Starting phenix.real_space_refine on Sun Sep 29 07:55:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ur6_26706/09_2024/7ur6_26706.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ur6_26706/09_2024/7ur6_26706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ur6_26706/09_2024/7ur6_26706.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ur6_26706/09_2024/7ur6_26706.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ur6_26706/09_2024/7ur6_26706.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ur6_26706/09_2024/7ur6_26706.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.025 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 129 5.16 5 C 13497 2.51 5 N 3429 2.21 5 O 4578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21633 Number of models: 1 Model: "" Number of chains: 60 Chain: "G" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3556 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 23, 'TRANS': 428} Chain breaks: 4 Chain: "B" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1045 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1021 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3556 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 23, 'TRANS': 428} Chain breaks: 4 Chain: "C" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1045 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "D" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1021 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "F" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3556 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 23, 'TRANS': 428} Chain breaks: 4 Chain: "I" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1045 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "J" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1021 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "K" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" 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: "P" 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: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" 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: 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: "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: 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: 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: "Y" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: "d" 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: "e" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 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: "m" 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: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 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: "r" 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: "s" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 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: 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: 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: "1" 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" 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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 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: "F" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "I" 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: 14.43, per 1000 atoms: 0.67 Number of scatterers: 21633 At special positions: 0 Unit cell: (148.371, 153.786, 124.545, 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 129 16.00 O 4578 8.00 N 3429 7.00 C 13497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.04 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " 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 P 5 " - " MAN P 6 " " MAN P 8 " - " MAN P 9 " " MAN Q 4 " - " MAN Q 5 " " MAN d 5 " - " MAN d 6 " " MAN d 8 " - " MAN d 9 " " MAN e 4 " - " MAN e 5 " " MAN r 5 " - " MAN r 6 " " MAN r 8 " - " MAN r 9 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 8 " " MAN P 4 " - " MAN P 7 " " BMA Q 3 " - " MAN Q 4 " " BMA Y 3 " - " MAN Y 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 8 " " MAN d 4 " - " MAN d 7 " " BMA e 3 " - " MAN e 4 " " BMA m 3 " - " MAN m 4 " " BMA q 3 " - " MAN q 4 " " BMA r 3 " - " MAN r 8 " " MAN r 4 " - " MAN r 7 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA 0 3 " - " MAN 0 5 " " BMA O 3 " - " MAN O 5 " " BMA P 3 " - " MAN P 4 " " MAN P 4 " - " MAN P 5 " " BMA Q 3 " - " MAN Q 6 " " BMA Y 3 " - " MAN Y 5 " " BMA c 3 " - " MAN c 5 " " BMA d 3 " - " MAN d 4 " " MAN d 4 " - " MAN d 5 " " BMA e 3 " - " MAN e 6 " " BMA m 3 " - " MAN m 5 " " BMA q 3 " - " MAN q 5 " " BMA r 3 " - " MAN r 4 " " MAN r 4 " - " MAN r 5 " " BMA s 3 " - " MAN s 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " 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 X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG 0 1 " - " ASN F 339 " " NAG 1 1 " - " ASN I 637 " " NAG A 601 " - " ASN A 130 " " NAG A 602 " - " ASN A 230 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 289 " " NAG A 606 " - " ASN A 301 " " NAG A 607 " - " ASN A 332 " " NAG A 608 " - " ASN A 386 " " NAG A 609 " - " ASN A 442 " " NAG A 610 " - " ASN A 448 " " NAG A 611 " - " ASN A 133 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 625 " " NAG B 703 " - " ASN B 616 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 625 " " NAG C 703 " - " ASN C 616 " " NAG F 601 " - " ASN F 130 " " NAG F 602 " - " ASN F 230 " " NAG F 603 " - " ASN F 234 " " NAG F 604 " - " ASN F 276 " " NAG F 605 " - " ASN F 289 " " NAG F 606 " - " ASN F 301 " " NAG F 607 " - " ASN F 332 " " NAG F 608 " - " ASN F 386 " " NAG F 609 " - " ASN F 442 " " NAG F 610 " - " ASN F 448 " " NAG F 611 " - " ASN F 133 " " NAG G 601 " - " ASN G 130 " " NAG G 602 " - " ASN G 230 " " NAG G 603 " - " ASN G 234 " " NAG G 604 " - " ASN G 276 " " NAG G 605 " - " ASN G 289 " " NAG G 606 " - " ASN G 301 " " NAG G 607 " - " ASN G 332 " " NAG G 608 " - " ASN G 386 " " NAG G 609 " - " ASN G 442 " " NAG G 610 " - " ASN G 448 " " NAG G 611 " - " ASN G 133 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 625 " " NAG I 703 " - " ASN I 616 " " NAG M 1 " - " ASN G 156 " " NAG N 1 " - " ASN G 197 " " NAG O 1 " - " ASN G 262 " " NAG P 1 " - " ASN G 241 " " NAG Q 1 " - " ASN G 88 " " NAG R 1 " - " ASN G 160 " " NAG S 1 " - " ASN G 407 " " NAG T 1 " - " ASN G 402 " " NAG U 1 " - " ASN G 398 " " NAG V 1 " - " ASN G 358 " " NAG W 1 " - " ASN G 362 " " NAG X 1 " - " ASN G 392 " " NAG Y 1 " - " ASN G 339 " " NAG Z 1 " - " ASN B 637 " " NAG a 1 " - " ASN A 156 " " NAG b 1 " - " ASN A 197 " " NAG c 1 " - " ASN A 262 " " NAG d 1 " - " ASN A 241 " " NAG e 1 " - " ASN A 88 " " NAG f 1 " - " ASN A 160 " " NAG g 1 " - " ASN A 407 " " NAG h 1 " - " ASN A 402 " " NAG i 1 " - " ASN A 398 " " NAG j 1 " - " ASN A 358 " " NAG k 1 " - " ASN A 362 " " NAG l 1 " - " ASN A 392 " " NAG m 1 " - " ASN A 339 " " NAG n 1 " - " ASN C 637 " " NAG o 1 " - " ASN F 156 " " NAG p 1 " - " ASN F 197 " " NAG q 1 " - " ASN F 262 " " NAG r 1 " - " ASN F 241 " " NAG s 1 " - " ASN F 88 " " NAG t 1 " - " ASN F 160 " " NAG u 1 " - " ASN F 407 " " NAG v 1 " - " ASN F 402 " " NAG w 1 " - " ASN F 398 " " NAG x 1 " - " ASN F 358 " " NAG y 1 " - " ASN F 362 " " NAG z 1 " - " ASN F 392 " Time building additional restraints: 8.25 Conformation dependent library (CDL) restraints added in 2.8 seconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4572 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 48 sheets defined 20.2% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 98 through 117 removed outlier: 3.929A pdb=" N ASP G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU G 106 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 335 through 353 removed outlier: 3.774A pdb=" N GLU G 351 " --> pdb=" O ARG G 347 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N HIS G 352 " --> pdb=" O LYS G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.535A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 406 removed outlier: 3.569A pdb=" N ALA G 405 " --> pdb=" O ASN G 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 481 removed outlier: 3.574A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 544 removed outlier: 4.233A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 597 removed outlier: 3.625A pdb=" N VAL B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.514A pdb=" N ASN B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.661A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.531A pdb=" N LYS H 64 " --> pdb=" O LEU H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.632A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.876A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.501A pdb=" N THR A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N HIS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.562A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 406 removed outlier: 3.560A pdb=" N ALA A 405 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.583A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 544 removed outlier: 4.274A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 544 " --> pdb=" O GLN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 597 removed outlier: 3.634A pdb=" N VAL C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 624 removed outlier: 3.514A pdb=" N ASN C 624 " --> pdb=" O GLU C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 662 removed outlier: 3.673A pdb=" N GLU C 657 " --> pdb=" O GLN C 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.579A pdb=" N LYS D 64 " --> pdb=" O LEU D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.628A pdb=" N THR D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 74 Processing helix chain 'F' and resid 98 through 117 removed outlier: 3.952A pdb=" N ASP F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE F 109 " --> pdb=" O HIS F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 195 through 198 Processing helix chain 'F' and resid 335 through 353 removed outlier: 3.765A pdb=" N GLU F 351 " --> pdb=" O ARG F 347 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HIS F 352 " --> pdb=" O LYS F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.533A pdb=" N THR F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 406 removed outlier: 3.569A pdb=" N ALA F 405 " --> pdb=" O ASN F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 484 removed outlier: 3.629A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 544 removed outlier: 4.272A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA I 541 " --> pdb=" O LEU I 537 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN I 543 " --> pdb=" O VAL I 539 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU I 544 " --> pdb=" O GLN I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 569 through 597 removed outlier: 3.675A pdb=" N VAL I 589 " --> pdb=" O ARG I 585 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 624 removed outlier: 3.528A pdb=" N ASN I 624 " --> pdb=" O GLU I 620 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 662 removed outlier: 3.670A pdb=" N GLU I 657 " --> pdb=" O GLN I 653 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.613A pdb=" N LYS J 64 " --> pdb=" O LEU J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.608A pdb=" N THR J 87 " --> pdb=" O PRO J 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 494 through 499 removed outlier: 3.532A pdb=" N ALA G 497 " --> pdb=" O THR G 37 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N TYR G 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N CYS B 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'G' and resid 202 through 203 removed outlier: 7.438A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.434A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY G 451 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 10.900A pdb=" N GLU G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 12.033A pdb=" N LEU G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 12.335A pdb=" N LEU G 288 " --> pdb=" O LEU G 453 " (cutoff:3.500A) removed outlier: 10.947A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.037A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 284 through 298 current: chain 'G' and resid 359 through 361 removed outlier: 3.753A pdb=" N GLY G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 271 through 273 removed outlier: 11.037A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.947A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 12.335A pdb=" N LEU G 288 " --> pdb=" O LEU G 453 " (cutoff:3.500A) removed outlier: 12.033A pdb=" N LEU G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 10.900A pdb=" N GLU G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY G 451 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 443 through 456 current: chain 'G' and resid 413 through 415 Processing sheet with id=AB1, first strand: chain 'G' and resid 302 through 312 removed outlier: 6.489A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 374 through 378 removed outlier: 3.617A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 513 through 514 removed outlier: 7.071A pdb=" N ASP H 100H" --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N TYR H 100 " --> pdb=" O ASP H 100H" (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL H 100J" --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ARG H 98 " --> pdb=" O VAL H 100J" (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL H 100L" --> pdb=" O ARG H 96 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG H 96 " --> pdb=" O VAL H 100L" (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 513 through 514 removed outlier: 7.071A pdb=" N ASP H 100H" --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N TYR H 100 " --> pdb=" O ASP