Starting phenix.real_space_refine on Thu Apr 11 14:50:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v8l_8643/04_2024/5v8l_8643_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v8l_8643/04_2024/5v8l_8643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v8l_8643/04_2024/5v8l_8643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v8l_8643/04_2024/5v8l_8643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v8l_8643/04_2024/5v8l_8643_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v8l_8643/04_2024/5v8l_8643_neut.pdb" } resolution = 4.3 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 36 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 14310 2.51 5 N 3784 2.21 5 O 4711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 91": "OE1" <-> "OE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "H PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "K TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 22934 Number of models: 1 Model: "" Number of chains: 63 Chain: "A" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3545 Classifications: {'peptide': 450} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 426} Chain breaks: 2 Chain: "B" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Chain: "D" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3562 Classifications: {'peptide': 452} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "E" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "G" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "H" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "I" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "J" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1094 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "K" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "M" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "N" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 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: "U" 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: 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: 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: 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 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: "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: 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: "t" 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: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 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: "y" 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: "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: 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: "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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 78 residue: pdb=" C1 NAG P 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG P 1 " occ=0.00 residue: pdb=" C1 NAG P 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG P 2 " occ=0.00 residue: pdb=" C1 NAG R 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG R 1 " occ=0.00 residue: pdb=" C1 NAG R 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG R 2 " occ=0.00 residue: pdb=" C1 NAG S 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG S 1 " occ=0.00 residue: pdb=" C1 NAG S 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG S 2 " occ=0.00 residue: pdb=" C1 BMA S 3 " occ=0.00 ... (9 atoms not shown) pdb=" O6 BMA S 3 " occ=0.00 residue: pdb=" C1 NAG T 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG T 1 " occ=0.00 residue: pdb=" C1 NAG T 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG T 2 " occ=0.00 residue: pdb=" C1 BMA T 3 " occ=0.00 ... (9 atoms not shown) pdb=" O6 BMA T 3 " occ=0.00 residue: pdb=" C1 MAN T 4 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN T 4 " occ=0.00 residue: pdb=" C1 MAN T 5 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN T 5 " occ=0.00 ... (remaining 66 not shown) Time building chain proxies: 11.97, per 1000 atoms: 0.52 Number of scatterers: 22934 At special positions: 0 Unit cell: (148.03, 144.1, 171.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 4711 8.00 N 3784 7.00 C 14310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.06 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.23 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.12 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=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.12 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.20 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.09 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=2.09 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.17 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.08 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.02 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.05 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.12 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS E 605 " distance=2.08 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.05 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.10 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.09 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.14 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.05 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 "HETATM21625 O5 NAG g 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN T 4 " - " MAN T 5 " " MAN f 4 " - " MAN f 5 " " MAN g 4 " - " MAN g 5 " " MAN q 4 " - " MAN q 5 " " MAN s 4 " - " MAN s 5 " " MAN t 4 " - " MAN t 5 " ALPHA1-3 " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 7 " " MAN U 4 " - " MAN U 5 " " BMA Y 3 " - " MAN Y 4 " " BMA f 3 " - " MAN f 4 " " MAN f 6 " - " MAN f 7 " " BMA g 3 " - " MAN g 4 " " MAN g 6 " - " MAN g 7 " " BMA k 3 " - " MAN k 4 " " BMA q 3 " - " MAN q 4 " " MAN q 6 " - " MAN q 7 " " BMA s 3 " - " MAN s 4 " " MAN s 6 " - " MAN s 7 " " BMA t 3 " - " MAN t 4 " " MAN t 6 " - " MAN t 7 " " BMA x 3 " - " MAN x 4 " ALPHA1-6 " BMA T 3 " - " MAN T 6 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 6 " " BMA Y 3 " - " MAN Y 5 " " BMA f 3 " - " MAN f 6 " " BMA g 3 " - " MAN g 6 " " MAN g 6 " - " MAN g 8 " " BMA k 3 " - " MAN k 5 " " BMA q 3 " - " MAN q 6 " " MAN q 6 " - " MAN q 8 " " BMA s 3 " - " MAN s 6 " " BMA t 3 " - " MAN t 6 " " MAN t 6 " - " MAN t 8 " " BMA x 3 " - " MAN x 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " 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 T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN E 637 " " NAG 1 1 " - " ASN F 611 " " NAG 2 1 " - " ASN K 72 " " NAG 3 1 " - " ASN L 72 " " NAG 4 1 " - " ASN M 72 " " NAG A 612 " - " ASN A 234 " " NAG A 633 " - " ASN A 339 " " NAG A 634 " - " ASN A 355 " " NAG A 642 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 611 " - " ASN C 234 " " NAG C 633 " - " ASN C 339 " " NAG C 634 " - " ASN C 355 " " NAG D 603 " - " ASN D 133 " " NAG D 616 " - " ASN D 234 " " NAG D 638 " - " ASN D 339 " " NAG D 639 " - " ASN D 355 " " NAG D 648 " - " ASN D 392 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 618 " " NAG F 703 " - " ASN F 618 " " NAG F 704 " - " ASN F 637 " " NAG O 1 " - " ASN A 88 " " NAG P 1 " - " ASN A 133 " " NAG Q 1 " - " ASN A 156 " " NAG R 1 " - " ASN A 160 " " NAG S 1 " - " ASN A 197 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN A 276 " " NAG V 1 " - " ASN A 295 " " NAG W 1 " - " ASN A 301 " " NAG X 1 " - " ASN A 332 " " NAG Y 1 " - " ASN A 363 " " NAG Z 1 " - " ASN A 386 " " NAG a 1 " - " ASN A 448 " " NAG b 1 " - " ASN C 133 " " NAG c 1 " - " ASN C 156 " " NAG d 1 " - " ASN C 160 " " NAG e 1 " - " ASN C 197 " " 