimal weight: 8.9990 chunk 333 optimal weight: 4.9990 chunk 266 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 80 ASN ** 5 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 42 GLN ** 7 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 105 GLN ** c 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 55 GLN ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.090230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.063349 restraints weight = 124927.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.065661 restraints weight = 66542.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.067182 restraints weight = 44157.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.068136 restraints weight = 33602.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.068781 restraints weight = 28204.557| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32778 Z= 0.135 Angle : 0.715 14.040 44787 Z= 0.349 Chirality : 0.046 0.236 5322 Planarity : 0.005 0.089 5454 Dihedral : 8.092 74.707 6945 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.03 % Allowed : 0.42 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.14), residues: 3786 helix: 0.72 (0.26), residues: 417 sheet: -0.63 (0.14), residues: 1260 loop : -1.22 (0.14), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 3 81 TYR 0.036 0.002 TYR A 643 PHE 0.030 0.001 PHE d 519 TRP 0.031 0.002 TRP m 34 HIS 0.003 0.001 HIS c 374 Details of bonding type rmsd covalent geometry : bond 0.00302 (32598) covalent geometry : angle 0.68438 (44292) SS BOND : bond 0.00251 ( 45) SS BOND : angle 1.53710 ( 90) hydrogen bonds : bond 0.03414 ( 1043) hydrogen bonds : angle 5.43127 ( 2832) link_ALPHA1-2 : bond 0.00566 ( 6) link_ALPHA1-2 : angle 1.73579 ( 18) link_ALPHA1-3 : bond 0.00818 ( 18) link_ALPHA1-3 : angle 1.63703 ( 54) link_ALPHA1-6 : bond 0.00562 ( 9) link_ALPHA1-6 : angle 1.50972 ( 27) link_BETA1-4 : bond 0.00384 ( 57) link_BETA1-4 : angle 2.59880 ( 171) link_NAG-ASN : bond 0.00340 ( 45) link_NAG-ASN : angle 1.92923 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 480 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 45 TRP cc_start: 0.8994 (p90) cc_final: 0.8539 (p90) REVERT: 2 52 LEU cc_start: 0.9415 (mt) cc_final: 0.9167 (mm) REVERT: 2 83 GLU cc_start: 0.8700 (pt0) cc_final: 0.8262 (pm20) REVERT: 2 119 CYS cc_start: 0.6365 (m) cc_final: 0.5968 (m) REVERT: 2 140 ASP cc_start: 0.7523 (m-30) cc_final: 0.7010 (t0) REVERT: 2 492 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8501 (mm-30) REVERT: 3 81 ARG cc_start: 0.8539 (ttp-110) cc_final: 0.7907 (ptp90) REVERT: 5 34 TRP cc_start: 0.6589 (m100) cc_final: 0.6124 (m100) REVERT: 5 82 LEU cc_start: 0.9083 (tt) cc_final: 0.8376 (mp) REVERT: 5 100 LYS cc_start: 0.9485 (mmmm) cc_final: 0.8621 (tmtt) REVERT: 5 103 LYS cc_start: 0.9060 (mmmt) cc_final: 0.8569 (mmtm) REVERT: 7 48 TYR cc_start: 0.8471 (p90) cc_final: 0.7958 (p90) REVERT: 7 77 LEU cc_start: 0.9264 (mt) cc_final: 0.9049 (tp) REVERT: 7 78 ASP cc_start: 0.9258 (t70) cc_final: 0.8992 (t70) REVERT: 8 80 MET cc_start: 0.7441 (tmm) cc_final: 0.7060 (tmm) REVERT: A 530 MET cc_start: 0.7436 (mmp) cc_final: 0.7060 (mmp) REVERT: A 573 ILE cc_start: 0.9349 (mp) cc_final: 0.9143 (mp) REVERT: A 588 ARG cc_start: 0.9128 (mtt180) cc_final: 0.8651 (ttm110) REVERT: A 626 MET cc_start: 0.7854 (tpt) cc_final: 0.7422 (tpp) REVERT: A 632 ASP cc_start: 0.8816 (t70) cc_final: 0.8566 (t70) REVERT: A 655 LYS cc_start: 0.8983 (pttp) cc_final: 0.8739 (pttm) REVERT: C 45 TRP cc_start: 0.8967 (p90) cc_final: 0.8535 (p90) REVERT: C 140 ASP cc_start: 0.7952 (m-30) cc_final: 0.7320 (t0) REVERT: C 161 MET cc_start: 0.9350 (tpp) cc_final: 0.8787 (tpp) REVERT: C 425 ASN cc_start: 0.8843 (t0) cc_final: 0.8573 (t0) REVERT: C 492 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8476 (mm-30) REVERT: D 542 ARG cc_start: 0.9226 (ttp-110) cc_final: 0.8982 (ttp-110) REVERT: D 580 VAL cc_start: 0.9610 (m) cc_final: 0.9340 (m) REVERT: D 632 ASP cc_start: 0.8826 (t70) cc_final: 0.8592 (t70) REVERT: D 633 LYS cc_start: 0.9366 (mmmm) cc_final: 0.8978 (mmtm) REVERT: D 655 LYS cc_start: 0.8886 (pttp) cc_final: 0.8535 (mmmt) REVERT: H 51 MET cc_start: 0.1180 (ttm) cc_final: 0.0796 (ttm) REVERT: H 55 GLU cc_start: 0.5280 (mm-30) cc_final: 