H 100H" (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL H 100J" --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ARG H 98 " --> pdb=" O VAL H 100J" (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL H 100L" --> pdb=" O ARG H 96 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG H 96 " --> pdb=" O VAL H 100L" (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLY H 35 " --> pdb=" O ILE H 95 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE H 35A" --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLY H 50 " --> pdb=" O ILE H 35A" (cutoff:3.500A) removed outlier: 6.840A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.737A pdb=" N THR H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.576A pdb=" N ILE L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS L 23 " --> pdb=" O ALA L 71 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.565A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE L 97 " --> pdb=" O THR L 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 494 through 499 removed outlier: 3.512A pdb=" N ALA A 497 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL C 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL A 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N THR C 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N TYR A 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N CYS C 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'A' and resid 154 through 162 Processing sheet with id=AC3, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AC4, first strand: chain 'A' and resid 202 through 203 removed outlier: 7.415A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.391A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.965A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.036A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.368A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.001A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 359 through 361 removed outlier: 3.637A pdb=" N GLY A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.001A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.368A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.036A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.965A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 413 through 415 Processing sheet with id=AC7, first strand: chain 'A' and resid 302 through 312 removed outlier: 6.539A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.610A pdb=" N PHE A 376 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 513 through 514 removed outlier: 7.024A pdb=" N ASP D 100H" --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TYR D 100 " --> pdb=" O ASP D 100H" (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL D 100J" --> pdb=" O ARG D 98 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ARG D 98 " --> pdb=" O VAL D 100J" (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL D 100L" --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG D 96 " --> pdb=" O VAL D 100L" (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 513 through 514 removed outlier: 7.024A pdb=" N ASP D 100H" --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TYR D 100 " --> pdb=" O ASP D 100H" (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL D 100J" --> pdb=" O ARG D 98 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ARG D 98 " --> pdb=" O VAL D 100J" (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL D 100L" --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG D 96 " --> pdb=" O VAL D 100L" (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLY D 35 " --> pdb=" O ILE D 95 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE D 35A" --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY D 50 " --> pdb=" O ILE D 35A" (cutoff:3.500A) removed outlier: 6.898A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.755A pdb=" N THR D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 25 " --> pdb=" O THR D 3 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 19 through 24 removed outlier: 3.584A pdb=" N ILE E 21 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS E 23 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.547A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 494 through 499 removed outlier: 3.517A pdb=" N ALA F 497 " --> pdb=" O THR F 37 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AD7, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AD8, first strand: chain 'F' and resid 66 through 67 removed outlier: 6.893A pdb=" N HIS F 66 " --> pdb=" O THR F 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AE1, first strand: chain 'F' and resid 130 through 133 Processing sheet with id=AE2, first strand: chain 'F' and resid 181 through 183 Processing sheet with id=AE3, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.416A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL F 292 " --> pdb=" O ILE F 449 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLY F 451 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 10.858A pdb=" N GLU F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 12.005A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 12.270A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 10.975A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.109A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 284 through 298 current: chain 'F' and resid 359 through 361 removed outlier: 3.755A pdb=" N GLY F 393 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 271 through 273 removed outlier: 11.109A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 10.975A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 12.270A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 12.005A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.858A pdb=" N GLU F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLY F 451 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL F 292 " --> pdb=" O ILE F 449 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 443 through 456 current: chain 'F' and resid 413 through 415 Processing sheet with id=AE5, first strand: chain 'F' and resid 302 through 312 removed outlier: 6.514A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 374 through 378 removed outlier: 3.627A pdb=" N PHE F 376 " --> pdb=" O PHE F 383 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 423 through 424 removed outlier: 3.706A pdb=" N ILE F 424 " --> pdb=" O MET F 434 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 513 through 514 removed outlier: 7.098A pdb=" N ASP J 100H" --> pdb=" O TYR J 100 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N TYR J 100 " --> pdb=" O ASP J 100H" (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL J 100J" --> pdb=" O ARG J 98 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ARG J 98 " --> pdb=" O VAL J 100J" (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL J 