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 363 " " NAG l 1 " - " ASN C 386 " " NAG m 1 " - " ASN C 392 " " NAG n 1 " - " ASN C 448 " " NAG o 1 " - " ASN D 88 " " NAG p 1 " - " ASN D 156 " " NAG q 1 " - " ASN D 160 " " NAG r 1 " - " ASN D 197 " " NAG s 1 " - " ASN D 262 " " NAG t 1 " - " ASN D 276 " " NAG u 1 " - " ASN D 295 " " NAG v 1 " - " ASN D 301 " " NAG w 1 " - " ASN D 332 " " NAG x 1 " - " ASN D 363 " " NAG y 1 " - " ASN D 386 " " NAG z 1 " - " ASN D 448 " Time building additional restraints: 11.40 Conformation dependent library (CDL) restraints added in 3.7 seconds 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4892 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 49 sheets defined 23.3% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 56 through 64 removed outlier: 5.630A pdb=" N TYR A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.511A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.811A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.362A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 597 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.810A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 650 removed outlier: 3.786A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'C' and resid 59 through 64 removed outlier: 3.634A pdb=" N THR C 63 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 377 through 381 Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'D' and resid 59 through 64 Processing helix chain 'D' and resid 99 through 117 Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.559A pdb=" N VAL D 127 " --> pdb=" O PRO D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 335 through 350 Processing helix chain 'D' and resid 351 through 353 No H-bonds generated for 'chain 'D' and resid 351 through 353' Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 377 through 381 Processing helix chain 'D' and resid 387 through 392 Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'E' and resid 523 through 528 Processing helix chain 'E' and resid 529 through 534 removed outlier: 3.619A pdb=" N SER E 534 " --> pdb=" O MET E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 543 removed outlier: 4.465A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 597 Processing helix chain 'E' and resid 611 through 615 Processing helix chain 'E' and resid 618 through 624 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 649 Processing helix chain 'E' and resid 650 through 663 Processing helix chain 'F' and resid 523 through 528 Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.813A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 541 Processing helix chain 'F' and resid 542 through 544 No H-bonds generated for 'chain 'F' and resid 542 through 544' Processing helix chain 'F' and resid 569 through 597 Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 649 Processing helix chain 'F' and resid 650 through 663 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.613A pdb=" N ASP G 31 " --> pdb=" O ASN G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 60 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 26 through 32 removed outlier: 5.887A pdb=" N PHE J 29 " --> pdb=" O GLY J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 62 Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.066A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 202 removed outlier: 6.621A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.211A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.897A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 40 Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.702A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 172 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 201 through 202 removed outlier: 6.838A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.207A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.110A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.404A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.394A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.957A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.394A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.404A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.110A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AC1, first strand: chain 'D' and resid 494 through 499 Processing sheet with id=AC2, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'D' and resid 76 through 77 removed outlier: 7.021A pdb=" N THR D 77 " --> pdb=" O CYS D 54 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER D 56 " --> pdb=" O THR D 77 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AC5, first strand: chain 'D' and resid 130 through 133 Processing sheet with id=AC6, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AC7, first strand: chain 'D' and resid 201 through 203 removed outlier: 6.715A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.222A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 10.494A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.384A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.924A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.384A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 10.494A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 304 through 306 Processing sheet with id=AD2, first strand: chain 'G' and resid 5 through 6 Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.390A pdb=" N ALA G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE G 33 " --> pdb=" O GLN G 95 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.390A pdb=" N ALA G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.566A pdb=" N ALA H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE H 33 " --> pdb=" O GLN H 95 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.449A pdb=" N ALA I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE I 33 " --> pdb=" O GLN I 95 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.449A pdb=" N ALA I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 6 removed outlier: 4.453A pdb=" N SER J 16 " --> pdb=" O GLY J 82B" (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY J 82B" --> pdb=" O SER J 16 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.473A pdb=" N VAL J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TRP J 50 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 10 through 12 removed outlier: 7.770A pdb=" N CYS J 92 " --> pdb=" O VAL J 107 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL J 107 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N THR J 94 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU J 105 " --> pdb=" O THR J 94 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER J 96 " --> pdb=" O ALA J 103 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLU J 100O" --> pdb=" O ASP J 100B" (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE J 100D" --> pdb=" O TYR J 100M" (cutoff:3.500A) removed outlier: 6.414A pdb=" N TYR J 100M" --> pdb=" O PHE J 100D" (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 5 through 6 Processing sheet with id=AE5, first strand: chain 'K' and resid 10 through 11 Processing sheet with id=AE6, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.406A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.484A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 5 through 6 Processing sheet with id=AF1, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.434A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.289A pdb=" N LEU N 33 " --> pdb=" O HIS N 49 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N HIS N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 10 through 13 853 hydrogen bonds defined for protein. 