Starting phenix.real_space_refine on Mon Mar 18 11:35:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fuu_3308/03_2024/5fuu_3308_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fuu_3308/03_2024/5fuu_3308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fuu_3308/03_2024/5fuu_3308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fuu_3308/03_2024/5fuu_3308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fuu_3308/03_2024/5fuu_3308_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fuu_3308/03_2024/5fuu_3308_neut_updated.pdb" } resolution = 4.19 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= 0.000 sd= 0.006 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 116 5.16 5 C 12882 2.51 5 N 3274 2.21 5 O 4463 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20735 Number of models: 1 Model: "" Number of chains: 70 Chain: "A" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3553 Classifications: {'peptide': 449} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "B" Number of atoms: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1150 Classifications: {'peptide': 144} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 141} Chain: "C" Number of atoms: 3506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3506 Classifications: {'peptide': 444} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1159 Classifications: {'peptide': 147} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 142} Chain: "E" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3537 Classifications: {'peptide': 448} Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Chain: "F" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1209 Classifications: {'peptide': 153} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 148} Chain: "H" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1073 Classifications: {'peptide': 135} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "L" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 881 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 107} Chain: "M" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1067 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "N" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 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: "O" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 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: 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: "V" 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: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 135 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 5} 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: "Z" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 160 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 3, 'MAN': 2, 'NAG': 6} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "a" 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 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: "f" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: "n" 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: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 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: "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: 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: "y" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: "0" 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: "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: "2" 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: "3" 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: "4" 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: "5" 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: "6" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "7" 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: "8" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "9" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 135 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 5} 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: "AA" 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: "BA" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 149 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 6} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "A" 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: "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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.33, per 1000 atoms: 0.55 Number of scatterers: 20735 At special positions: 0 Unit cell: (137.55, 153.27, 140.17, 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 116 16.00 O 4463 8.00 N 3274 7.00 C 12882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.02 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 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 M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM20028 O5 NAG 3 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM18843 O5 NAG a 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 8 4 " - " MAN 8 5 " " MAN O 4 " - " MAN O 5 " " MAN f 4 " - " MAN f 5 " " MAN p 4 " - " MAN p 5 " " MAN x 4 " - " MAN x 5 " " MAN y 4 " - " MAN y 5 " ALPHA1-3 " BMA 8 3 " - " MAN 8 4 " " MAN 8 6 " - " MAN 8 7 " " BMA 9 3 " - " MAN 9 9 " " BMA O 3 " - " MAN O 4 " " MAN O 6 " - " MAN O 7 " " BMA Y 3 " - " MAN Y 9 " " BMA Z 3 " - " MAN Z 4 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 4 " " MAN f 6 " - " MAN f 7 " " BMA p 3 " - " MAN p 4 " " MAN p 6 " - " MAN p 7 " " BMA x 3 " - " MAN x 4 " " BMA y 3 " - " MAN y 4 " " MAN y 6 " - " MAN y 7 " " BMABA 3 " - " MANBA 4 " ALPHA1-6 " BMA 6 3 " - " MAN 6 4 " " BMA 8 3 " - " MAN 8 6 " " MAN 8 6 " - " MAN 