100L" --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG J 96 " --> pdb=" O VAL J 100L" (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA J 88 " --> pdb=" O VAL J 109 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 513 through 514 removed outlier: 7.098A pdb=" N ASP J 100H" --> pdb=" O TYR J 100 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N TYR J 100 " --> pdb=" O ASP J 100H" (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL J 100J" --> pdb=" O ARG J 98 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ARG J 98 " --> pdb=" O VAL J 100J" (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL J 100L" --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG J 96 " --> pdb=" O VAL J 100L" (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLY J 35 " --> pdb=" O ILE J 95 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE J 35A" --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLY J 50 " --> pdb=" O ILE J 35A" (cutoff:3.500A) removed outlier: 6.934A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.716A pdb=" N THR J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR J 21 " --> pdb=" O SER J 7 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 19 through 24 removed outlier: 3.619A pdb=" N ILE K 21 " --> pdb=" O LEU K 73 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS K 23 " --> pdb=" O ALA K 71 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.573A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 665 hydrogen bonds defined for protein. 1743 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: 7.52 Time building geometry restraints manager: 9.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6506 1.35 - 1.47: 5853 1.47 - 1.59: 9508 1.59 - 1.71: 0 1.71 - 1.83: 174 Bond restraints: 22041 Sorted by residual: bond pdb=" C1 BMA Y 3 " pdb=" C2 BMA Y 3 " ideal model delta sigma weight residual 1.519 1.588 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1 BMA m 3 " pdb=" C2 BMA m 3 " ideal model delta sigma weight residual 1.519 1.587 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C1 BMA 0 3 " pdb=" C2 BMA 0 3 " ideal model delta sigma weight residual 1.519 1.586 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C1 BMA X 3 " pdb=" C2 BMA X 3 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.78e+00 bond pdb=" C1 BMA l 3 " pdb=" C2 BMA l 3 " ideal model delta sigma weight residual 1.519 1.557 -0.038 2.00e-02 2.50e+03 3.70e+00 ... (remaining 22036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 28275 1.58 - 3.16: 1282 3.16 - 4.74: 282 4.74 - 6.32: 89 6.32 - 7.91: 15 Bond angle restraints: 29943 Sorted by residual: angle pdb=" CA GLU G 164 " pdb=" C GLU G 164 " pdb=" O GLU G 164 " ideal model delta sigma weight residual 120.55 116.89 3.66 1.06e+00 8.90e-01 1.19e+01 angle pdb=" N GLU G 164 " pdb=" CA GLU G 164 " pdb=" C GLU G 164 " ideal model delta sigma weight residual 111.28 107.57 3.71 1.09e+00 8.42e-01 1.16e+01 angle pdb=" O GLU G 164 " pdb=" C GLU G 164 " pdb=" N ILE G 165 " ideal model delta sigma weight residual 122.12 125.46 -3.34 1.06e+00 8.90e-01 9.91e+00 angle pdb=" N VAL K 39 " pdb=" CA VAL K 39 " pdb=" C VAL K 39 " ideal model delta sigma weight residual 109.02 106.10 2.92 9.30e-01 1.16e+00 9.88e+00 angle pdb=" N GLU F 164 " pdb=" CA GLU F 164 " pdb=" C GLU F 164 " ideal model delta sigma weight residual 111.82 108.22 3.60 1.16e+00 7.43e-01 9.64e+00 ... (remaining 29938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.21: 14061 24.21 - 48.42: 1085 48.42 - 72.63: 146 72.63 - 96.84: 116 96.84 - 121.05: 63 Dihedral angle restraints: 15471 sinusoidal: 8367 harmonic: 7104 Sorted by residual: dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -143.45 57.45 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -143.44 57.44 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -143.18 57.18 1 1.00e+01 1.00e-02 4.40e+01 ... (remaining 15468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 3654 0.105 - 0.210: 243 0.210 - 0.315: 21 0.315 - 0.420: 0 0.420 - 0.525: 6 Chirality restraints: 3924 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN G 398 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.89e+00 chirality pdb=" C1 NAG w 1 " pdb=" ND2 ASN F 398 " pdb=" C2 NAG w 1 " pdb=" O5 NAG w 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.85e+00 chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN A 398 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.73e+00 ... (remaining 3921 not shown) Planarity restraints: 3615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 39 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO D 40 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 40 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 40 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO J 40 " 0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO J 41 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO J 41 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 41 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 78 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO G 79 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO G 79 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 79 " -0.027 5.00e-02 4.00e+02 ... (remaining 3612 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 406 2.64 - 3.21: 19600 3.21 - 3.77: 30846 3.77 - 4.34: 43053 4.34 - 4.90: 71166 Nonbonded interactions: 165071 Sorted by model distance: nonbonded pdb=" OG SER K 12 " pdb=" O ILE K 105 " model vdw 2.075 3.040 nonbonded pdb=" OG SER E 12 " pdb=" O ILE E 105 " model vdw 2.083 3.040 nonbonded pdb=" OG SER L 12 " pdb=" O ILE L 105 " model vdw 2.084 3.040 nonbonded pdb=" OG1 THR A 404 " pdb=" O5 NAG h 1 " model vdw 2.103 3.040 nonbonded pdb=" OG1 THR G 404 " pdb=" O5 NAG T 1 " model vdw 2.106 3.040 ... (remaining 165066 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'O' selection = chain 'Y' selection = chain 'c' selection = chain 'm' selection = chain 'q' } ncs_group { reference = chain '1' selection = chain 'M' selection = chain 'N' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'P' selection = chain 'd' selection = chain 'r' } ncs_group { reference = chain 'Q' selection = chain 'e' selection = chain 's' } ncs_group { reference = chain 'X' selection = chain 'l' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.040 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 52.750 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.005 0.069 22041 Z= 0.316 Angle : 0.809 7.906 29943 Z= 0.342 Chirality : 0.056 0.525 3924 Planarity : 0.004 0.074 3531 Dihedral : 18.664 121.048 10773 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.23 % Allowed : 17.83 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2412 helix: 0.97 (0.29), residues: 375 sheet: -0.05 (0.20), residues: 720 loop : -0.45 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 47 HIS 0.004 0.000 HIS F 66 PHE 0.004 0.001 PHE