2022 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: 8.97 Time building geometry restraints manager: 12.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6011 1.33 - 1.46: 6563 1.46 - 1.58: 10649 1.58 - 1.71: 6 1.71 - 1.84: 175 Bond restraints: 23404 Sorted by residual: bond pdb=" CA PHE I 78 " pdb=" C PHE I 78 " ideal model delta sigma weight residual 1.521 1.462 0.059 1.20e-02 6.94e+03 2.46e+01 bond pdb=" CA ILE F 641 " pdb=" C ILE F 641 " ideal model delta sigma weight residual 1.524 1.464 0.060 1.23e-02 6.61e+03 2.38e+01 bond pdb=" C3 MAN t 5 " pdb=" C4 MAN t 5 " ideal model delta sigma weight residual 1.524 1.615 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" CA PHE H 78 " pdb=" C PHE H 78 " ideal model delta sigma weight residual 1.522 1.467 0.055 1.21e-02 6.83e+03 2.04e+01 bond pdb=" C3 MAN g 5 " pdb=" C4 MAN g 5 " ideal model delta sigma weight residual 1.524 1.614 -0.090 2.00e-02 2.50e+03 2.03e+01 ... (remaining 23399 not shown) Histogram of bond angle deviations from ideal: 95.76 - 103.45: 211 103.45 - 111.13: 9783 111.13 - 118.82: 10178 118.82 - 126.50: 11225 126.50 - 134.19: 392 Bond angle restraints: 31789 Sorted by residual: angle pdb=" C LYS C 252 " pdb=" N PRO C 253 " pdb=" CA PRO C 253 " ideal model delta sigma weight residual 120.12 131.29 -11.17 1.11e+00 8.12e-01 1.01e+02 angle pdb=" C ALA A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 119.66 126.49 -6.83 7.20e-01 1.93e+00 9.00e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 129.01 -9.45 1.02e+00 9.61e-01 8.58e+01 angle pdb=" C CYS D 239 " pdb=" N PRO D 240 " pdb=" CA PRO D 240 " ideal model delta sigma weight residual 119.56 128.83 -9.27 1.02e+00 9.61e-01 8.27e+01 angle pdb=" C VAL B 608 " pdb=" N PRO B 609 " pdb=" CA PRO B 609 " ideal model delta sigma weight residual 119.85 129.03 -9.18 1.01e+00 9.80e-01 8.26e+01 ... (remaining 31784 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.34: 15054 20.34 - 40.67: 536 40.67 - 61.01: 219 61.01 - 81.34: 89 81.34 - 101.68: 65 Dihedral angle restraints: 15963 sinusoidal: 8366 harmonic: 7597 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 -171.44 85.44 1 1.00e+01 1.00e-02 8.84e+01 dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual -86.00 -131.27 45.27 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual 93.00 136.53 -43.53 1 1.00e+01 1.00e-02 2.64e+01 ... (remaining 15960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.445: 3948 0.445 - 0.890: 26 0.890 - 1.336: 1 1.336 - 1.781: 0 1.781 - 2.226: 2 Chirality restraints: 3977 Sorted by residual: chirality pdb=" C1 MAN U 4 " pdb=" O6 BMA U 3 " pdb=" C2 MAN U 4 " pdb=" O5 MAN U 4 " both_signs ideal model delta sigma weight residual False 2.40 1.52 0.88 2.00e-02 2.50e+03 1.93e+03 chirality pdb=" C1 MAN g 6 " pdb=" O6 BMA g 3 " pdb=" C2 MAN g 6 " pdb=" O5 MAN g 6 " both_signs ideal model delta sigma weight residual False 2.40 1.52 0.88 2.00e-02 2.50e+03 1.93e+03 chirality pdb=" C1 MAN t 6 " pdb=" O6 BMA t 3 " pdb=" C2 MAN t 6 " pdb=" O5 MAN t 6 " both_signs ideal model delta sigma weight residual False 2.40 1.52 0.88 2.00e-02 2.50e+03 1.92e+03 ... (remaining 3974 not shown) Planarity restraints: 3901 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 386 " -0.259 2.00e-02 2.50e+03 3.18e-01 1.26e+03 pdb=" CG ASN C 386 " 0.111 2.00e-02 2.50e+03 pdb=" OD1 ASN C 386 " 0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN C 386 " 0.511 2.00e-02 2.50e+03 pdb=" C1 NAG l 1 " -0.404 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 363 " 0.265 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" CG ASN C 363 " -0.115 2.00e-02 2.50e+03 pdb=" OD1 ASN C 363 " -0.093 2.00e-02 2.50e+03 pdb=" ND2 ASN C 363 " -0.458 2.00e-02 2.50e+03 pdb=" C1 NAG k 1 " 0.401 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 363 " 0.218 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" CG ASN D 363 " -0.094 2.00e-02 2.50e+03 pdb=" OD1 ASN D 363 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN D 363 " -0.492 2.00e-02 2.50e+03 pdb=" C1 NAG x 1 " 0.342 2.00e-02 2.50e+03 ... (remaining 3898 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 63 2.41 - 3.03: 15575 3.03 - 3.65: 33158 3.65 - 4.28: 53138 4.28 - 4.90: 83439 Nonbonded interactions: 185373 Sorted by model distance: nonbonded pdb=" OG SER C 388 " pdb=" O6 NAG l 1 " model vdw 1.786 2.440 nonbonded pdb=" O ASN C 392 " pdb=" OD1 ASN C 392 " model vdw 1.902 3.040 nonbonded pdb=" NH2 ARG J 100A" pdb=" OE2 GLU J 100N" model vdw 2.035 2.520 nonbonded pdb=" OH TYR C 61 " pdb=" C HIS C 66 " model vdw 2.039 3.270 nonbonded pdb=" OE2 GLU L 70 " pdb=" N2 NAG 3 1 " model vdw 2.059 2.520 ... (remaining 185368 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 '2' selection = chain '3' selection = chain '4' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'z' } ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 32 through 398 or resid 412 through 506 or resid 601 throu \ gh 634)) selection = (chain 'D' and (resid 32 through 185 or resid 189 through 398 or resid 412 throu \ gh 506 or resid 603 through 639)) } ncs_group { reference = (chain 'B' and (resid 520 through 545 or resid 569 through 664 or resid 701 thro \ ugh 702)) selection = (chain 'E' and (resid 520 through 545 or resid 569 through 664 or resid 701 thro \ ugh 702)) selection = (chain 'F' and (resid 520 through 545 or resid 569 through 664 or resid 703 thro \ ugh 704)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'S' selection = chain 'X' selection = chain 'd' selection = chain 'l' selection = chain 'y' } ncs_group { reference = (chain 'T' and (resid 1 or resid 4 through 6)) selection = (chain 'U' and (resid 2 or resid 5 through 7)) selection = (chain 'f' and (resid 2 or resid 5 through 7)) selection = (chain 's' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'Y' selection = chain 'k' selection = chain 'x' } ncs_group { reference = chain 'g' selection = chain 'q' selection = chain 't' } 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=0.00 max=1.00 mean=0.96 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: 0.010 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.020 Extract box with map and model: 6.460 Check model and map are aligned: 0.320 Set scattering table: 0.250 Process input model: 62.160 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 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 : 0.015 0.091 23404 Z= 0.945 Angle : 1.852 12.668 31789 Z= 1.140 Chirality : 0.123 2.226 3977 Planarity : 0.013 0.112 3838 Dihedral : 14.727 101.676 10948 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.74 % Favored : 98.07 % Rotamer: Outliers : 0.39 % Allowed : 0.91 % Favored : 98.70 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.17), residues: 2589 helix: -0.59 (0.22), residues: 419 sheet: 0.60 (0.16), residues: 830 loop : 3.32 (0.18), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.009 TRP H 103 HIS 0.016 0.002 HIS A 374 PHE 0.023 0.005 PHE I 78 TYR 0.046 0.006 TYR N 36 ARG 0.007 0.001 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 829 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8893 (mt) cc_final: 0.8619 (mm) REVERT: A 96 TRP cc_start: 0.8585 (m-90) cc_final: 0.7446 (m-90) REVERT: A 100 MET cc_start: 0.8688 (mtp) cc_final: 0.8454 (ttp) REVERT: A 111 LEU cc_start: 0.9581 (mt) cc_final: 0.9195 (mt) REVERT: A 116 LEU cc_start: 0.9364 (tp) cc_final: 0.9117 (tt) REVERT: A 257 THR cc_start: 0.8540 (p) cc_final: 0.8257 (t) REVERT: A 359 ILE cc_start: 0.9194 (mt) cc_final: 0.8954 (mm) REVERT: A 434 MET cc_start: 0.8813 (ptm) cc_final: 0.8430 (ptm) REVERT: A 435 TYR cc_start: 0.8224 (t80) cc_final: 0.7847 (t80) REVERT: B 530 MET cc_start: 0.8813 (mtp) cc_final: 0.8609 (mtp) REVERT: B 623 TRP cc_start: 0.8035 (m100) cc_final: 0.7782 (m100) REVERT: B 630 GLN cc_start: 0.8664 (mt0) cc_final: 0.8191 (mp10) REVERT: B 634 GLU cc_start: 0.7964 (tt0) cc_final: 0.6845 (tp30) REVERT: B 658 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8782 (tm-30) REVERT: C 107 ASP cc_start: 0.8428 (t70) cc_final: 0.8218 (t70) REVERT: C 111 LEU cc_start: 0.9321 (mt) cc_final: 0.9051 (tt) REVERT: C 260 LEU cc_start: 0.9284 (mt) cc_final: 0.9072 (mp) REVERT: C 271 MET cc_start: 0.8266 (mmm) cc_final: 0.7751 (mmm) REVERT: C 308 ARG cc_start: 0.8932 (ttm170) cc_final: 0.8719 (ttp80) REVERT: C 309 ILE cc_start: 0.9508 (mt) cc_final: 0.9301 (mt) REVERT: C 368 ASP cc_start: 0.8101 (m-30) cc_final: 0.7880 (m-30) REVERT: C 443 ILE cc_start: 0.8898 (mt) cc_final: 0.8274 (mm) REVERT: D 107 ASP cc_start: 0.8992 (t70) cc_final: 0.8708 (t0) REVERT: D 226 LEU cc_start: 0.8860 (mt) cc_final: 0.8628 (mt) REVERT: D 300 ASN cc_start: 0.8822 (m-40) cc_final: 0.7993 (m-40) REVERT: D 303 THR cc_start: 0.8702 (p) cc_final: 0.8183 (t) REVERT: D 368 ASP cc_start: 0.8647 (t70) cc_final: 0.8389 (t0) REVERT: D 370 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8230 (mt-10) REVERT: D 443 ILE cc_start: 0.9296 (mm) cc_final: 0.9027 (mm) REVERT: E 544 LEU cc_start: 0.9095 (mt) cc_final: 0.8844 (mt) REVERT: E 571 TRP cc_start: 0.6541 (m-10) cc_final: 0.5628 (m-10) REVERT: E 618 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7229 (m-40) REVERT: F 575 GLN cc_start: 0.8879 (tt0) cc_final: 0.8288 (tm-30) REVERT: F 601 LYS cc_start: 0.8596 (mppt) cc_final: 0.8123 (mtmm) REVERT: F 607 ASN cc_start: 0.7709 (t0) cc_final: 0.7422 (t0) REVERT: F 624 ASP cc_start: 0.8110 (m-30) cc_final: 0.7528 (p0) REVERT: G 36 TRP cc_start: 0.9046 (m100) cc_final: 0.8588 (m100) REVERT: G 100 PHE cc_start: 0.9415 (m-80) cc_final: 0.8722 (m-80) REVERT: H 23 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7040 (mm-30) REVERT: H 37 TRP cc_start: 0.9466 (m100) cc_final: 0.8666 (m-10) REVERT: H 56 GLN cc_start: 0.8127 (tp40) cc_final: 0.7721 (tp-100) REVERT: H 72 ASP cc_start: 0.8948 (p0) cc_final: 0.8138 (p0) REVERT: H 80 MET cc_start: 0.8756 (tmm) cc_final: 0.8310 (tmm) REVERT: H 86 ASP cc_start: 0.8442 (m-30) cc_final: 0.8068 (m-30) REVERT: H 99 TYR cc_start: 0.8197 (m-80) cc_final: 0.7879 (m-80) REVERT: H 100 ASP cc_start: 0.7968 (m-30) cc_final: 0.7718 (t0) REVERT: I 58 ASN cc_start: 0.8870 (t0) cc_final: 0.8596 (t0) REVERT: I 59 ASN cc_start: 0.9581 (m-40) cc_final: 0.8869 (m-40) REVERT: I 61 ARG cc_start: 0.8899 (ttp80) cc_final: 0.8594 (tmm-80) REVERT: I 62 GLN cc_start: 0.9194 (tt0) cc_final: 0.8948 (tt0) REVERT: I 81 ASP cc_start: 0.8454 (m-30) cc_final: 0.8220 (m-30) REVERT: J 41 THR cc_start: 0.8646 (m) cc_final: 0.8334 (t) REVERT: J 80 MET cc_start: 0.6444 (ttp) cc_final: 0.6231 (ttt) REVERT: J 81 GLU cc_start: 0.6996 (tt0) cc_final: 0.6758 (tm-30) REVERT: K 5 THR cc_start: 0.8247 (p) cc_final: 0.7527 (p) REVERT: K 15 VAL cc_start: 0.8813 (t) cc_final: 0.8580 (m) REVERT: K 17 ASP cc_start: 0.8440 (m-30) cc_final: 0.8221 (m-30) REVERT: K 33 LEU cc_start: 0.8839 (tp) cc_final: 0.8637 (tp) REVERT: K 36 TYR cc_start: 0.8743 (m-80) cc_final: 0.7665 (m-80) REVERT: K 42 LYS cc_start: 0.8643 (mttt) cc_final: 0.8141 (tptp) REVERT: K 62 PHE cc_start: 0.7776 (m-80) cc_final: 0.7358 (m-80) REVERT: K 75 ILE cc_start: 0.8329 (mt) cc_final: 0.7746 (mt) REVERT: L 46 LEU cc_start: 0.9176 (tp) cc_final: 0.8718 (tp) REVERT: L 82 ASP cc_start: 0.6842 (m-30) cc_final: 0.6539 (m-30) REVERT: L 97 PHE cc_start: 0.8545 (m-80) cc_final: 0.8265 (m-10) REVERT: M 34 ASN cc_start: 0.8756 (m-40) cc_final: 0.8061 (m110) REVERT: M 50 ASP cc_start: 0.8957 (t0) cc_final: 0.8574 (t0) REVERT: M 99 VAL cc_start: 0.9324 (p) cc_final: 0.8918 (p) REVERT: N 35 TRP cc_start: 0.4092 (m100) cc_final: 0.2668 (m100) REVERT: N 44 PRO cc_start: 0.7209 (Cg_exo) cc_final: 0.6992 (Cg_endo) REVERT: N 73 LEU cc_start: 0.7970 (tp) cc_final: 0.7218 (pp) REVERT: N 78 VAL cc_start: 0.5635 (t) cc_final: 0.5295 (t) REVERT: N 81 ASP cc_start: 0.8404 (m-30) cc_final: 0.7897 (m-30) outliers start: 9 outliers final: 3 residues processed: 838 average time/residue: 0.3974 time to fit residues: 491.7804 Evaluate side-chains 471 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 467 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 4.9990 chunk 196 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 203 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 235 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS A 352 HIS A 356 ASN B 625 ASN C 66 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS C 352 HIS C 425 ASN D 315 GLN D 352 HIS G 64 GLN H 56 GLN ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 HIS L 24 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23404 Z= 0.280 Angle : 0.879 9.999 31789 Z= 0.437 Chirality : 0.054 0.595 3977 Planarity : 0.006 0.089 3838 Dihedral : 13.782 77.395 6038 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.09 % Allowed : 3.30 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.16), residues: 2589 helix: 0.65 (0.26), residues: 408 sheet: 0.39 (0.17), residues: 813 loop : 1.87 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP I 37 HIS 0.004 0.001 HIS H 71A PHE 0.041 0.002 PHE H 73 TYR 0.028 0.002 TYR E 638 ARG 0.006 0.001 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 629 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.8501 (m-90) cc_final: 0.7855 (m-10) REVERT: A 111 LEU cc_start: 0.9533 (mt) cc_final: 0.9145 (mt) REVERT: A 116 LEU cc_start: 0.9320 (tp) cc_final: 0.9029 (tt) REVERT: A 125 LEU cc_start: 0.9405 (mt) cc_final: 0.9171 (mt) REVERT: A 150 MET cc_start: 0.8990 (mmm) cc_final: 0.8500 (mtp) REVERT: A 180 ASP cc_start: 0.8282 (m-30) cc_final: 0.7979 (m-30) REVERT: A 257 THR cc_start: 0.8568 (p) cc_final: 0.8237 (t) REVERT: A 377 ASN cc_start: 0.9136 (t0) cc_final: 0.8831 (t0) REVERT: B 530 MET cc_start: 0.8974 (mtp) cc_final: 0.8756 (mtt) REVERT: B 571 TRP cc_start: 0.7893 (m100) cc_final: 0.7338 (m100) REVERT: B 634 GLU cc_start: 0.8388 (tt0) cc_final: 0.7253 (tp30) REVERT: C 61 TYR cc_start: 0.3328 (t80) cc_final: 0.3098 (t80) REVERT: C 80 ASN cc_start: 0.8519 (t0) cc_final: 0.8102 (p0) REVERT: C 161 MET cc_start: 0.6786 (ttm) cc_final: 0.6386 (ttm) REVERT: C 201 ILE cc_start: 0.8761 (tt) cc_final: 0.8386 (tt) REVERT: C 211 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8454 (mm-30) REVERT: C 308 ARG cc_start: 0.8958 (ttm170) cc_final: 0.8421 (mtp85) REVERT: C 309 ILE cc_start: 0.9334 (mt) cc_final: 0.9025 (mm) REVERT: C 426 MET cc_start: 0.9001 (tpt) cc_final: 0.8684 (ttm) REVERT: D 69 TRP cc_start: 0.8761 (m100) cc_final: 0.8272 (m100) REVERT: D 279 ASN cc_start: 0.9137 (t0) cc_final: 0.8670 (t0) REVERT: D 300 ASN cc_start: 0.8557 (m-40) cc_final: 0.8320 (m-40) REVERT: D 368 ASP cc_start: 0.8821 (t70) cc_final: 0.8578 (t0) REVERT: D 370 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8295 (mt-10) REVERT: E 530 MET cc_start: 0.9444 (mmm) cc_final: 0.8855 (mmm) REVERT: E 538 THR cc_start: 0.9554 (t) cc_final: 0.8554 (t) REVERT: E 571 TRP cc_start: 0.6366 (m-10) cc_final: 0.5471 (m-10) REVERT: E 574 LYS cc_start: 0.8858 (mtmt) cc_final: 0.8505 (pttp) REVERT: E 610 TRP cc_start: 0.6735 (p-90) cc_final: 0.6462 (p-90) REVERT: E 626 MET cc_start: 0.8309 (ttt) cc_final: 0.7790 (ttt) REVERT: F 530 MET cc_start: 0.8619 (ptm) cc_final: 0.8345 (ptm) REVERT: F 575 GLN cc_start: 0.8853 (tt0) cc_final: 0.8314 (tm-30) REVERT: F 584 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8383 (tm-30) REVERT: F 607 ASN