8 8 " " BMA 9 3 " - " MAN 9 4 " " BMA O 3 " - " MAN O 6 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 9 " " BMA e 3 " - " MAN e 5 " " BMA f 3 " - " MAN f 6 " " BMA p 3 " - " MAN p 6 " " MAN p 6 " - " MAN p 8 " " BMA x 3 " - " MAN x 6 " " BMA y 3 " - " MAN y 6 " " BMABA 3 " - " MANBA 9 " BETA1-2 " MAN 9 4 " - " NAG 9 5 " " MAN 9 9 " - " NAG 9 10 " " MAN Y 4 " - " NAG Y 5 " " MAN Y 9 " - " NAG Y 10 " " MAN Z 4 " - " NAG Z 5 " " MAN Z 9 " - " NAG Z 10 " " MANBA 4 " - " NAGBA 5 " " MANBA 9 " - " NAGBA 10 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG 9 5 " - " GAL 9 6 " " NAG 9 7 " - " GAL 9 8 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Y 5 " - " GAL Y 6 " " NAG Y 7 " - " GAL Y 8 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " MAN Z 4 " - " NAG Z 7 " " NAG Z 5 " - " GAL Z 6 " " NAG Z 7 " - " GAL Z 8 " " NAG Z 10 " - " GAL Z 11 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " MANBA 4 " - " NAGBA 7 " " NAGBA 5 " - " GALBA 6 " " NAGBA 7 " - " GALBA 8 " BETA1-6 " NAG 9 1 " - " FUC 9 11 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " MAN 9 4 " - " NAG 9 7 " " NAG Y 1 " - " FUC Y 11 " " MAN Y 4 " - " NAG Y 7 " " NAG Z 1 " - " FUC Z 13 " " MAN Z 9 " - " NAG Z 12 " " NAG q 1 " - " FUC q 3 " " NAGBA 1 " - " FUCBA 12 " " MANBA 9 " - " NAGBA 11 " NAG-ASN " NAG 0 1 " - " ASN E 295 " " NAG 1 1 " - " ASN E 301 " " NAG 2 1 " - " ASN E 332 " " NAG 3 1 " - " ASN E 339 " " NAG 4 1 " - " ASN E 355 " " NAG 5 1 " - " ASN E 362 " " NAG 6 1 " - " ASN E 386 " " NAG 7 1 " - " ASN E 392 " " NAG 8 1 " - " ASN E 448 " " NAG 9 1 " - " ASN F 611 " " NAG A1135 " - " ASN A 135 " " NAG A1355 " - " ASN A 355 " " NAG A1397 " - " ASN A 397 " " NAG B1600 " - " ASN B 616 " " NAG B1625 " - " ASN B 625 " " NAG C1397 " - " ASN C 397 " " NAG D1600 " - " ASN D 616 " " NAG E1187 " - " ASN E 187 " " NAG E1397 " - " ASN E 397 " " NAG F1600 " - " ASN F 616 " " NAG G 1 " - " ASN A 88 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 160 " " NAG K 1 " - " ASN A 241 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 276 " " NAG Q 1 " - " ASN A 295 " " NAG R 1 " - " ASN A 301 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 339 " " NAG U 1 " - " ASN A 362 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 392 " " NAG X 1 " - " ASN A 448 " " NAG Y 1 " - " ASN B 611 " " NAG Z 1 " - " ASN B 637 " " NAG a 1 " - " ASN C 88 " " NAG b 1 " - " ASN C 135 " " NAG c 1 " - " ASN C 156 " " NAG d 1 " - " ASN C 160 " " NAG e 1 " - " ASN C 241 " " NAG f 1 " - " ASN C 262 " " NAG g 1 " - " ASN C 276 " " NAG h 1 " - " ASN C 295 " " NAG i 1 " - " ASN C 301 " " NAG j 1 " - " ASN C 332 " " NAG k 1 " - " ASN C 339 " " NAG l 1 " - " ASN C 355 " " NAG m 1 " - " ASN C 362 " " NAG n 1 " - " ASN C 386 " " NAG o 1 " - " ASN C 392 " " NAG p 1 " - " ASN C 448 " " NAG q 1 " - " ASN D 611 " " NAG r 1 " - " ASN D 625 " " NAG s 1 " - " ASN D 637 " " NAG t 1 " - " ASN E 88 " " NAG u 1 " - " ASN E 135 " " NAG v 1 " - " ASN E 156 " " NAG w 1 " - " ASN E 160 " " NAG x 1 " - " ASN E 241 " " NAG y 1 " - " ASN E 262 " " NAG z 1 " - " ASN E 276 " " NAGAA 1 " - " ASN F 625 " " NAGBA 1 " - " ASN F 637 " Time building additional restraints: 11.42 Conformation dependent library (CDL) restraints added in 3.0 seconds 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4240 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 43 sheets defined 21.0% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 100 through 116 Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 335 through 352 Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 475 through 485 removed outlier: 3.549A pdb=" N SER A 481 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 527 Processing helix chain 'B' and resid 530 through 540 removed outlier: 6.551A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 565 removed outlier: 4.110A pdb=" N ALA B 561 " --> pdb=" O ARG B 557 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 removed outlier: 3.802A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 628 through 634 removed outlier: 3.581A pdb=" N ARG B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU B 634 " --> pdb=" O GLU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 650 removed outlier: 4.402A pdb=" N SER B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 662 Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.550A pdb=" N ASP C 107 " --> pdb=" O MET C 104 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE C 108 " --> pdb=" O GLN C 105 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP C 112 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 126 No H-bonds generated for 'chain 'C' and resid 124 through 126' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 335 through 352 removed outlier: 3.689A pdb=" N LYS C 348 " --> pdb=" O GLN C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'D' and resid 524 through 527 removed outlier: 3.649A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 524 through 527' Processing helix chain 'D' and resid 530 through 533 No H-bonds generated for 'chain 'D' and resid 530 through 533' Processing helix chain 'D' and resid 537 through 543 removed outlier: 4.379A pdb=" N LEU D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 565 removed outlier: 3.511A pdb=" N GLN D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 596 removed outlier: 3.852A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 628 through 656 removed outlier: 5.435A pdb=" N ASN D 637 " --> pdb=" O ARG D 633 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N TYR D 638 " --> pdb=" O GLU D 634 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU D 641 " --> pdb=" O ASN D 