G 210 TYR 0.008 0.001 TYR K 36 ARG 0.010 0.001 ARG I 617 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 418 time to evaluate : 2.497 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: G 449 ILE cc_start: 0.9015 (mt) cc_final: 0.8772 (tt) REVERT: B 652 GLN cc_start: 0.8477 (tp-100) cc_final: 0.7848 (tp40) REVERT: H 46 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7716 (tm-30) REVERT: H 82 ASN cc_start: 0.8644 (t0) cc_final: 0.8184 (t0) REVERT: H 86 ASP cc_start: 0.8876 (t0) cc_final: 0.8640 (t0) REVERT: H 90 TYR cc_start: 0.8276 (m-80) cc_final: 0.8056 (m-10) REVERT: L 28 ILE cc_start: 0.9207 (mm) cc_final: 0.8790 (tt) REVERT: L 78 LEU cc_start: 0.8240 (tp) cc_final: 0.7950 (tt) REVERT: L 82 ASP cc_start: 0.8373 (m-30) cc_final: 0.7977 (m-30) REVERT: L 85 ASP cc_start: 0.7700 (m-30) cc_final: 0.7295 (m-30) REVERT: A 217 TYR cc_start: 0.7360 (m-80) cc_final: 0.7050 (m-80) REVERT: C 652 GLN cc_start: 0.8470 (tp-100) cc_final: 0.7870 (tp40) REVERT: D 46 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7201 (tm-30) REVERT: D 82 ASN cc_start: 0.8823 (t0) cc_final: 0.8577 (t0) REVERT: D 82 MET cc_start: 0.7854 (mpp) cc_final: 0.7505 (mpp) REVERT: D 95 ILE cc_start: 0.9052 (pt) cc_final: 0.8785 (pt) REVERT: E 28 ILE cc_start: 0.9300 (mm) cc_final: 0.8944 (tt) REVERT: E 78 LEU cc_start: 0.8159 (mp) cc_final: 0.7862 (tt) REVERT: F 426 MET cc_start: 0.7639 (ttm) cc_final: 0.6807 (ttp) REVERT: F 434 MET cc_start: 0.7419 (mtm) cc_final: 0.7144 (mtm) REVERT: I 648 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8330 (tm-30) REVERT: J 29 MET cc_start: 0.8905 (mmm) cc_final: 0.8698 (tpt) REVERT: J 46 GLU cc_start: 0.7706 (tm-30) cc_final: 0.6890 (tm-30) REVERT: J 82 ASN cc_start: 0.8797 (t0) cc_final: 0.8334 (t0) REVERT: K 28 ILE cc_start: 0.9380 (mm) cc_final: 0.8996 (tt) outliers start: 5 outliers final: 3 residues processed: 423 average time/residue: 0.3624 time to fit residues: 227.1437 Evaluate side-chains 309 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 306 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 339 ASN Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain F residue 339 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 0.0040 chunk 124 optimal weight: 0.0970 chunk 98 optimal weight: 0.9990 chunk 190 optimal weight: 0.0970 chunk 73 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 220 optimal weight: 8.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN L 31 ASN C 653 GLN E 31 ASN E 79 GLN F 280 ASN F 336 GLN F 343 GLN F 374 HIS I 653 GLN J 100CASN K 79 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22041 Z= 0.183 Angle : 0.666 9.069 29943 Z= 0.318 Chirality : 0.049 0.389 3924 Planarity : 0.004 0.049 3531 Dihedral : 14.609 116.826 6306 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.00 % Allowed : 18.66 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2412 helix: 1.37 (0.28), residues: 399 sheet: 0.26 (0.21), residues: 675 loop : -0.74 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 427 HIS 0.003 0.001 HIS G 216 PHE 0.009 0.001 PHE B 522 TYR 0.016 0.001 TYR J 90 ARG 0.007 0.001 ARG E 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 325 time to evaluate : 2.390 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: G 154 MET cc_start: 0.6613 (mtm) cc_final: 0.6292 (mtm) REVERT: G 449 ILE cc_start: 0.9272 (mt) cc_final: 0.9060 (tt) REVERT: B 652 GLN cc_start: 0.8016 (tp-100) cc_final: 0.7439 (tp40) REVERT: H 46 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7696 (tm-30) REVERT: H 82 ASN cc_start: 0.8752 (t0) cc_final: 0.8337 (t0) REVERT: H 86 ASP cc_start: 0.8955 (t0) cc_final: 0.8678 (t0) REVERT: L 28 ILE cc_start: 0.9316 (mm) cc_final: 0.8927 (tt) REVERT: L 54 ARG cc_start: 0.8817 (ptt180) cc_final: 0.8581 (ptt180) REVERT: L 82 ASP cc_start: 0.8486 (m-30) cc_final: 0.8157 (m-30) REVERT: C 652 GLN cc_start: 0.7965 (tp-100) cc_final: 0.7360 (tp40) REVERT: D 46 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7345 (tm-30) REVERT: E 28 ILE cc_start: 0.9305 (mm) cc_final: 0.8971 (tt) REVERT: F 104 MET cc_start: 0.8241 (ppp) cc_final: 0.7958 (ttt) REVERT: I 575 GLN cc_start: 0.8954 (tt0) cc_final: 0.8752 (tt0) REVERT: I 630 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7970 (mt-10) REVERT: J 46 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7099 (tm-30) REVERT: J 82 ASN cc_start: 0.8907 (t0) cc_final: 0.8525 (t0) REVERT: K 28 ILE cc_start: 0.9426 (mm) cc_final: 0.9215 (tt) REVERT: K 78 LEU cc_start: 0.8120 (tt) cc_final: 0.7681 (tt) REVERT: K 85 ASP cc_start: 0.7865 (m-30) cc_final: 0.7537 (m-30) outliers start: 43 outliers final: 17 residues processed: 358 average time/residue: 0.3389 time to fit residues: 185.4692 Evaluate side-chains 303 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 286 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 339 ASN Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain G residue 401 TYR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain K residue 97 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 221 optimal weight: 8.9990 chunk 238 optimal weight: 0.0670 chunk 196 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN K 53 GLN K 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22041 Z= 0.247 Angle : 0.644 9.636 29943 Z= 0.308 Chirality : 0.048 0.400 3924 Planarity : 0.004 0.047 3531 Dihedral : 13.225 116.759 6304 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.37 % Allowed : 19.55 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2412 helix: 1.50 (0.29), residues: 402 sheet: 0.35 (0.22), residues: 636 loop : -0.82 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 427 HIS 0.005 0.001 HIS G 396 PHE 0.011 0.001 PHE G 53 TYR 0.015 0.002 TYR B 586 ARG 0.008 0.001 ARG K 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 289 time to evaluate : 2.325 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: G 217 TYR cc_start: 0.7334 (m-80) cc_final: 0.7104 (m-80) REVERT: H 82 ASN cc_start: 0.8741 (t0) cc_final: 0.8344 (t0) REVERT: L 28 ILE cc_start: 0.9306 (mm) cc_final: 0.8922 (tt) REVERT: L 54 ARG cc_start: 0.8807 (ptt180) cc_final: 0.8492 (ptt180) REVERT: L 82 ASP cc_start: 0.8428 (m-30) cc_final: 0.8076 (m-30) REVERT: A 434 MET cc_start: 0.7896 (ptp) cc_final: 0.7530 (ptp) REVERT: C 642 ILE cc_start: 0.9346 (mt) cc_final: 0.9024 (mm) REVERT: C 652 GLN cc_start: 0.8297 (tp-100) cc_final: 0.7668 (tp40) REVERT: D 35 TYR cc_start: 0.8630 (m-10) cc_final: 0.8371 (m-80) REVERT: D 46 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7571 (tm-30) REVERT: E 28 ILE cc_start: 0.9289 (mm) cc_final: 0.8960 (tt) REVERT: F 84 MET cc_start: 0.8829 (tpp) cc_final: 0.8396 (tpp) REVERT: F 217 TYR cc_start: 0.7864 (m-80) cc_final: 0.7347 (m-80) REVERT: I 630 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7970 (mt-10) REVERT: J 46 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7200 (tm-30) REVERT: J 82 ASN cc_start: 0.8904 (t0) cc_final: 