0.5052 (mm-30) REVERT: L 4 MET cc_start: 0.5527 (ptp) cc_final: 0.5306 (mpp) REVERT: M 100 LYS cc_start: 0.9468 (mmmm) cc_final: 0.8813 (tmtt) REVERT: M 103 LYS cc_start: 0.9074 (mmmt) cc_final: 0.8616 (mmtm) REVERT: M 105 THR cc_start: 0.8017 (m) cc_final: 0.7766 (p) REVERT: Q 82 PHE cc_start: 0.8594 (t80) cc_final: 0.8318 (t80) REVERT: R 46 LEU cc_start: 0.9195 (mp) cc_final: 0.8776 (mp) REVERT: c 83 GLU cc_start: 0.8795 (pt0) cc_final: 0.8366 (pm20) REVERT: c 95 MET cc_start: 0.8913 (ptp) cc_final: 0.8570 (pmm) REVERT: c 123 THR cc_start: 0.9183 (p) cc_final: 0.8724 (t) REVERT: c 140 ASP cc_start: 0.7512 (m-30) cc_final: 0.6858 (t70) REVERT: c 259 LEU cc_start: 0.8818 (mp) cc_final: 0.8585 (pp) REVERT: c 321 ASP cc_start: 0.8221 (t0) cc_final: 0.8007 (t0) REVERT: c 370 GLU cc_start: 0.7731 (pm20) cc_final: 0.7479 (pm20) REVERT: c 425 ASN cc_start: 0.8992 (t0) cc_final: 0.8550 (t0) REVERT: c 434 MET cc_start: 0.7971 (ttm) cc_final: 0.7771 (mtp) REVERT: c 466 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7927 (mp0) REVERT: c 492 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8441 (mp0) REVERT: d 530 MET cc_start: 0.7675 (mmp) cc_final: 0.7294 (mmp) REVERT: d 589 ASP cc_start: 0.8778 (m-30) cc_final: 0.8469 (m-30) REVERT: d 632 ASP cc_start: 0.8720 (t70) cc_final: 0.8519 (t70) REVERT: d 633 LYS cc_start: 0.9145 (mmmm) cc_final: 0.8747 (ptpp) REVERT: d 655 LYS cc_start: 0.9384 (mmmm) cc_final: 0.8974 (pttp) REVERT: n 30 SER cc_start: 0.9328 (m) cc_final: 0.8816 (p) REVERT: q 19 LYS cc_start: 0.7948 (mmpt) cc_final: 0.7738 (tppt) REVERT: q 28 ASN cc_start: 0.8941 (t0) cc_final: 0.8655 (t0) REVERT: q 52 LYS cc_start: 0.9307 (mtmm) cc_final: 0.8658 (mtmm) REVERT: q 76 ASP cc_start: 0.8623 (m-30) cc_final: 0.8335 (m-30) REVERT: r 46 LEU cc_start: 0.9460 (mp) cc_final: 0.9217 (mp) outliers start: 1 outliers final: 0 residues processed: 481 average time/residue: 0.1996 time to fit residues: 152.8548 Evaluate side-chains 373 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 180 optimal weight: 3.9990 chunk 254 optimal weight: 0.4980 chunk 228 optimal weight: 0.9980 chunk 372 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 300 optimal weight: 2.9990 chunk 367 optimal weight: 0.9990 chunk 200 optimal weight: 10.0000 chunk 271 optimal weight: 0.2980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 42 GLN ** 7 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 HIS ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 105 GLN ** c 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.090475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.063613 restraints weight = 124375.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.065914 restraints weight = 66120.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.067413 restraints weight = 43933.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.068336 restraints weight = 33494.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.068984 restraints weight = 28224.380| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32778 Z= 0.130 Angle : 0.711 14.051 44787 Z= 0.347 Chirality : 0.046 0.281 5322 Planarity : 0.005 0.075 5454 Dihedral : 7.923 73.742 6945 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: -1.16 (0.14), residues: 3786 helix: 0.84 (0.27), residues: 411 sheet: -0.60 (0.14), residues: 1251 loop : -1.20 (0.14), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 3 31 TYR 0.025 0.001 TYR D 586 PHE 0.021 0.001 PHE d 519 TRP 0.046 0.002 TRP m 34 HIS 0.003 0.001 HIS m 52 Details of bonding type rmsd covalent geometry : bond 0.00293 (32598) covalent geometry : angle 0.68201 (44292) SS BOND : bond 0.00259 ( 45) SS BOND : angle 1.54150 ( 90) hydrogen bonds : bond 0.03387 ( 1043) hydrogen bonds : angle 5.33638 ( 2832) link_ALPHA1-2 : bond 0.00602 ( 6) link_ALPHA1-2 : angle 1.70694 ( 18) link_ALPHA1-3 : bond 0.00789 ( 18) link_ALPHA1-3 : angle 1.59595 ( 54) link_ALPHA1-6 : bond 0.00594 ( 9) link_ALPHA1-6 : angle 1.51129 ( 27) link_BETA1-4 : bond 0.00384 ( 57) link_BETA1-4 : angle 2.56165 ( 171) link_NAG-ASN : bond 0.00322 ( 45) link_NAG-ASN : angle 1.87700 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6902.03 seconds wall clock time: 120 minutes 6.96 seconds (7206.96 seconds total)