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 336 through 352 removed outlier: 3.668A pdb=" N VAL E 346 " --> pdb=" O LYS E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 426 through 428 No H-bonds generated for 'chain 'E' and resid 426 through 428' Processing helix chain 'E' and resid 461 through 463 No H-bonds generated for 'chain 'E' and resid 461 through 463' Processing helix chain 'E' and resid 475 through 483 removed outlier: 4.272A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 535 removed outlier: 4.874A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.719A pdb=" N LEU F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 568 removed outlier: 3.843A pdb=" N GLN F 567 " --> pdb=" O GLN F 563 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU F 568 " --> pdb=" O ARG F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 595 removed outlier: 4.170A pdb=" N LEU F 592 " --> pdb=" O GLY F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 622 No H-bonds generated for 'chain 'F' and resid 619 through 622' Processing helix chain 'F' and resid 628 through 651 removed outlier: 3.619A pdb=" N GLU F 634 " --> pdb=" O GLU F 630 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASN F 637 " --> pdb=" O ARG F 633 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N SER F 640 " --> pdb=" O ASP F 636 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 662 Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'M' and resid 29 through 31 No H-bonds generated for 'chain 'M' and resid 29 through 31' Processing helix chain 'M' and resid 84 through 86 No H-bonds generated for 'chain 'M' and resid 84 through 86' Processing sheet with id= A, first strand: chain 'A' and resid 37 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= E, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= F, first strand: chain 'A' and resid 181 through 184 removed outlier: 4.593A pdb=" N SER A 190 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 200 through 203 Processing sheet with id= H, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.048A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ASN A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 413 through 417 removed outlier: 4.677A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 374 through 378 Processing sheet with id= K, first strand: chain 'A' and resid 301 through 308 removed outlier: 3.705A pdb=" N GLU A 321A" --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= M, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.080A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= O, first strand: chain 'C' and resid 91 through 94 Processing sheet with id= P, first strand: chain 'C' and resid 155 through 157 Processing sheet with id= Q, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.741A pdb=" N ARG C 192 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.127A pdb=" N THR C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE C 468 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N ASN C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 445 through 449 removed outlier: 3.575A pdb=" N CYS C 445 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.335A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 301 through 308 removed outlier: 3.942A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU C 321A" --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= W, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.934A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= Y, first strand: chain 'E' and resid 91 through 94 Processing sheet with id= Z, first strand: chain 'E' and resid 154 through 162 Processing sheet with id= AA, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= AB, first strand: chain 'E' and resid 200 through 203 Processing sheet with id= AC, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.615A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 443 through 449 Processing sheet with id= AE, first strand: chain 'E' and resid 359 through 362 removed outlier: 6.409A pdb=" N GLU E 466 " --> pdb=" O VAL E 360 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ASN E 362 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE E 468 " --> pdb=" O ASN E 362 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'E' and resid 374 through 377 Processing sheet with id= AG, first strand: chain 'E' and resid 302 through 308 removed outlier: 3.692A pdb=" N GLU E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= AI, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.843A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 93 through 95 removed outlier: 3.631A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.599A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.389A pdb=" N LYS L 103 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL L 13 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASP L 105 " --> pdb=" O VAL L 13 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU L 46 " --> pdb=" O ARG L 37 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'M' and resid 4 through 7 Processing sheet with id= AN, first strand: chain 'M' and resid 10 through 12 removed outlier: 5.811A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'M' and resid 93 through 95 removed outlier: 3.701A pdb=" N VAL M 102 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'N' and resid 4 through 7 Processing sheet with id= AQ, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.887A pdb=" N LYS N 103 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU N 46 " --> pdb=" O ARG N 37 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1479 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: 6.78 Time building geometry restraints manager: 11.