0.8573 (t0) REVERT: K 28 ILE cc_start: 0.9427 (mm) cc_final: 0.9085 (tt) REVERT: K 85 ASP cc_start: 0.8208 (m-30) cc_final: 0.7783 (m-30) REVERT: K 90 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8642 (m) REVERT: K 103 ARG cc_start: 0.8769 (mmm-85) cc_final: 0.8359 (mmm160) outliers start: 51 outliers final: 31 residues processed: 326 average time/residue: 0.3403 time to fit residues: 168.8270 Evaluate side-chains 300 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 268 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 151 PHE Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 327 ARG Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain C residue 601 LYS Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 151 PHE Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain I residue 523 LEU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 95 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 221 optimal weight: 0.0870 chunk 234 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 210 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 396 HIS K 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22041 Z= 0.161 Angle : 0.621 9.621 29943 Z= 0.292 Chirality : 0.048 0.389 3924 Planarity : 0.003 0.045 3531 Dihedral : 12.058 116.787 6300 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.95 % Allowed : 21.03 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2412 helix: 1.56 (0.29), residues: 402 sheet: 0.48 (0.22), residues: 603 loop : -0.82 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS A 396 PHE 0.007 0.001 PHE L 98 TYR 0.012 0.001 TYR F 217 ARG 0.009 0.001 ARG K 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 296 time to evaluate : 2.412 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: G 217 TYR cc_start: 0.7318 (m-80) cc_final: 0.7048 (m-80) REVERT: G 401 TYR cc_start: 0.5742 (OUTLIER) cc_final: 0.5427 (m-80) REVERT: H 82 ASN cc_start: 0.8706 (t0) cc_final: 0.8306 (t0) REVERT: L 28 ILE cc_start: 0.9308 (mm) cc_final: 0.8957 (tt) REVERT: A 84 MET cc_start: 0.8311 (tpp) cc_final: 0.7965 (tpp) REVERT: C 588 GLU cc_start: 0.7973 (pt0) cc_final: 0.7655 (pt0) REVERT: C 652 GLN cc_start: 0.8283 (tp-100) cc_final: 0.7489 (tp40) REVERT: C 656 ASN cc_start: 0.8608 (p0) cc_final: 0.8357 (p0) REVERT: D 35 TYR cc_start: 0.8524 (m-10) cc_final: 0.8309 (m-10) REVERT: D 46 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7503 (tm-30) REVERT: E 28 ILE cc_start: 0.9249 (mm) cc_final: 0.8920 (tt) REVERT: F 84 MET cc_start: 0.8875 (tpp) cc_final: 0.8357 (tpp) REVERT: I 630 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8007 (mt-10) REVERT: J 46 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7225 (tm-30) REVERT: J 82 ASN cc_start: 0.8874 (t0) cc_final: 0.8510 (t0) REVERT: K 28 ILE cc_start: 0.9426 (mm) cc_final: 0.9111 (tt) REVERT: K 85 ASP cc_start: 0.8022 (m-30) cc_final: 0.7628 (m-30) REVERT: K 103 ARG cc_start: 0.8744 (mmm-85) cc_final: 0.8398 (mmm160) outliers start: 42 outliers final: 20 residues processed: 327 average time/residue: 0.3465 time to fit residues: 172.7505 Evaluate side-chains 292 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 271 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 327 ARG Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain G residue 401 TYR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain K residue 95 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 162 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 210 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 575 GLN I 653 GLN K 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22041 Z= 0.194 Angle : 0.626 9.680 29943 Z= 0.293 Chirality : 0.049 0.401 3924 Planarity : 0.003 0.048 3531 Dihedral : 11.184 116.055 6300 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.86 % Allowed : 22.33 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.17), residues: 2412 helix: 1.61 (0.29), residues: 402 sheet: 0.57 (0.22), residues: 600 loop : -0.83 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 427 HIS 0.004 0.001 HIS A 396 PHE 0.008 0.001 PHE G 53 TYR 0.012 0.001 TYR B 586 ARG 0.011 0.001 ARG C 585 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 281 time to evaluate : 2.335 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: G 154 MET cc_start: 0.6158 (mtm) cc_final: 0.5741 (mtm) REVERT: G 217 TYR cc_start: 0.7449 (m-80) cc_final: 0.7132 (m-80) REVERT: G 401 TYR cc_start: 0.5764 (OUTLIER) cc_final: 0.5472 (m-80) REVERT: H 46 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7650 (tm-30) REVERT: H 82 ASN cc_start: 0.8723 (t0) cc_final: 0.8332 (t0) REVERT: L 28 ILE cc_start: 0.9298 (mm) cc_final: 0.8944 (tt) REVERT: L 78 LEU cc_start: 0.8255 (tt) cc_final: 0.8053 (tt) REVERT: C 652 GLN cc_start: 0.8414 (tp-100) cc_final: 0.8095 (tp40) REVERT: C 656 ASN cc_start: 0.8599 (p0) cc_final: 0.8318 (p0) REVERT: D 35 TYR cc_start: 0.8499 (m-10) cc_final: 0.8292 (m-10) REVERT: D 46 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7525 (tm-30) REVERT: E 28 ILE cc_start: 0.9213 (mm) cc_final: 0.8910 (tt) REVERT: E 78 LEU cc_start: 0.8009 (tt) cc_final: 0.7710 (tt) REVERT: E 103 ARG cc_start: 0.8879 (mmm-85) cc_final: 0.8239 (mmm160) REVERT: F 84 MET cc_start: 0.8902 (tpp) cc_final: 0.8341 (tpp) REVERT: F 426 MET cc_start: 0.8041 (ttm) cc_final: 0.7595 (ttm) REVERT: I 630 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8047 (mt-10) REVERT: J 82 ASN cc_start: 0.8917 (t0) cc_final: 0.8594 (t0) REVERT: K 28 ILE cc_start: 0.9410 (mm) cc_final: 0.9067 (tt) REVERT: K 38 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: K 90 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8614 (m) outliers start: 40 outliers final: 25 residues processed: 313 average time/residue: 0.3399 time to fit residues: 162.3447 Evaluate side-chains 292 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 264 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 327 ARG Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain G residue 401 TYR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 95 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 235 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 336 GLN G 356 ASN L 53 GLN A 94 ASN A 356 ASN A 374 HIS C 619 GLN D 82BASN F 356 ASN I 619 GLN K 53 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.063 22041 Z= 0.606 Angle : 0.870 10.186 29943 Z= 0.408 Chirality : 0.055 0.467 3924 Planarity : 0.005 0.049 3531 Dihedral : 11.277 115.784 6300 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.11 % Allowed : 21.87 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2412 helix: 1.22 (0.28), residues: 384 sheet: 0.50 (0.20), residues: 657 loop : -1.14 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 427 HIS 0.007 0.002 HIS F 330 PHE 0.019 0.002 PHE G 53 TYR 0.025 0.002 TYR F 401 ARG 0.010 0.001 ARG J 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 255 