cc_start: 0.7912 (t0) cc_final: 0.7123 (t0) REVERT: F 624 ASP cc_start: 0.7775 (m-30) cc_final: 0.7485 (p0) REVERT: G 23 GLU cc_start: 0.9110 (pm20) cc_final: 0.8768 (pm20) REVERT: G 54 THR cc_start: 0.8484 (p) cc_final: 0.7921 (p) REVERT: G 82 LEU cc_start: 0.8552 (tp) cc_final: 0.8269 (tp) REVERT: G 91 PHE cc_start: 0.8127 (p90) cc_final: 0.7455 (p90) REVERT: G 95 GLN cc_start: 0.9404 (tt0) cc_final: 0.9086 (tt0) REVERT: G 100 PHE cc_start: 0.9267 (m-80) cc_final: 0.8646 (m-80) REVERT: H 72 ASP cc_start: 0.8585 (p0) cc_final: 0.8273 (p0) REVERT: H 74 ASP cc_start: 0.7517 (p0) cc_final: 0.7226 (p0) REVERT: H 79 TYR cc_start: 0.8981 (m-80) cc_final: 0.8584 (m-10) REVERT: H 80 MET cc_start: 0.8738 (tmm) cc_final: 0.8199 (tmm) REVERT: H 86 ASP cc_start: 0.8493 (m-30) cc_final: 0.8145 (m-30) REVERT: H 95 GLN cc_start: 0.8530 (tm-30) cc_final: 0.7959 (tm-30) REVERT: I 23 GLU cc_start: 0.8438 (tt0) cc_final: 0.7867 (tp30) REVERT: I 58 ASN cc_start: 0.9019 (t0) cc_final: 0.8765 (t0) REVERT: I 59 ASN cc_start: 0.9178 (m-40) cc_final: 0.8910 (m110) REVERT: I 76 TYR cc_start: 0.8059 (m-80) cc_final: 0.7826 (m-10) REVERT: I 78 PHE cc_start: 0.9095 (m-10) cc_final: 0.8805 (m-10) REVERT: K 33 LEU cc_start: 0.9047 (tp) cc_final: 0.8611 (tp) REVERT: K 36 TYR cc_start: 0.8722 (m-80) cc_final: 0.7997 (m-10) REVERT: K 42 LYS cc_start: 0.8878 (mttt) cc_final: 0.8499 (mmtm) REVERT: K 46 LEU cc_start: 0.9157 (tp) cc_final: 0.8426 (tp) REVERT: K 49 TYR cc_start: 0.7312 (m-80) cc_final: 0.5952 (m-10) REVERT: K 58 VAL cc_start: 0.8087 (t) cc_final: 0.7701 (t) REVERT: K 76 ASN cc_start: 0.8767 (m-40) cc_final: 0.8393 (p0) REVERT: L 46 LEU cc_start: 0.9089 (tp) cc_final: 0.8866 (tp) REVERT: L 87 PHE cc_start: 0.7740 (m-80) cc_final: 0.7496 (m-10) REVERT: M 34 ASN cc_start: 0.8581 (m-40) cc_final: 0.8312 (m-40) REVERT: M 36 TYR cc_start: 0.8789 (m-80) cc_final: 0.8374 (m-80) REVERT: M 50 ASP cc_start: 0.9055 (t0) cc_final: 0.8645 (t0) REVERT: M 99 VAL cc_start: 0.9424 (p) cc_final: 0.9191 (p) REVERT: N 44 PRO cc_start: 0.7340 (Cg_exo) cc_final: 0.7027 (Cg_endo) REVERT: N 75 ILE cc_start: 0.3894 (mp) cc_final: 0.3513 (mp) REVERT: N 79 GLU cc_start: 0.3707 (pp20) cc_final: 0.3045 (tm-30) REVERT: N 86 TYR cc_start: 0.5893 (m-80) cc_final: 0.5517 (m-80) outliers start: 2 outliers final: 2 residues processed: 631 average time/residue: 0.3818 time to fit residues: 376.8109 Evaluate side-chains 422 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 420 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 195 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 235 optimal weight: 0.0470 chunk 254 optimal weight: 20.0000 chunk 209 optimal weight: 20.0000 chunk 233 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 189 optimal weight: 0.9980 overall best weight: 2.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 GLN D 203 GLN D 411 ASN E 577 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN H 108 GLN J 1 GLN ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 23404 Z= 0.348 Angle : 0.829 13.930 31789 Z= 0.410 Chirality : 0.050 0.443 3977 Planarity : 0.005 0.061 3838 Dihedral : 11.798 75.145 6038 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.17 % Allowed : 3.17 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.16), residues: 2589 helix: 0.73 (0.26), residues: 409 sheet: 0.19 (0.17), residues: 811 loop : 1.17 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP J 108 HIS 0.008 0.002 HIS C 105 PHE 0.032 0.003 PHE I 73 TYR 0.023 0.002 TYR G 32 ARG 0.010 0.001 ARG N 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 548 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8847 (m-90) cc_final: 0.8631 (m-90) REVERT: A 96 TRP cc_start: 0.8519 (m-90) cc_final: 0.7528 (m-90) REVERT: A 104 MET cc_start: 0.9179 (ttm) cc_final: 0.8967 (ttt) REVERT: A 111 LEU cc_start: 0.9550 (mt) cc_final: 0.9252 (mt) REVERT: A 116 LEU cc_start: 0.9297 (tp) cc_final: 0.9095 (tt) REVERT: A 377 ASN cc_start: 0.9121 (t0) cc_final: 0.8791 (t0) REVERT: B 530 MET cc_start: 0.9098 (mtp) cc_final: 0.8769 (mtt) REVERT: B 571 TRP cc_start: 0.8032 (m100) cc_final: 0.7267 (m100) REVERT: B 622 ILE cc_start: 0.8805 (mm) cc_final: 0.8539 (mm) REVERT: B 634 GLU cc_start: 0.8268 (tt0) cc_final: 0.7224 (tp30) REVERT: C 80 ASN cc_start: 0.8873 (t0) cc_final: 0.8484 (p0) REVERT: C 159 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.7635 (m-10) REVERT: C 161 MET cc_start: 0.7477 (ttm) cc_final: 0.6996 (ttm) REVERT: C 426 MET cc_start: 0.8953 (tpt) cc_final: 0.8561 (tpp) REVERT: D 69 TRP cc_start: 0.8846 (m100) cc_final: 0.8536 (m100) REVERT: D 95 MET cc_start: 0.8411 (ttm) cc_final: 0.7992 (ttm) REVERT: D 300 ASN cc_start: 0.8551 (m-40) cc_final: 0.8341 (m-40) REVERT: D 370 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8483 (mt-10) REVERT: E 536 THR cc_start: 0.8944 (p) cc_final: 0.8729 (p) REVERT: E 571 TRP cc_start: 0.6630 (m-10) cc_final: 0.5843 (m-10) REVERT: E 575 GLN cc_start: 0.9004 (tt0) cc_final: 0.8751 (tt0) REVERT: E 622 ILE cc_start: 0.8809 (mp) cc_final: 0.8203 (mp) REVERT: F 584 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8568 (tm-30) REVERT: F 591 GLN cc_start: 0.9316 (tp40) cc_final: 0.9099 (tp40) REVERT: G 23 GLU cc_start: 0.9059 (pm20) cc_final: 0.8791 (mp0) REVERT: G 31 ASP cc_start: 0.8770 (p0) cc_final: 0.8339 (p0) REVERT: G 78 PHE cc_start: 0.8924 (m-10) cc_final: 0.8697 (m-10) REVERT: G 80 MET cc_start: 0.8965 (ptm) cc_final: 0.8722 (ptm) REVERT: G 95 GLN cc_start: 0.9468 (tt0) cc_final: 0.9150 (tt0) REVERT: G 96 ARG cc_start: 0.8717 (ttp80) cc_final: 0.8502 (ttp80) REVERT: G 100 PHE cc_start: 0.9267 (m-80) cc_final: 0.8477 (m-80) REVERT: H 28 ASN cc_start: 0.8002 (t0) cc_final: 0.7538 (t0) REVERT: H 30 ARG cc_start: 0.8697 (mtt-85) cc_final: 0.8393 (mtt-85) REVERT: H 79 TYR cc_start: 0.9145 (m-80) cc_final: 0.8837 (m-80) REVERT: H 80 MET cc_start: 0.9081 (tmm) cc_final: 0.8448 (tmm) REVERT: H 86 ASP cc_start: 0.8353 (m-30) cc_final: 0.8124 (m-30) REVERT: H 99 TYR cc_start: 0.9125 (m-80) cc_final: 0.8571 (m-10) REVERT: I 28 ASN cc_start: 0.8181 (t0) cc_final: 0.7654 (t0) REVERT: I 59 ASN cc_start: 0.9183 (m-40) cc_final: 0.8657 (m110) REVERT: J 48 MET cc_start: 0.6695 (mmp) cc_final: 0.6202 (mmm) REVERT: J 60 LYS cc_start: 0.7210 (pttt) cc_final: 0.6894 (pttm) REVERT: K 5 THR cc_start: 0.7656 (p) cc_final: 0.7384 (p) REVERT: K 33 LEU cc_start: 0.9019 (tp) cc_final: 0.8779 (tp) REVERT: K 36 TYR cc_start: 0.9102 (m-80) cc_final: 0.7797 (m-10) REVERT: K 42 LYS cc_start: 0.8964 (mttt) cc_final: 0.8716 (mmtm) REVERT: K 46 LEU cc_start: 0.8932 (tp) cc_final: 0.8699 (tp) REVERT: K 49 TYR cc_start: 0.7776 (m-80) cc_final: 0.6832 (m-80) REVERT: K 54 LEU cc_start: 0.9140 (pp) cc_final: 0.8893 (pp) REVERT: K 55 GLU cc_start: 0.8670 (tp30) cc_final: 0.8007 (tp30) REVERT: K 75 ILE cc_start: 0.8380 (mm) cc_final: 0.8074 (mm) REVERT: K 76 ASN cc_start: 0.8524 (m-40) cc_final: 0.8271 (p0) REVERT: L 37 GLN cc_start: 0.8705 (pp30) cc_final: 0.8434 (pp30) REVERT: M 36 TYR cc_start: 0.8919 (m-80) cc_final: 0.8608 (m-10) REVERT: M 50 ASP cc_start: 0.8893 (t0) cc_final: 0.8604 (t0) REVERT: M 78 LEU cc_start: 0.9082 (tp) cc_final: 0.8834 (pp) REVERT: N 95 PRO cc_start: 0.5812 (Cg_endo) cc_final: 0.5141 (Cg_exo) outliers start: 4 outliers final: 1 residues processed: 550 average time/residue: 0.3572 time to fit residues: 300.7072 Evaluate side-chains 402 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 400 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 236 optimal weight: 1.9990 chunk 250 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23404 Z= 0.246 Angle : 0.731 10.218 31789 Z= 0.361 Chirality : 0.049 0.510 3977 