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4977 1.33 - 1.45: 5227 1.45 - 1.57: 10733 1.57 - 1.69: 0 1.69 - 1.81: 164 Bond restraints: 21101 Sorted by residual: bond pdb=" CA ASN A 229 " pdb=" CB ASN A 229 " ideal model delta sigma weight residual 1.530 1.412 0.117 1.64e-02 3.72e+03 5.11e+01 bond pdb=" N PRO E 118 " pdb=" CD PRO E 118 " ideal model delta sigma weight residual 1.473 1.553 -0.080 1.40e-02 5.10e+03 3.25e+01 bond pdb=" N PRO A 118 " pdb=" CD PRO A 118 " ideal model delta sigma weight residual 1.473 1.549 -0.076 1.40e-02 5.10e+03 2.91e+01 bond pdb=" CA SER F 599 " pdb=" C SER F 599 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.28e-02 6.10e+03 2.58e+01 bond pdb=" C ASN E 80 " pdb=" N PRO E 81 " ideal model delta sigma weight residual 1.334 1.389 -0.055 1.11e-02 8.12e+03 2.45e+01 ... (remaining 21096 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.78: 1038 106.78 - 114.32: 12689 114.32 - 121.86: 10639 121.86 - 129.40: 4096 129.40 - 136.95: 168 Bond angle restraints: 28630 Sorted by residual: angle pdb=" C GLY M 100 " pdb=" N PRO M 100A" pdb=" CA PRO M 100A" ideal model delta sigma weight residual 119.66 128.29 -8.63 7.30e-01 1.88e+00 1.40e+02 angle pdb=" C ASN C 80 " pdb=" N PRO C 81 " pdb=" CA PRO C 81 " ideal model delta sigma weight residual 119.99 130.47 -10.48 1.08e+00 8.57e-01 9.42e+01 angle pdb=" C GLY C 237 " pdb=" N PRO C 238 " pdb=" CA PRO C 238 " ideal model delta sigma weight residual 119.76 128.86 -9.10 1.00e+00 1.00e+00 8.29e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.32 129.28 -9.96 1.14e+00 7.69e-01 7.64e+01 angle pdb=" C ALA C 436 " pdb=" N PRO C 437 " pdb=" CA PRO C 437 " ideal model delta sigma weight residual 119.66 125.92 -6.26 7.20e-01 1.93e+00 7.57e+01 ... (remaining 28625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.70: 14752 26.70 - 53.39: 271 53.39 - 80.09: 230 80.09 - 106.78: 135 106.78 - 133.48: 4 Dihedral angle restraints: 15392 sinusoidal: 8822 harmonic: 6570 Sorted by residual: dihedral pdb=" CA ASN E 412 " pdb=" C ASN E 412 " pdb=" N THR E 413 " pdb=" CA THR E 413 " ideal model delta harmonic sigma weight residual -180.00 -46.52 -133.48 0 5.00e+00 4.00e-02 7.13e+02 dihedral pdb=" CA VAL C 65 " pdb=" C VAL C 65 " pdb=" N HIS C 66 " pdb=" CA HIS C 66 " ideal model delta harmonic sigma weight residual 0.00 -37.56 37.56 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" C GLN C 352 " pdb=" N GLN C 352 " pdb=" CA GLN C 352 " pdb=" CB GLN C 352 " ideal model delta harmonic sigma weight residual -122.60 -140.88 18.28 0 2.50e+00 1.60e-01 5.35e+01 ... (remaining 15389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 3170 0.158 - 0.317: 638 0.317 - 0.475: 19 0.475 - 0.634: 13 0.634 - 0.792: 10 Chirality restraints: 3850 Sorted by residual: chirality pdb=" C1 MAN f 7 " pdb=" O3 MAN f 6 " pdb=" C2 MAN f 7 " pdb=" O5 MAN f 7 " both_signs ideal model delta sigma weight residual False 2.40 1.62 0.78 2.00e-02 2.50e+03 1.51e+03 chirality pdb=" C1 MAN O 7 " pdb=" O3 MAN O 6 " pdb=" C2 MAN O 7 " pdb=" O5 MAN O 7 " both_signs ideal model delta sigma weight residual False 2.40 1.63 0.77 2.00e-02 2.50e+03 1.50e+03 chirality pdb=" C1 MAN y 7 " pdb=" O3 MAN y 6 " pdb=" C2 MAN y 7 " pdb=" O5 MAN y 7 " both_signs ideal model delta sigma weight residual False 2.40 1.63 0.77 2.00e-02 2.50e+03 1.50e+03 ... (remaining 3847 not shown) Planarity restraints: 3402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 301 " -0.300 2.00e-02 2.50e+03 3.39e-01 1.44e+03 pdb=" CG ASN C 301 " 0.146 2.00e-02 2.50e+03 pdb=" OD1 ASN C 301 " 0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN C 301 " 0.505 2.00e-02 2.50e+03 pdb=" C1 NAG i 1 " -0.446 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 156 " 0.258 2.00e-02 2.50e+03 3.37e-01 1.42e+03 pdb=" CG ASN A 156 " -0.143 2.00e-02 2.50e+03 pdb=" OD1 ASN A 156 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN A 156 " -0.526 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.450 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 156 " -0.308 2.00e-02 2.50e+03 3.32e-01 1.38e+03 pdb=" CG ASN C 156 " 0.146 2.00e-02 2.50e+03 pdb=" OD1 ASN C 156 " 0.128 2.00e-02 2.50e+03 pdb=" ND2 ASN C 156 " 0.474 2.00e-02 2.50e+03 pdb=" C1 NAG c 1 " -0.440 2.00e-02 2.50e+03 ... (remaining 3399 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 173 2.47 - 3.08: 15582 3.08 - 3.68: 28470 3.68 - 4.29: 45074 4.29 - 4.90: 70402 Nonbonded interactions: 159701 Sorted by model distance: nonbonded pdb=" NE ARG A 298 " pdb=" CD1 ILE A 443 " model vdw 1.862 3.540 nonbonded pdb=" CA PRO E 183 " pdb=" CD1 TYR E 191 " model vdw 1.869 3.770 nonbonded pdb=" OD1 ASN A 339 " pdb=" N ASP A 340 " model vdw 1.900 2.520 nonbonded pdb=" O ALA E 336 " pdb=" OD1 ASN E 339 " model vdw 1.967 3.040 nonbonded pdb=" OE1 GLU A 87 " pdb=" O7 NAG G 1 " model vdw 1.996 3.040 ... (remaining 159696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain 'AA' selection = chain 'G' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'X' selection = chain 'b' selection = chain 'c' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'o' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'w' selection = chain 'z' } ncs_group { reference = (chain '2' and resid 1 through 2) selection = (chain '7' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'n' and resid 1 through 2) selection = (chain 'q' and resid 1 through 2) selection = (chain 't' and resid 1 through 2) selection = (chain 'v' and resid 1 through 2) } ncs_group { reference = (chain '8' and (resid 2 or resid 5 through 8)) selection = (chain 'O' and (resid 1 or resid 4 through 7)) selection = (chain 'f' and (resid 1 or resid 4 through 7)) selection = (chain 'p' and (resid 2 or resid 5 through 8)) selection = (chain 'y' and (resid 1 or resid 4 through 7)) } ncs_group { reference = (chain '9' and (resid 1 or resid 10 through 11)) selection = (chain 'BA' and (resid 2 or resid 11 through 12)) selection = (chain 'Y' and (resid 1 or resid 10 through 11)) } ncs_group { reference = (chain 'A' and (resid 31 through 136 or resid 152 through 401 or resid 410 throu \ gh 506 or resid 1397)) selection = (chain 'C' and (resid 31 through 57 or resid 64 through 401 or resid 410 through \ 506 or resid 1397)) selection = (chain 'E' and (resid 31 through 57 or resid 64 through 136 or resid 152 through \ 401 or resid 410 through 506 or resid 1397)) } ncs_group { reference = (chain 'B' and resid 521 through 658) selection = (chain 'D' and resid 521 through 658) selection = (chain 'F' and resid 521 through 658) } ncs_group { reference = (chain 'H' and resid 2 through 113) selection = (chain 'M' and resid 2 through 113) } ncs_group { reference = (chain 'L' and resid 2 through 108) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.010 Extract box with map and model: 4.760 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 56.950 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.270 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 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 : 0.014 0.117 21101 Z= 0.872 Angle : 1.862 13.033 28630 Z= 1.055 Chirality : 0.120 0.792 3850 Planarity : 0.017 0.137 3338 Dihedral : 17.626 133.475 11050 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 1.69 % Allowed : 6.15 % Favored : 92.15 % Rotamer: Outliers : 1.20 % Allowed : 1.54 % Favored : 97.26 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.78 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.15), residues: 2243 helix: -1.70 (0.20), residues: 431 sheet: -1.02 (0.20), residues: 600 loop : -1.82 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP M 100G HIS 0.003 0.000 HIS C 330 PHE 0.010 0.000 PHE B 522 TYR 0.003 0.000 TYR M 100N ARG 0.007 0.003 ARG C 503 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 562 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.8288 (m-90) cc_final: 0.7339 (m-10) REVERT: A 100 MET cc_start: 0.8292 (mtp) cc_final: 0.8077 (mtm) REVERT: A 115 SER cc_start: 0.8924 (p) cc_final: 0.8719 (p) REVERT: A 229 ASN cc_start: 0.6352 (m110) cc_final: 0.5970 (m110) REVERT: A 434 MET cc_start: 0.8581 (tmm) cc_final: 0.8283 (ttm) REVERT: A 499 THR cc_start: 0.7061 (OUTLIER) cc_final: 0.6459 (t) REVERT: B 543 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7612 (mp) REVERT: B 554 ASN cc_start: 0.7501 (m-40) cc_final: 0.7024 (t0) REVERT: B 606 THR cc_start: 0.8556 (t) cc_final: 0.8325 (p) REVERT: B 628 TRP cc_start: 0.8507 (t-100) cc_final: 0.8269 (t-100) REVERT: B 663 LEU cc_start: 0.7516 (mt) cc_final: 0.7282 (mt) REVERT: C 100 MET cc_start: 0.7585 (mtp) cc_final: 0.7276 (mtm) REVERT: C 297 THR cc_start: 0.7138 (p) cc_final: 0.6856 (p) REVERT: C 434 MET cc_start: 0.8329 (ppp) cc_final: 0.8116 (ptp) REVERT: C 482 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7441 (mm-30) REVERT: D 584 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7313 (mt-10) REVERT: E 42 VAL cc_start: 0.9667 (t) cc_final: 0.9447 (p) REVERT: E 45 TRP cc_start: 0.7838 (m-10) cc_final: 0.7631 (m-10) REVERT: E 56 SER cc_start: 0.9043 (p) cc_final: 0.8819 (m) REVERT: E 57 ASP cc_start: 0.7473 (t0) cc_final: 0.7104 (t70) REVERT: E 213 ILE cc_start: 0.9177 (mt) cc_final: 0.8879 (tt) REVERT: F 629 MET cc_start: 0.7662 (mtm) cc_final: 0.6197 (mtm) REVERT: H 22 CYS cc_start: 0.3418 (t) cc_final: 0.2751 (t) REVERT: M 82 MET cc_start: 0.6699 (mtm) cc_final: 0.6449 (mtp) outliers start: 24 outliers final: 11 residues processed: 583 average time/residue: 0.3720 time to fit residues: 311.9878 Evaluate side-chains 247 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 234 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 0.3980 chunk 169 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 202 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS C 99 ASN C 389 GLN D 624 ASN E 66 HIS E 428 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN F 624 ASN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN M 76 ASN ** M 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21101 Z= 0.237 Angle : 0.952 12.070 28630 Z= 0.440 Chirality : 0.058 0.900 3850 Planarity : 0.005 0.045 3338 Dihedral : 15.427 85.314 6745 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.71 % Allowed : 4.64 % Favored : 94.65 % Rotamer: Outliers : 0.20 % Allowed : 2.14 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.78 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.16), residues: 2243 helix: -0.58 (0.24), residues: 426 sheet: -0.64 (0.20), residues: 591 loop : -1.37 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 479 HIS 0.005 0.001 HIS C 374 PHE 0.018 0.002 PHE C 53 TYR 0.021 0.002 TYR C 173 ARG 0.009 0.001 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 365 time to evaluate : 2.311 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: A 96 TRP cc_start: 0.7948 (m-90) cc_final: 0.7251 (m-10) REVERT: A 434 MET cc_start: 0.8323 (tmm) cc_final: 0.8002 (ttm) REVERT: B 554 ASN cc_start: 0.7140 (m-40) cc_final: 0.5124 (t0) REVERT: B 628 TRP cc_start: 0.8478 (t-100) cc_final: 0.8108 (t-100) REVERT: B 663 LEU cc_start: 0.7949 (mt) cc_final: 0.7671 (mt) REVERT: C 34 LEU cc_start: 0.7718 (mt) cc_final: 0.7281 (mp) REVERT: C 297 THR cc_start: 0.7900 (p) cc_final: 0.7626 (p) REVERT: C 434 MET cc_start: 0.8267 (ppp) cc_final: 0.7800 (ptp) REVERT: C 482 