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 154 MET cc_start: 0.6525 (mtm) cc_final: 0.6042 (mtt) REVERT: G 217 TYR cc_start: 0.8046 (m-80) cc_final: 0.7834 (m-80) REVERT: H 46 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7750 (tm-30) REVERT: H 72 ASP cc_start: 0.8567 (t0) cc_final: 0.8036 (p0) REVERT: H 75 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8727 (ttpt) REVERT: H 77 GLN cc_start: 0.8815 (pt0) cc_final: 0.8445 (pt0) REVERT: H 82 ASN cc_start: 0.8923 (t0) cc_final: 0.8610 (t0) REVERT: L 28 ILE cc_start: 0.9339 (mm) cc_final: 0.8996 (tt) REVERT: L 78 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8117 (tp) REVERT: C 646 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9245 (mm) REVERT: C 648 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8343 (tp30) REVERT: D 39 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8545 (tt0) REVERT: D 46 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7591 (tm-30) REVERT: D 71 LYS cc_start: 0.9201 (ptmm) cc_final: 0.8908 (ptmt) REVERT: E 28 ILE cc_start: 0.9236 (mm) cc_final: 0.8921 (tt) REVERT: E 103 ARG cc_start: 0.8959 (mmm-85) cc_final: 0.8367 (mmm160) REVERT: F 84 MET cc_start: 0.8948 (tpp) cc_final: 0.8218 (tpp) REVERT: F 217 TYR cc_start: 0.8451 (m-10) cc_final: 0.8121 (m-80) REVERT: J 46 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7326 (tm-30) REVERT: J 82 ASN cc_start: 0.8971 (t0) cc_final: 0.8695 (t0) REVERT: K 28 ILE cc_start: 0.9496 (mm) cc_final: 0.9127 (tt) REVERT: K 79 GLN cc_start: 0.8634 (mp-120) cc_final: 0.8154 (mp-120) outliers start: 67 outliers final: 43 residues processed: 304 average time/residue: 0.3179 time to fit residues: 150.0420 Evaluate side-chains 295 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 248 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 151 PHE Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 327 ARG Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 53 GLN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 151 PHE Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 291 SER Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 95 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 197 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 234 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 280 ASN C 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22041 Z= 0.216 Angle : 0.707 11.207 29943 Z= 0.333 Chirality : 0.049 0.406 3924 Planarity : 0.004 0.044 3531 Dihedral : 10.581 115.699 6300 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.09 % Allowed : 22.33 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2412 helix: 1.50 (0.29), residues: 384 sheet: 0.59 (0.20), residues: 666 loop : -1.03 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 427 HIS 0.004 0.001 HIS F 216 PHE 0.008 0.001 PHE L 98 TYR 0.021 0.001 TYR F 401 ARG 0.010 0.001 ARG L 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 265 time to evaluate : 2.340 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: G 178 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8765 (tptp) REVERT: G 217 TYR cc_start: 0.7905 (m-80) cc_final: 0.7651 (m-80) REVERT: H 46 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7744 (tm-30) REVERT: H 82 ASN cc_start: 0.8905 (t0) cc_final: 0.8599 (t0) REVERT: L 28 ILE cc_start: 0.9333 (mm) cc_final: 0.8964 (tt) REVERT: L 78 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8155 (tp) REVERT: A 475 MET cc_start: 0.7866 (tmm) cc_final: 0.7548 (tmm) REVERT: C 648 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8256 (tp30) REVERT: C 652 GLN cc_start: 0.8566 (tp-100) cc_final: 0.8219 (tp40) REVERT: D 39 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8460 (tt0) REVERT: D 46 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7702 (tm-30) REVERT: D 71 LYS cc_start: 0.9145 (ptmm) cc_final: 0.8867 (ptmt) REVERT: D 77 GLN cc_start: 0.8607 (pt0) cc_final: 0.8395 (pm20) REVERT: E 28 ILE cc_start: 0.9242 (mm) cc_final: 0.8924 (tt) REVERT: E 103 ARG cc_start: 0.8951 (mmm-85) cc_final: 0.8377 (mmm160) REVERT: F 84 MET cc_start: 0.8897 (tpp) cc_final: 0.8245 (tpp) REVERT: F 217 TYR cc_start: 0.8307 (m-10) cc_final: 0.8093 (m-80) REVERT: J 46 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7615 (tm-30) REVERT: J 82 ASN cc_start: 0.8952 (t0) cc_final: 0.8643 (t0) REVERT: K 28 ILE cc_start: 0.9476 (mm) cc_final: 0.9086 (tt) REVERT: K 90 THR cc_start: 0.8842 (t) cc_final: 0.8581 (m) REVERT: K 103 ARG cc_start: 0.8837 (mmm-85) cc_final: 0.8262 (mmm160) outliers start: 45 outliers final: 28 residues processed: 303 average time/residue: 0.3431 time to fit residues: 160.1658 Evaluate side-chains 277 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 247 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 327 ARG Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain G residue 407 ASN Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 95 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 148 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 213 optimal weight: 0.7980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN C 575 GLN E 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 22041 Z= 0.309 Angle : 0.841 59.191 29943 Z= 0.423 Chirality : 0.051 0.612 3924 Planarity : 0.004 0.045 3531 Dihedral : 10.570 115.628 6300 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.95 % Allowed : 22.70 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.17), residues: 2412 helix: 1.41 (0.29), residues: 384 sheet: 0.56 (0.20), residues: 654 loop : -1.05 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 427 HIS 0.004 0.001 HIS G 396 PHE 0.010 0.001 PHE G 53 TYR 0.021 0.002 TYR D 35B ARG 0.010 0.001 ARG E 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 249 time to evaluate : 2.444 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: G 217 TYR cc_start: 0.7938 (m-80) cc_final: 0.7680 (m-80) REVERT: H 46 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7711 (tm-30) REVERT: H 82 ASN cc_start: 0.8924 (t0) cc_final: 0.8607 (t0) REVERT: L 28 ILE cc_start: 0.9334 (mm) cc_final: 0.8969 (tt) REVERT: L 78 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8211 (tp) REVERT: A 84 MET cc_start: 0.8604 (tpp) cc_final: 0.8151 (tpp) REVERT: C 648 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8262 (tp30) REVERT: C 652 GLN cc_start: 0.8524 (tp-100) cc_final: 0.8319 (tp40) REVERT: D 39 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8470 (tt0) REVERT: D 46 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7707 (tm-30) REVERT: D 71 LYS cc_start: 0.9149 (ptmm) cc_final: 0.8869 (ptmt) REVERT: E 28 ILE cc_start: 0.9257 (mm) cc_final: 0.8926 (tt) REVERT: F 84 MET cc_start: 0.8909 (tpp) cc_final: 0.8246 (tpp) REVERT: F 217 TYR cc_start: 0.8326 (m-80) cc_final: 0.8095 (m-80) REVERT: J 46 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7622 (tm-30) REVERT: J 82 ASN cc_start: 0.8956 (t0) cc_final: 0.8647 (t0) REVERT: K 28 ILE cc_start: 