Planarity : 0.005 0.066 3838 Dihedral : 10.566 65.718 6038 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.04 % Allowed : 2.47 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.16), residues: 2589 helix: 0.99 (0.27), residues: 403 sheet: 0.06 (0.17), residues: 849 loop : 0.95 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 50 HIS 0.008 0.001 HIS C 72 PHE 0.018 0.002 PHE J 29 TYR 0.024 0.002 TYR M 32 ARG 0.010 0.001 ARG G 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 529 time to evaluate : 2.411 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: A 83 GLU cc_start: 0.7334 (tm-30) cc_final: 0.7128 (tm-30) REVERT: A 111 LEU cc_start: 0.9499 (mt) cc_final: 0.9202 (mt) REVERT: A 257 THR cc_start: 0.8043 (p) cc_final: 0.7770 (t) REVERT: B 530 MET cc_start: 0.9092 (mtp) cc_final: 0.8617 (mtt) REVERT: B 623 TRP cc_start: 0.8063 (m100) cc_final: 0.7757 (m100) REVERT: B 634 GLU cc_start: 0.8211 (tt0) cc_final: 0.7121 (tp30) REVERT: C 80 ASN cc_start: 0.8943 (t0) cc_final: 0.8653 (p0) REVERT: C 309 ILE cc_start: 0.9363 (mm) cc_final: 0.9049 (tt) REVERT: C 426 MET cc_start: 0.8949 (tpt) cc_final: 0.8580 (tpp) REVERT: D 69 TRP cc_start: 0.8746 (m100) cc_final: 0.8471 (m100) REVERT: D 95 MET cc_start: 0.8372 (ttm) cc_final: 0.7735 (ttm) REVERT: D 365 SER cc_start: 0.8038 (t) cc_final: 0.7814 (t) REVERT: D 368 ASP cc_start: 0.8553 (t0) cc_final: 0.8210 (t0) REVERT: E 571 TRP cc_start: 0.6519 (m-10) cc_final: 0.5798 (m-10) REVERT: E 626 MET cc_start: 0.8057 (ttt) cc_final: 0.7564 (ttt) REVERT: E 655 LYS cc_start: 0.9380 (mttp) cc_final: 0.8893 (mttm) REVERT: F 575 GLN cc_start: 0.8697 (tt0) cc_final: 0.8109 (tm-30) REVERT: F 584 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8644 (tm-30) REVERT: F 591 GLN cc_start: 0.9308 (tp40) cc_final: 0.9079 (tp40) REVERT: F 624 ASP cc_start: 0.7968 (m-30) cc_final: 0.7767 (m-30) REVERT: G 23 GLU cc_start: 0.8943 (pm20) cc_final: 0.8666 (mp0) REVERT: G 31 ASP cc_start: 0.8871 (p0) cc_final: 0.8640 (p0) REVERT: G 78 PHE cc_start: 0.8987 (m-10) cc_final: 0.8746 (m-10) REVERT: G 80 MET cc_start: 0.8978 (ptm) cc_final: 0.8655 (ptm) REVERT: G 96 ARG cc_start: 0.8579 (ttp80) cc_final: 0.8322 (ttp80) REVERT: G 100 PHE cc_start: 0.9053 (m-80) cc_final: 0.8610 (m-80) REVERT: H 28 ASN cc_start: 0.8052 (t0) cc_final: 0.7845 (t0) REVERT: H 30 ARG cc_start: 0.8670 (mtt-85) cc_final: 0.8438 (mtt-85) REVERT: H 79 TYR cc_start: 0.9098 (m-80) cc_final: 0.8776 (m-10) REVERT: H 80 MET cc_start: 0.9203 (tmm) cc_final: 0.8520 (tmm) REVERT: H 98 ASP cc_start: 0.8575 (t0) cc_final: 0.8347 (t0) REVERT: I 23 GLU cc_start: 0.8545 (tt0) cc_final: 0.8207 (tp30) REVERT: I 28 ASN cc_start: 0.8177 (t0) cc_final: 0.7814 (t0) REVERT: I 53 LYS cc_start: 0.9606 (ttmm) cc_final: 0.9232 (ttmt) REVERT: I 59 ASN cc_start: 0.8992 (m-40) cc_final: 0.8565 (m110) REVERT: J 108 TRP cc_start: 0.5106 (m-10) cc_final: 0.4716 (m-10) REVERT: K 5 THR cc_start: 0.7831 (p) cc_final: 0.7349 (p) REVERT: K 33 LEU cc_start: 0.9055 (tp) cc_final: 0.8837 (tp) REVERT: K 36 TYR cc_start: 0.8751 (m-80) cc_final: 0.7900 (m-10) REVERT: K 42 LYS cc_start: 0.9131 (mttt) cc_final: 0.8749 (mmtm) REVERT: K 54 LEU cc_start: 0.9146 (pp) cc_final: 0.8943 (pp) REVERT: K 75 ILE cc_start: 0.8650 (mm) cc_final: 0.8388 (mm) REVERT: M 34 ASN cc_start: 0.9107 (m-40) cc_final: 0.8907 (m-40) REVERT: M 50 ASP cc_start: 0.9009 (t0) cc_final: 0.8505 (t0) REVERT: M 69 GLN cc_start: 0.7849 (pm20) cc_final: 0.6469 (mm110) REVERT: M 70 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7216 (tp30) REVERT: N 73 LEU cc_start: 0.8185 (tp) cc_final: 0.7826 (pt) REVERT: N 79 GLU cc_start: 0.7357 (tm-30) cc_final: 0.7023 (tm-30) outliers start: 1 outliers final: 0 residues processed: 530 average time/residue: 0.3602 time to fit residues: 294.7517 Evaluate side-chains 412 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 0.0470 chunk 142 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 213 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 127 optimal weight: 0.6980 chunk 224 optimal weight: 8.9990 chunk 63 optimal weight: 0.4980 overall best weight: 1.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN H 56 GLN ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23404 Z= 0.201 Angle : 0.690 9.785 31789 Z= 0.340 Chirality : 0.048 0.563 3977 Planarity : 0.004 0.047 3838 Dihedral : 9.776 62.862 6038 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.04 % Allowed : 2.04 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.16), residues: 2589 helix: 1.15 (0.27), residues: 402 sheet: 0.09 (0.17), residues: 842 loop : 0.81 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 96 HIS 0.011 0.001 HIS C 72 PHE 0.029 0.002 PHE A 53 TYR 0.027 0.001 TYR C 217 ARG 0.007 0.000 ARG M 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 523 time to evaluate : 2.077 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: A 109 ILE cc_start: 0.9552 (mt) cc_final: 0.9334 (mt) REVERT: A 111 LEU cc_start: 0.9494 (mt) cc_final: 0.9222 (mt) REVERT: A 377 ASN cc_start: 0.9201 (t0) cc_final: 0.8987 (t0) REVERT: A 426 MET cc_start: 0.8969 (tpt) cc_final: 0.8738 (tpp) REVERT: A 434 MET cc_start: 0.8520 (ptm) cc_final: 0.8307 (ptm) REVERT: B 530 MET cc_start: 0.9039 (mtp) cc_final: 0.8695 (mtt) REVERT: B 630 GLN cc_start: 0.8384 (mp10) cc_final: 0.8079 (mp10) REVERT: B 634 GLU cc_start: 0.8225 (tt0) cc_final: 0.7156 (tp30) REVERT: C 80 ASN cc_start: 0.8999 (t0) cc_final: 0.8724 (p0) REVERT: C 161 MET cc_start: 0.7150 (ttm) cc_final: 0.6788 (ttm) REVERT: C 309 ILE cc_start: 0.9374 (mm) cc_final: 0.9049 (mm) REVERT: C 426 MET cc_start: 0.9065 (tpt) cc_final: 0.8667 (tpp) REVERT: D 69 TRP cc_start: 0.8684 (m100) cc_final: 0.8409 (m100) REVERT: D 95 MET cc_start: 0.8315 (ttm) cc_final: 0.7814 (ttm) REVERT: D 370 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7991 (mt-10) REVERT: E 538 THR cc_start: 0.9100 (t) cc_final: 0.8858 (t) REVERT: E 571 TRP cc_start: 0.6490 (m-10) cc_final: 0.5712 (m-10) REVERT: E 655 LYS cc_start: 0.9383 (mttp) cc_final: 0.8932 (mttm) REVERT: F 584 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8659 (tm-30) REVERT: F 591 GLN cc_start: 0.9274 (tp40) cc_final: 0.9074 (tp40) REVERT: F 658 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8348 (tm-30) REVERT: G 23 GLU cc_start: 0.8921 (pm20) cc_final: 0.8598 (mp0) REVERT: G 80 MET cc_start: 0.8890 (ptm) cc_final: 0.8668 (ptm) REVERT: G 100 PHE cc_start: 0.9051 (m-80) cc_final: 0.8628 (m-80) REVERT: H 28 ASN cc_start: 0.8121 (t0) cc_final: 0.7849 (t0) REVERT: H 79 TYR cc_start: 0.9053 (m-80) cc_final: 0.8687 (m-10) REVERT: H 80 MET cc_start: 0.9253 (tmm) cc_final: 0.8586 (tmm) REVERT: H 86 ASP cc_start: 0.8175 (m-30) cc_final: 0.7952 (m-30) REVERT: H 99 TYR cc_start: 0.9020 (m-80) cc_final: 0.8686 (m-80) REVERT: I 23 GLU cc_start: 0.8483 (tt0) cc_final: 0.8216 (tp30) REVERT: I 28 ASN cc_start: 0.8109 (t0) cc_final: 0.7607 (t0) REVERT: J 38 ARG cc_start: 0.7835 (ttp80) cc_final: 0.7483 (ttp80) REVERT: J 48 MET cc_start: 0.6956 (mmp) cc_final: 0.6527 (mmm) REVERT: J 100 ARG cc_start: 0.7355 (ptm160) cc_final: 0.7081 (ptm160) REVERT: J 100 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7852 (mm-30) REVERT: K 33 LEU cc_start: 0.9114 (tp) cc_final: 0.8896 (tp) REVERT: K 36 TYR cc_start: 0.8700 (m-80) cc_final: 0.8073 (m-10) REVERT: K 37 GLN cc_start: 0.8552 (pp30) cc_final: 0.8266 (pp30) REVERT: K 42 LYS cc_start: 0.9099 (mttt) cc_final: 0.8751 (mmtm) REVERT: K 58 VAL cc_start: 0.8028 (t) cc_final: 0.7478 (t) REVERT: K 75 ILE cc_start: 0.8699 (mm) cc_final: 0.8397 (mm) REVERT: K 87 PHE cc_start: 0.8642 (p90) cc_final: 0.8434 (p90) REVERT: L 96 GLU cc_start: 0.8926 (pt0) cc_final: 0.8423 (pt0) REVERT: M 34 ASN cc_start: 0.8944 (m-40) cc_final: 0.8692 (m-40) REVERT: M 36 TYR cc_start: 0.8619 (m-10) cc_final: 0.8128 (m-10) REVERT: M 50 ASP cc_start: 0.8923 (t0) cc_final: 0.8541 (t0) REVERT: M 69 GLN cc_start: 0.7849 (pm20) cc_final: 0.6814 (mm110) REVERT: M 70 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7190 (tm-30) REVERT: N 47 LEU cc_start: 0.7351 (mp) cc_final: 0.7084 (mp) REVERT: N 95 PRO cc_start: 0.5434 (Cg_endo) cc_final: 0.5217 (Cg_exo) outliers start: 1 outliers final: 0 residues processed: 524 average time/residue: 0.3833 time to fit residues: 314.7529 Evaluate side-chains 413 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 10.0000 chunk 225 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 656 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.113 23404 Z= 0.566 Angle : 0.977 10.508 31789 Z= 0.478 Chirality : 0.054 0.431 3977 Planarity : 0.006 0.106 3838 Dihedral : 10.751 65.294 6038 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.04 % Allowed : 2.86 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.16), residues: 2589 helix: 0.15 (0.25), residues: 412 sheet: -0.37 (0.17), residues: 796 loop : 0.08 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A 96 HIS 0.011 0.003 HIS C 72 PHE 0.032 0.003 PHE A 53 TYR 0.038 0.003 TYR G 76 ARG 0.016 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 452 time to evaluate : 2.653 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: A 180 ASP cc_start: 0.8671 (m-30) cc_final: 0.8436 (m-30) REVERT: A 356 ASN cc_start: 0.7808 (m-40) cc_final: 0.7136 (p0) REVERT: A 426 MET cc_start: 0.8815 (tpt) cc_final: 0.8614 (tpp) REVERT: B 530 MET cc_start: 0.9281 (mtp) cc_final: 0.8961 (mtt) REVERT: B 575 GLN cc_start: 0.8728 (mm110) cc_final: 0.8355 (tp40) REVERT: B 588 ARG cc_start: 0.9079 (ttp-170) cc_final: 0.8863 (ttp-110) REVERT: B 622 ILE cc_start: 0.8996 (mm) cc_final: 0.8661 (mm) REVERT: B 634 GLU cc_start: 0.8456 (tt0) cc_final: 0.7580 (tp30) REVERT: C 80 ASN cc_start: 0.9067 (t0) cc_final: 0.8845 (p0) REVERT: C 150 MET cc_start: 0.8977 (mmp) cc_final: 0.8439 (mmt) REVERT: C 195 ASN cc_start: 0.9053 (p0) cc_final: 0.8842 (p0) REVERT: C 426 MET cc_start: 0.9042 (tpt) cc_final: 0.8841 (tpp) REVERT: D 86 LEU cc_start: 0.9387 (mp) cc_final: 0.9181 (mp) REVERT: E 544 LEU cc_start: 0.9315 (mt) cc_final: 0.9011 (tt) REVERT: E 571 TRP cc_start: 0.6432 (m-10) cc_final: 0.5730 (m-10) REVERT: E 601 LYS cc_start: 0.9165 (mttm) cc_final: 0.8964 (mtpp) REVERT: E 655 LYS cc_start: 0.9386 (mttp) cc_final: 0.9011 (mttm) REVERT: F 575 GLN cc_start: 0.8844 (tt0) cc_final: 0.8607 (tm-30) REVERT: F 584 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8722 (tm-30) REVERT: F 624 ASP cc_start: 0.8414 (m-30) cc_final: 0.8176 (m-30) REVERT: G 31 ASP cc_start: 0.8785 (p0) cc_final: 0.8474 (p0) REVERT: G 100 PHE cc_start: 0.9134 (m-80) cc_final: 0.8861 (m-80) REVERT: H 18 VAL cc_start: 0.9250 (p) cc_final: 0.9022 (t) REVERT: H 79 TYR cc_start: 0.9083 (m-80) cc_final: 0.8767 (m-80) REVERT: H 80 MET cc_start: 0.9370 (tmm) cc_final: 0.8573 (tmm) REVERT: H 99 TYR cc_start: 0.9142 (m-80) cc_final: 0.8917 (m-80) REVERT: I 23 GLU cc_start: 0.8696 (tt0) cc_final: 0.8378 (tp30) REVERT: I 28 ASN cc_start: 0.8372 (t0) cc_final: 0.7816 (t0) REVERT: I 62 GLN cc_start: 0.9334 (tt0) cc_final: 0.9102 (tt0) REVERT: I 98 ASP cc_start: 0.9039 (m-30) cc_final: 0.8671 (t70) REVERT: J 48 MET cc_start: 0.6980 (mmp) cc_final: 0.6516 (mmm) REVERT: J 60 LYS cc_start: 0.7165 (pttm) cc_final: 0.6714 (pttm) REVERT: K 36 TYR cc_start: 0.8931 (m-80) cc_final: 0.8100 (m-10) REVERT: K 42 LYS cc_start: 0.9165 (mttt) cc_final: 0.8787 (mmtm) REVERT: K 58 VAL cc_start: 0.8405 (t) cc_final: 0.7977 (t) REVERT: K 75 ILE cc_start: 0.8344 (mm) cc_final: 0.8066 (mm) REVERT: L 37 GLN cc_start: 0.8807 (pp30) cc_final: 0.8555 (pp30) REVERT: L 97 PHE cc_start: 0.8984 (m-80) cc_final: 0.8519 (m-80) REVERT: M 34 ASN cc_start: 0.8996 (m-40) cc_final: 0.8700 (m-40) REVERT: M 69 GLN cc_start: 0.7959 (pm20) cc_final: 0.6720 (mm110) REVERT: M 70 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7330 (tm-30) REVERT: N 47 LEU cc_start: 0.7186 (mp) cc_final: 0.6663 (mp) REVERT: N 95 PRO cc_start: 0.5955 (Cg_endo) cc_final: 0.5696 (Cg_exo) outliers start: 1 outliers final: 0 residues processed: 453 average time/residue: 0.3586 time to fit residues: 252.3785 Evaluate side-chains 346 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 142 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 249 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN A 300 ASN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.6156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23404 Z= 0.277 Angle : 0.741 9.591 31789 Z= 0.363 Chirality : 0.049 0.511 3977 Planarity : 0.004 0.058 3838 Dihedral : 9.865 61.312 6038 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.09 % Allowed : 1.61 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2589 helix: 0.70 (0.26), residues: 402 sheet: -0.27 (0.17), residues: 833 loop : 0.21 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP J 47 HIS 0.010 0.001 HIS C 72 PHE 0.025 0.002 PHE A 53 TYR 0.022 0.002 TYR M 32 ARG 0.008 0.001 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 474 time to evaluate : 2.318 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 102 GLU cc_start: 0.9244 (mp0) cc_final: 0.8974 (mp0) REVERT: A 111 LEU cc_start: 0.9561 (mt) cc_final: 0.9290 (mt) REVERT: A 203 GLN cc_start: 0.6993 (tp-100) cc_final: 0.6566 (tm-30) REVERT: A 356 ASN cc_start: 0.7582 (m-40) cc_final: 0.6936 (p0) REVERT: A 395 TRP cc_start: 0.8759 (m100) cc_final: 0.8259 (m100) REVERT: B 530 MET cc_start: 0.9159 (mtp) cc_final: 0.8721 (mtt) REVERT: B 587 LEU cc_start: 0.9349 (tp) cc_final: 0.9037 (tt) REVERT: B 622 ILE cc_start: 0.8918 (mm) cc_final: 0.8694 (mm) REVERT: B 623 TRP cc_start: 0.8281 (m100) cc_final: 0.7455 (m100) REVERT: B 634 GLU cc_start: 0.8413 (tt0) cc_final: 0.7551 (tp30) REVERT: B 657 GLU cc_start: 0.9020 (mp0) cc_final: 0.8607 (mp0) REVERT: C 80 ASN cc_start: 0.9232 (t0) cc_final: 0.8822 (p0) REVERT: D 86 LEU cc_start: 0.9398 (mp) cc_final: 0.9182 (mp) REVERT: D 100 MET cc_start: 0.8954 (ttp) cc_final: 0.8635 (ttm) REVERT: D 107 ASP cc_start: 0.8942 (t0) cc_final: 0.8738 (t0) REVERT: E 544 LEU cc_start: 0.9244 (mt) cc_final: 0.8991 (tt) REVERT: E 571 TRP cc_start: 0.6436 (m-10) cc_final: 0.5571 (m-10) REVERT: E 655 LYS cc_start: 0.9419 (mttp) cc_final: 0.8964 (mttm) REVERT: F 584 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8735 (tm-30) REVERT: F 591 GLN cc_start: 0.9410 (tp40) cc_final: 0.9181 (tp40) REVERT: F 607 ASN cc_start: 0.8373 (t0) cc_final: 0.8135 (t0) REVERT: F 624 ASP cc_start: 0.8292 (m-30) cc_final: 0.8049 (m-30) REVERT: G 31 ASP cc_start: 0.8966 (p0) cc_final: 0.8678 (p0) REVERT: G 80 MET cc_start: 0.8920 (ptm) cc_final: 0.8653 (ptm) REVERT: G 95 GLN cc_start: 0.9449 (tt0) cc_final: 0.9039 (tt0) REVERT: G 100 PHE cc_start: 0.9222 (m-80) cc_final: 0.8807 (m-80) REVERT: H 18 VAL cc_start: 0.9251 (p) cc_final: 0.8961 (t) REVERT: H 28 ASN cc_start: 0.8344 (t0) cc_final: 0.8107 (t0) REVERT: H 79 TYR cc_start: 0.8966 (m-80) cc_final: 0.8464 (m-10) REVERT: H 80 MET cc_start: 0.9357 (tmm) cc_final: 0.8508 (tmm) REVERT: I 23 GLU cc_start: 0.8511 (tt0) cc_final: 0.8245 (tp30) REVERT: I 28 ASN cc_start: 0.8167 (t0) cc_final: 0.7607 (t0) REVERT: J 4 LEU cc_start: 0.5158 (tp) cc_final: 0.4849 (tp) REVERT: J 38 ARG cc_start: 0.7545 (ttp80) cc_final: 0.7290 (ttp80) REVERT: J 48 MET cc_start: 0.6942 (mmp) cc_final: 0.6691 (mmm) REVERT: J 100 ARG cc_start: 0.8085 (ptm160) cc_final: 0.7114 (ptm-80) REVERT: K 36 TYR cc_start: 0.8805 (m-80) cc_final: 0.8128 (m-10) REVERT: K 37 GLN cc_start: 0.8380 (pp30) cc_final: 0.8029 (pp30) REVERT: K 65 ARG cc_start: 0.6723 (mtm110) cc_final: 0.6362 (mtm110) REVERT: L 96 GLU cc_start: 0.8837 (pt0) cc_final: 0.8553 (pt0) REVERT: L 97 PHE cc_start: 0.8938 (m-80) cc_final: 0.8528 (m-80) REVERT: M 34 ASN cc_start: 0.9054 (m-40) cc_final: 0.8815 (m-40) REVERT: M 36 TYR cc_start: 0.8645 (m-10) cc_final: 0.8252 (m-10) REVERT: M 69 GLN cc_start: 0.8057 (pm20) cc_final: 0.7180 (mm-40) REVERT: M 70 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7413 (tm-30) REVERT: N 21 LEU cc_start: 0.2698 (mt) cc_final: 0.2416 (mt) REVERT: N 47 LEU cc_start: 0.6943 (mp) cc_final: 0.6730 (mp) outliers start: 2 outliers final: 0 residues processed: 475 average time/residue: 0.3565 time to fit residues: 261.6664 Evaluate side-chains 371 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 149 optimal weight: 0.3980 chunk 75 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 158 optimal weight: 9.9990 chunk 170 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 196 optimal weight: 8.