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7431 (mm-30) REVERT: D 536 THR cc_start: 0.7743 (p) cc_final: 0.7424 (p) REVERT: D 603 ILE cc_start: 0.9288 (mt) cc_final: 0.9025 (mt) REVERT: E 42 VAL cc_start: 0.9519 (t) cc_final: 0.9305 (p) REVERT: E 122 LEU cc_start: 0.6503 (tt) cc_final: 0.6081 (tp) REVERT: E 318 TYR cc_start: 0.7049 (m-80) cc_final: 0.6810 (m-80) REVERT: F 629 MET cc_start: 0.7475 (mtm) cc_final: 0.6084 (mtm) REVERT: H 100 LEU cc_start: 0.9368 (tp) cc_final: 0.9152 (tt) REVERT: H 101 ASP cc_start: 0.7247 (p0) cc_final: 0.7006 (p0) REVERT: M 82 MET cc_start: 0.6771 (mtm) cc_final: 0.6403 (mtp) outliers start: 4 outliers final: 0 residues processed: 365 average time/residue: 0.3166 time to fit residues: 178.4481 Evaluate side-chains 224 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 246 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN E 103 GLN ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN M 76 ASN ** M 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 21101 Z= 0.345 Angle : 0.948 30.725 28630 Z= 0.431 Chirality : 0.055 0.478 3850 Planarity : 0.005 0.046 3338 Dihedral : 12.476 77.260 6745 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.11 % Favored : 93.18 % Rotamer: Outliers : 0.40 % Allowed : 1.69 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.17), residues: 2243 helix: -0.67 (0.23), residues: 430 sheet: -0.52 (0.20), residues: 600 loop : -1.31 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 427 HIS 0.007 0.001 HIS C 330 PHE 0.025 0.002 PHE H 67 TYR 0.016 0.002 TYR M 59 ARG 0.006 0.001 ARG D 557 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 300 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 LEU cc_start: 0.7607 (mt) cc_final: 0.7193 (mp) REVERT: C 297 THR cc_start: 0.8087 (p) cc_final: 0.7840 (p) REVERT: C 434 MET cc_start: 0.8383 (ppp) cc_final: 0.7919 (ptp) REVERT: C 482 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7595 (mm-30) REVERT: E 318 TYR cc_start: 0.7137 (m-80) cc_final: 0.6903 (m-80) REVERT: E 374 HIS cc_start: 0.8153 (OUTLIER) cc_final: 0.7738 (t-170) REVERT: F 569 THR cc_start: 0.8931 (t) cc_final: 0.8684 (t) REVERT: F 629 MET cc_start: 0.7718 (mtm) cc_final: 0.6869 (mtm) REVERT: H 32 TYR cc_start: 0.7656 (m-80) cc_final: 0.7383 (m-10) REVERT: H 101 ASP cc_start: 0.7347 (p0) cc_final: 0.6978 (p0) REVERT: L 5 THR cc_start: 0.6878 (p) cc_final: 0.6661 (p) REVERT: M 95 MET cc_start: 0.8476 (ttm) cc_final: 0.8087 (ttp) REVERT: N 4 MET cc_start: 0.7168 (tpp) cc_final: 0.6478 (tpp) outliers start: 8 outliers final: 3 residues processed: 305 average time/residue: 0.3098 time to fit residues: 147.3246 Evaluate side-chains 201 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 197 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 200 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 203 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 192 optimal weight: 0.0770 chunk 58 optimal weight: 6.9990 overall best weight: 2.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN B 553 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 21101 Z= 0.292 Angle : 0.857 28.746 28630 Z= 0.395 Chirality : 0.052 0.436 3850 Planarity : 0.004 0.049 3338 Dihedral : 10.677 69.916 6745 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.87 % Favored : 92.64 % Rotamer: Outliers : 0.20 % Allowed : 2.94 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.17), residues: 2243 helix: -0.39 (0.25), residues: 432 sheet: -0.50 (0.20), residues: 607 loop : -1.23 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 45 HIS 0.007 0.001 HIS C 330 PHE 0.015 0.002 PHE E 93 TYR 0.017 0.002 TYR E 217 ARG 0.006 0.001 ARG L 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 282 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8017 (ppp) cc_final: 0.7803 (ppp) REVERT: A 104 MET cc_start: 0.8713 (tpp) cc_final: 0.8220 (tpp) REVERT: A 217 TYR cc_start: 0.8014 (m-80) cc_final: 0.7660 (m-10) REVERT: C 297 THR cc_start: 0.7920 (p) cc_final: 0.7642 (p) REVERT: C 482 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7620 (mm-30) REVERT: E 122 LEU cc_start: 0.6587 (tt) cc_final: 0.6255 (tp) REVERT: E 318 TYR cc_start: 0.7151 (m-80) cc_final: 0.6904 (m-80) REVERT: F 534 SER cc_start: 0.8679 (p) cc_final: 0.7833 (p) REVERT: F 569 THR cc_start: 0.8995 (t) cc_final: 0.8593 (p) REVERT: H 101 ASP cc_start: 0.7404 (p0) cc_final: 0.6989 (p0) REVERT: N 4 MET cc_start: 0.7171 (tpp) cc_final: 0.6818 (tpp) outliers start: 4 outliers final: 1 residues processed: 283 average time/residue: 0.3072 time to fit residues: 135.2727 Evaluate side-chains 205 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 179 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 183 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 ASN A 463 ASN B 577 GLN ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 21101 Z= 0.295 Angle : 0.840 27.228 28630 Z= 0.390 Chirality : 0.051 0.451 3850 Planarity : 0.004 0.058 3338 Dihedral : 10.059 65.937 6745 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.51 % Favored : 93.00 % Rotamer: Outliers : 0.15 % Allowed : 1.94 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.17), residues: 2243 helix: -0.49 (0.24), residues: 435 sheet: -0.57 (0.20), residues: 646 loop : -1.27 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP E 45 HIS 0.009 0.001 HIS C 330 PHE 0.030 0.002 PHE H 27 TYR 0.012 0.001 TYR M 59 ARG 0.004 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 269 time to evaluate : 2.200 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: A 95 MET cc_start: 0.8023 (ppp) cc_final: 0.7779 (ppp) REVERT: A 346 VAL cc_start: 0.7739 (t) cc_final: 0.7537 (p) REVERT: B 557 ARG cc_start: 0.7888 (mtt180) cc_final: 0.7239 (mtt180) REVERT: C 297 THR cc_start: 0.8001 (p) cc_final: 0.7702 (p) REVERT: D 634 GLU cc_start: 0.8087 (tt0) cc_final: 0.7846 (tt0) REVERT: E 42 VAL cc_start: 0.9490 (t) cc_final: 0.9175 (p) REVERT: E 318 TYR cc_start: 0.7208 (m-80) cc_final: 0.6962 (m-80) REVERT: F 536 THR cc_start: 0.7965 (m) cc_final: 0.7622 (p) REVERT: F 569 THR cc_start: 0.8967 (t) cc_final: 0.8568 (p) REVERT: H 101 ASP cc_start: 0.7383 (p0) cc_final: 0.6712 (p0) REVERT: M 95 MET cc_start: 0.8177 (ttm) cc_final: 0.7762 (ttm) REVERT: M 100 ASP cc_start: 0.8152 (p0) cc_final: 0.7886 (p0) REVERT: N 4 MET cc_start: 0.7281 (tpp) cc_final: 0.6835 (tpp) outliers start: 3 outliers final: 0 residues processed: 271 average time/residue: 0.3080 time to fit residues: 130.0776 Evaluate side-chains 199 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 72 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN B 563 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN E 67 ASN ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN H 3 GLN M 97 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 21101 Z= 0.323 Angle : 0.831 23.731 28630 Z= 0.387 Chirality : 0.051 0.462 3850 Planarity : 0.004 0.052 3338 Dihedral : 9.765 62.990 6745 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.95 % Favored : 92.51 % Rotamer: Outliers : 0.10 % Allowed : 1.49 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.17), residues: 2243 helix: -0.46 (0.24), residues: 430 sheet: -0.55 (0.20), residues: 637 loop : -1.32 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 45 HIS 0.008 0.001 HIS C 330 PHE 0.027 0.002 PHE B 522 TYR 0.013 0.002 TYR M 59 ARG 0.003 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 260 time to evaluate : 2.156 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: A 346 VAL cc_start: 0.7651 (t) cc_final: 0.7346 (p) REVERT: C 297 THR cc_start: 0.7965 (p) cc_final: 0.7627 (p) REVERT: C 426 MET cc_start: 0.7226 (mtm) cc_final: 0.6283 (mtm) REVERT: F 534 SER cc_start: 0.8746 (p) cc_final: 0.7620 (p) REVERT: F 535 MET cc_start: 0.7509 (mpp) cc_final: 0.7259 (mpp) REVERT: F 536 THR cc_start: 0.7964 (m) cc_final: 0.7625 (p) REVERT: F 569 THR cc_start: 0.9012 (t) cc_final: 0.8619 (p) REVERT: H 32 TYR cc_start: 0.7827 (m-10) cc_final: 0.7445 (m-10) REVERT: H 79 TYR cc_start: 0.7122 (m-10) cc_final: 0.6871 (m-10) REVERT: M 95 MET cc_start: 0.8140 (ttm) cc_final: 0.7399 (ttm) REVERT: M 97 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: N 4 MET cc_start: 0.7347 (tpp) cc_final: 0.6862 (tpp) outliers start: 2 outliers final: 1 residues processed: 262 average time/residue: 0.2856 time to fit residues: 119.7970 Evaluate side-chains 191 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 208 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 181 optimal weight: 0.4980 chunk 120 optimal weight: 0.0370 chunk 214 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.9064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 461 ASN D 540 GLN ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN H 3 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21101 Z= 0.241 Angle : 0.794 29.907 28630 Z= 0.370 Chirality : 0.050 0.451 3850 Planarity : 0.004 0.075 3338 Dihedral : 9.344 60.189 6745 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.51 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.17), residues: 2243 helix: -0.40 (0.25), residues: 426 sheet: -0.54 (0.20), residues: 634 loop : -1.31 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 571 HIS 0.008 0.001 HIS C 330 PHE 0.025 0.002 PHE H 27 TYR 0.010 0.001 TYR M 59 ARG 0.008 0.000 ARG L 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 2.072 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: A 95 MET cc_start: 0.8124 (ppp) cc_final: 0.7804 (ppp) REVERT: B 557 ARG cc_start: 0.7793 (mtt180) cc_final: 0.7333 (mtt180) REVERT: C 297 THR cc_start: 0.7834 (p) cc_final: 0.7553 (p) REVERT: C 426 MET cc_start: 0.6936 (mtm) cc_final: 0.6601 (mtp) REVERT: D 520 LEU cc_start: 0.8722 (tp) cc_final: 0.8384 (mt) REVERT: E 434 MET cc_start: 0.7857 (ptp) cc_final: 0.7472 (ptp) REVERT: F 569 THR cc_start: 0.8971 (t) cc_final: 0.8529 (p) REVERT: H 32 TYR cc_start: 0.7666 (m-80) cc_final: 0.7347 (m-10) REVERT: H 79 TYR cc_start: 0.7085 (m-10) cc_final: 0.6804 (m-10) REVERT: H 101 ASP cc_start: 0.7301 (p0) cc_final: 0.7057 (p0) REVERT: M 95 MET cc_start: 0.8142 (ttm) cc_final: 0.7751 (ttm) REVERT: M 100 TYR cc_start: 0.7742 (m-80) cc_final: 0.7322 (m-80) REVERT: N 4 MET cc_start: 0.7259 (tpp) cc_final: 0.6874 (tpp) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.2982 time to fit residues: 129.6029 Evaluate side-chains 195 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 85 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 0.0670 chunk 41 optimal weight: 0.0980 chunk 136 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 168 optimal weight: 0.6980 chunk 195 optimal weight: 9.