0.9476 (mm) cc_final: 0.9089 (tt) REVERT: K 90 THR cc_start: 0.8869 (t) cc_final: 0.8604 (m) REVERT: K 103 ARG cc_start: 0.8845 (mmm-85) cc_final: 0.8279 (mmm160) outliers start: 42 outliers final: 32 residues processed: 284 average time/residue: 0.3278 time to fit residues: 144.5845 Evaluate side-chains 276 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 242 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 327 ARG Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain G residue 407 ASN Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 95 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 206 optimal weight: 0.9990 chunk 217 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 22041 Z= 0.226 Angle : 0.839 59.162 29943 Z= 0.421 Chirality : 0.054 1.078 3924 Planarity : 0.004 0.043 3531 Dihedral : 10.534 115.716 6300 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.76 % Allowed : 22.70 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2412 helix: 1.43 (0.28), residues: 384 sheet: 0.57 (0.20), residues: 666 loop : -1.04 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 427 HIS 0.003 0.001 HIS F 216 PHE 0.008 0.001 PHE G 53 TYR 0.020 0.001 TYR G 401 ARG 0.012 0.001 ARG E 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 247 time to evaluate : 2.351 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: G 154 MET cc_start: 0.5532 (mtt) cc_final: 0.5174 (mtm) REVERT: G 178 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8773 (tptp) REVERT: G 217 TYR cc_start: 0.7971 (m-80) cc_final: 0.7717 (m-80) REVERT: H 46 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7711 (tm-30) REVERT: H 82 ASN cc_start: 0.8925 (t0) cc_final: 0.8602 (t0) REVERT: L 28 ILE cc_start: 0.9328 (mm) cc_final: 0.8964 (tt) REVERT: L 78 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8176 (tp) REVERT: C 648 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8251 (tp30) REVERT: C 652 GLN cc_start: 0.8519 (tp-100) cc_final: 0.8311 (tp40) REVERT: D 39 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8456 (tt0) REVERT: D 46 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7702 (tm-30) REVERT: D 71 LYS cc_start: 0.9166 (ptmm) cc_final: 0.8868 (ptmt) REVERT: E 28 ILE cc_start: 0.9252 (mm) cc_final: 0.8922 (tt) REVERT: F 84 MET cc_start: 0.8900 (tpp) cc_final: 0.8244 (tpp) REVERT: F 217 TYR cc_start: 0.8289 (m-80) cc_final: 0.8060 (m-80) REVERT: J 46 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7616 (tm-30) REVERT: J 82 ASN cc_start: 0.8950 (t0) cc_final: 0.8669 (t0) REVERT: K 28 ILE cc_start: 0.9472 (mm) cc_final: 0.9086 (tt) REVERT: K 90 THR cc_start: 0.8857 (t) cc_final: 0.8588 (m) REVERT: K 103 ARG cc_start: 0.8844 (mmm-85) cc_final: 0.8283 (mmm160) outliers start: 38 outliers final: 34 residues processed: 279 average time/residue: 0.3306 time to fit residues: 142.4581 Evaluate side-chains 278 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 242 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 327 ARG Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain G residue 407 ASN Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 17 LYS Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 95 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 160 optimal weight: 9.9990 chunk 242 optimal weight: 7.9990 chunk 222 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 118 optimal weight: 0.1980 chunk 153 optimal weight: 0.6980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 22041 Z= 0.226 Angle : 0.839 59.200 29943 Z= 0.421 Chirality : 0.064 2.183 3924 Planarity : 0.004 0.043 3531 Dihedral : 10.534 115.716 6300 Min Nonbonded Distance : 1.598 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.67 % Allowed : 22.93 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2412 helix: 1.43 (0.28), residues: 384 sheet: 0.57 (0.20), residues: 666 loop : -1.04 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 427 HIS 0.003 0.001 HIS F 216 PHE 0.008 0.001 PHE G 53 TYR 0.020 0.001 TYR G 401 ARG 0.012 0.001 ARG E 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 242 time to evaluate : 2.536 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: G 154 MET cc_start: 0.5532 (mtt) cc_final: 0.5174 (mtm) REVERT: G 178 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8773 (tptp) REVERT: G 217 TYR cc_start: 0.7973 (m-80) cc_final: 0.7717 (m-80) REVERT: H 46 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7711 (tm-30) REVERT: H 82 ASN cc_start: 0.8931 (t0) cc_final: 0.8602 (t0) REVERT: L 28 ILE cc_start: 0.9327 (mm) cc_final: 0.8964 (tt) REVERT: L 78 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8176 (tp) REVERT: C 648 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8251 (tp30) REVERT: C 652 GLN cc_start: 0.8519 (tp-100) cc_final: 0.8311 (tp40) REVERT: D 39 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8456 (tt0) REVERT: D 46 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7702 (tm-30) REVERT: D 71 LYS cc_start: 0.9166 (ptmm) cc_final: 0.8868 (ptmt) REVERT: E 28 ILE cc_start: 0.9251 (mm) cc_final: 0.8922 (tt) REVERT: F 84 MET cc_start: 0.8900 (tpp) cc_final: 0.8244 (tpp) REVERT: F 217 TYR cc_start: 0.8290 (m-80) cc_final: 0.8060 (m-80) REVERT: J 46 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7616 (tm-30) REVERT: J 82 ASN cc_start: 0.8979 (t0) cc_final: 0.8669 (t0) REVERT: K 28 ILE cc_start: 0.9472 (mm) cc_final: 0.9086 (tt) REVERT: K 90 THR cc_start: 0.8857 (t) cc_final: 0.8588 (m) REVERT: K 103 ARG cc_start: 0.8847 (mmm-85) cc_final: 0.8283 (mmm160) outliers start: 36 outliers final: 34 residues processed: 272 average time/residue: 0.3244 time to fit residues: 136.9713 Evaluate side-chains 278 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 242 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 327 ARG Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain G residue 407 ASN Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 17 LYS Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 95 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.070034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.053346 restraints weight = 65362.973| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.70 r_work: 0.2683 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 22041 Z= 0.226 Angle : 0.839 59.200 29943 Z= 0.421 Chirality : 0.064 2.183 3924 Planarity : 0.004 0.043 3531 Dihedral : 10.534 115.716 6300 Min Nonbonded Distance : 1.598 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.67 % Allowed : 22.93 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2412 helix: 1.43 (0.28), residues: 384 sheet: 0.57 (0.20), residues: 666 loop : -1.04 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 427 HIS 0.003 0.001 HIS F 216 PHE 0.008 0.001 PHE G 53 TYR 0.020 0.001 TYR G 401 ARG 0.012 0.001 ARG E 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4354.03 seconds wall clock time: 79 minutes 37.87 seconds (4777.87 seconds total)