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN H 3 GLN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN M 76 ASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21101 Z= 0.168 Angle : 0.743 24.562 28630 Z= 0.349 Chirality : 0.049 0.442 3850 Planarity : 0.004 0.065 3338 Dihedral : 8.778 59.466 6745 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.58 % Allowed : 5.84 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.17), residues: 2243 helix: -0.08 (0.26), residues: 416 sheet: -0.42 (0.20), residues: 622 loop : -1.25 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP E 45 HIS 0.007 0.001 HIS C 330 PHE 0.015 0.001 PHE B 522 TYR 0.010 0.001 TYR A 486 ARG 0.006 0.000 ARG L 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 2.161 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: A 95 MET cc_start: 0.8138 (ppp) cc_final: 0.7924 (ppp) REVERT: B 557 ARG cc_start: 0.7802 (mtt180) cc_final: 0.7293 (mtt180) REVERT: C 297 THR cc_start: 0.7559 (p) cc_final: 0.7259 (p) REVERT: C 426 MET cc_start: 0.6944 (mtm) cc_final: 0.6736 (mtp) REVERT: C 434 MET cc_start: 0.8205 (ppp) cc_final: 0.7950 (ptp) REVERT: D 520 LEU cc_start: 0.8627 (tp) cc_final: 0.8377 (mt) REVERT: F 534 SER cc_start: 0.8039 (p) cc_final: 0.7467 (p) REVERT: F 535 MET cc_start: 0.7325 (mmp) cc_final: 0.7071 (mmm) REVERT: F 569 THR cc_start: 0.8944 (t) cc_final: 0.8660 (p) REVERT: H 79 TYR cc_start: 0.6872 (m-10) cc_final: 0.6667 (m-10) REVERT: H 84 ILE cc_start: 0.8296 (tp) cc_final: 0.8090 (tp) REVERT: L 73 LEU cc_start: 0.7059 (tp) cc_final: 0.5215 (tp) REVERT: M 95 MET cc_start: 0.7975 (ttm) cc_final: 0.7566 (ttm) REVERT: N 4 MET cc_start: 0.7134 (tpp) cc_final: 0.6712 (tpp) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.3041 time to fit residues: 131.9002 Evaluate side-chains 193 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 205 optimal weight: 7.9990 chunk 187 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 189 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 ASN M 97 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 21101 Z= 0.415 Angle : 0.909 23.121 28630 Z= 0.426 Chirality : 0.053 0.479 3850 Planarity : 0.005 0.062 3338 Dihedral : 9.216 59.942 6745 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.36 % Favored : 92.02 % Rotamer: Outliers : 0.05 % Allowed : 0.45 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.17), residues: 2243 helix: -0.43 (0.25), residues: 423 sheet: -0.52 (0.20), residues: 613 loop : -1.41 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.098 0.003 TRP E 45 HIS 0.009 0.002 HIS C 330 PHE 0.017 0.002 PHE C 53 TYR 0.017 0.002 TYR M 59 ARG 0.011 0.001 ARG L 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 236 time to evaluate : 2.177 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: C 297 THR cc_start: 0.7780 (p) cc_final: 0.7474 (p) REVERT: C 426 MET cc_start: 0.7406 (mtm) cc_final: 0.6952 (mtm) REVERT: C 434 MET cc_start: 0.8379 (ppp) cc_final: 0.8092 (ptm) REVERT: E 434 MET cc_start: 0.8092 (ptt) cc_final: 0.7849 (ptt) REVERT: H 32 TYR cc_start: 0.7788 (m-10) cc_final: 0.7535 (m-10) REVERT: H 86 ASP cc_start: 0.6235 (m-30) cc_final: 0.5805 (m-30) REVERT: H 101 ASP cc_start: 0.7486 (p0) cc_final: 0.7199 (p0) REVERT: M 95 MET cc_start: 0.8171 (ttm) cc_final: 0.7536 (ttm) REVERT: M 97 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.6943 (tm-30) REVERT: N 4 MET cc_start: 0.7332 (tpp) cc_final: 0.6955 (tpp) outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.3077 time to fit residues: 114.5615 Evaluate side-chains 173 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 211 optimal weight: 0.0370 chunk 129 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 222 optimal weight: 8.9990 chunk 204 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 246 GLN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21101 Z= 0.196 Angle : 0.793 25.009 28630 Z= 0.372 Chirality : 0.050 0.444 3850 Planarity : 0.004 0.059 3338 Dihedral : 8.753 59.839 6745 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.58 % Allowed : 5.93 % Favored : 93.49 % Rotamer: Outliers : 0.05 % Allowed : 0.05 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.17), residues: 2243 helix: -0.29 (0.25), residues: 427 sheet: -0.44 (0.21), residues: 602 loop : -1.38 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.002 TRP E 45 HIS 0.006 0.001 HIS C 330 PHE 0.027 0.001 PHE A 53 TYR 0.019 0.001 TYR H 79 ARG 0.006 0.000 ARG L 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 244 time to evaluate : 2.269 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: A 99 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7438 (p0) REVERT: C 297 THR cc_start: 0.7634 (p) cc_final: 0.7350 (p) REVERT: D 520 LEU cc_start: 0.8681 (tp) cc_final: 0.8373 (mt) REVERT: D 629 MET cc_start: 0.7972 (mmm) cc_final: 0.7765 (mmm) REVERT: H 101 ASP cc_start: 0.7459 (p0) cc_final: 0.7113 (p0) REVERT: L 36 TYR cc_start: 0.7380 (m-80) cc_final: 0.7109 (m-80) REVERT: M 95 MET cc_start: 0.8154 (ttm) cc_final: 0.7453 (ttm) REVERT: N 4 MET cc_start: 0.7211 (tpp) cc_final: 0.6780 (tpp) outliers start: 1 outliers final: 0 residues processed: 245 average time/residue: 0.2933 time to fit residues: 114.5171 Evaluate side-chains 185 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 26 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 177 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.078629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.061825 restraints weight = 70487.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.063296 restraints weight = 45674.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.063795 restraints weight = 33778.743| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.6047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21101 Z= 0.224 Angle : 0.778 22.822 28630 Z= 0.368 Chirality : 0.049 0.441 3850 Planarity : 0.004 0.058 3338 Dihedral : 8.541 59.731 6745 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.73 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2243 helix: -0.26 (0.25), residues: 427 sheet: -0.41 (0.20), residues: 609 loop : -1.39 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.002 TRP E 45 HIS 0.008 0.001 HIS C 374 PHE 0.029 0.002 PHE C 376 TYR 0.016 0.001 TYR A 217 ARG 0.017 0.000 ARG B 557 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3768.04 seconds wall clock time: 69 minutes 57.17 seconds (4197.17 seconds total)