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN J 52AHIS ** L 37 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: 0.6316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23404 Z= 0.185 Angle : 0.690 10.413 31789 Z= 0.338 Chirality : 0.048 0.431 3977 Planarity : 0.004 0.052 3838 Dihedral : 9.016 59.517 6038 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.04 % Allowed : 0.48 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2589 helix: 0.92 (0.27), residues: 408 sheet: -0.18 (0.17), residues: 843 loop : 0.41 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 96 HIS 0.010 0.001 HIS C 72 PHE 0.023 0.002 PHE A 53 TYR 0.023 0.002 TYR I 27 ARG 0.012 0.001 ARG G 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 516 time to evaluate : 2.496 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: A 69 TRP cc_start: 0.8735 (m-90) cc_final: 0.8214 (m-90) REVERT: A 102 GLU cc_start: 0.9165 (mp0) cc_final: 0.8866 (mp0) REVERT: A 111 LEU cc_start: 0.9514 (mt) cc_final: 0.9181 (mt) REVERT: A 203 GLN cc_start: 0.6910 (tp-100) cc_final: 0.6317 (tm-30) REVERT: A 356 ASN cc_start: 0.7461 (m-40) cc_final: 0.6874 (p0) REVERT: A 395 TRP cc_start: 0.8628 (m100) cc_final: 0.8148 (m100) REVERT: A 426 MET cc_start: 0.8850 (tpt) cc_final: 0.8599 (tpp) REVERT: B 530 MET cc_start: 0.9054 (mtp) cc_final: 0.8580 (mtt) REVERT: B 588 ARG cc_start: 0.8942 (ttp-170) cc_final: 0.8708 (ttp-110) REVERT: B 623 TRP cc_start: 0.8379 (m100) cc_final: 0.7566 (m100) REVERT: B 630 GLN cc_start: 0.8488 (mp10) cc_final: 0.8149 (mp10) REVERT: B 634 GLU cc_start: 0.8423 (tt0) cc_final: 0.7580 (tp30) REVERT: B 648 GLU cc_start: 0.7407 (tp30) cc_final: 0.7188 (tp30) REVERT: C 80 ASN cc_start: 0.9122 (t0) cc_final: 0.8801 (p0) REVERT: D 86 LEU cc_start: 0.9377 (mp) cc_final: 0.9169 (mp) REVERT: D 100 MET cc_start: 0.8941 (ttp) cc_final: 0.8667 (ttm) REVERT: D 492 GLU cc_start: 0.8677 (tt0) cc_final: 0.8000 (tm-30) REVERT: E 536 THR cc_start: 0.8884 (p) cc_final: 0.8403 (p) REVERT: E 571 TRP cc_start: 0.6627 (m-10) cc_final: 0.5760 (m-10) REVERT: E 634 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8301 (mt-10) REVERT: E 655 LYS cc_start: 0.9395 (mttp) cc_final: 0.9073 (mttt) REVERT: F 575 GLN cc_start: 0.8811 (tt0) cc_final: 0.8427 (pp30) REVERT: F 591 GLN cc_start: 0.9318 (tp40) cc_final: 0.9100 (tp40) REVERT: F 624 ASP cc_start: 0.8236 (m-30) cc_final: 0.7973 (m-30) REVERT: F 658 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8615 (tm-30) REVERT: G 28 ASN cc_start: 0.8069 (t0) cc_final: 0.7775 (t0) REVERT: G 31 ASP cc_start: 0.8831 (p0) cc_final: 0.8439 (p0) REVERT: G 95 GLN cc_start: 0.9349 (tt0) cc_final: 0.8936 (tt0) REVERT: G 100 PHE cc_start: 0.9219 (m-80) cc_final: 0.8783 (m-80) REVERT: H 18 VAL cc_start: 0.9256 (p) cc_final: 0.9013 (t) REVERT: H 30 ARG cc_start: 0.8674 (mtt-85) cc_final: 0.8433 (mtt-85) REVERT: H 80 MET cc_start: 0.9360 (tmm) cc_final: 0.8552 (tmm) REVERT: I 28 ASN cc_start: 0.7947 (t0) cc_final: 0.7324 (t0) REVERT: I 35 HIS cc_start: 0.9156 (m-70) cc_final: 0.8766 (m90) REVERT: I 75 THR cc_start: 0.9041 (p) cc_final: 0.8838 (p) REVERT: J 4 LEU cc_start: 0.5362 (tp) cc_final: 0.5086 (tp) REVERT: J 38 ARG cc_start: 0.7587 (ttp80) cc_final: 0.7189 (ttp80) REVERT: J 48 MET cc_start: 0.6954 (mmp) cc_final: 0.6601 (mmm) REVERT: J 60 LYS cc_start: 0.7504 (pttm) cc_final: 0.7205 (pttm) REVERT: J 100 ARG cc_start: 0.8202 (ptm160) cc_final: 0.7248 (ptm-80) REVERT: J 100 LEU cc_start: 0.9191 (mp) cc_final: 0.8979 (mp) REVERT: J 100 TYR cc_start: 0.8547 (m-10) cc_final: 0.8247 (m-10) REVERT: K 36 TYR cc_start: 0.8602 (m-80) cc_final: 0.8017 (m-10) REVERT: K 37 GLN cc_start: 0.8396 (pp30) cc_final: 0.8013 (pp30) REVERT: K 46 LEU cc_start: 0.9145 (tp) cc_final: 0.8772 (tp) REVERT: K 55 GLU cc_start: 0.8096 (tt0) cc_final: 0.7552 (tt0) REVERT: K 58 VAL cc_start: 0.8120 (t) cc_final: 0.7714 (t) REVERT: K 65 ARG cc_start: 0.6616 (mtm110) cc_final: 0.6268 (mtm110) REVERT: L 96 GLU cc_start: 0.8836 (pt0) cc_final: 0.8524 (pt0) REVERT: L 97 PHE cc_start: 0.8931 (m-80) cc_final: 0.8622 (m-80) REVERT: M 34 ASN cc_start: 0.9021 (m-40) cc_final: 0.8764 (m-40) REVERT: M 69 GLN cc_start: 0.8041 (pm20) cc_final: 0.7524 (mm-40) REVERT: M 70 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7418 (tm-30) REVERT: M 77 ASN cc_start: 0.8313 (t0) cc_final: 0.8111 (t0) REVERT: N 21 LEU cc_start: 0.3657 (mt) cc_final: 0.3386 (mt) REVERT: N 47 LEU cc_start: 0.6915 (mp) cc_final: 0.6647 (mp) outliers start: 1 outliers final: 0 residues processed: 517 average time/residue: 0.3485 time to fit residues: 279.3423 Evaluate side-chains 400 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 7.9990 chunk 239 optimal weight: 9.9990 chunk 218 optimal weight: 0.5980 chunk 232 optimal weight: 6.9990 chunk 140 optimal weight: 0.4980 chunk 101 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN ** K 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23404 Z= 0.274 Angle : 0.724 9.595 31789 Z= 0.354 Chirality : 0.047 0.410 3977 Planarity : 0.004 0.090 3838 Dihedral : 9.013 58.440 6038 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.04 % Allowed : 0.69 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 2589 helix: 0.83 (0.27), residues: 411 sheet: -0.22 (0.18), residues: 825 loop : 0.22 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP N 96 HIS 0.011 0.001 HIS C 72 PHE 0.030 0.002 PHE N 98 TYR 0.027 0.002 TYR J 100C ARG 0.008 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 485 time to evaluate : 2.653 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: A 69 TRP cc_start: 0.8713 (m-90) cc_final: 0.8390 (m-90) REVERT: A 98 ASN cc_start: 0.8871 (t0) cc_final: 0.8569 (t0) REVERT: A 102 GLU cc_start: 0.9193 (mp0) cc_final: 0.8892 (mp0) REVERT: A 111 LEU cc_start: 0.9532 (mt) cc_final: 0.9292 (mt) REVERT: A 271 MET cc_start: 0.8257 (mmm) cc_final: 0.7916 (mmm) REVERT: A 356 ASN cc_start: 0.7512 (m-40) cc_final: 0.6905 (p0) REVERT: A 395 TRP cc_start: 0.8743 (m100) cc_final: 0.8156 (m100) REVERT: A 426 MET cc_start: 0.8898 (tpt) cc_final: 0.8559 (tpp) REVERT: A 475 MET cc_start: 0.9057 (mmp) cc_final: 0.8789 (mmm) REVERT: B 530 MET cc_start: 0.9091 (mtp) cc_final: 0.8775 (mtt) REVERT: B 588 ARG cc_start: 0.8968 (ttp-170) cc_final: 0.8729 (ttp-110) REVERT: B 622 ILE cc_start: 0.8844 (mm) cc_final: 0.8524 (mm) REVERT: B 630 GLN cc_start: 0.8406 (mp10) cc_final: 0.8103 (mp10) REVERT: B 634 GLU cc_start: 0.8436 (tt0) cc_final: 0.7581 (tp30) REVERT: B 648 GLU cc_start: 0.7498 (tp30) cc_final: 0.7259 (tp30) REVERT: C 80 ASN cc_start: 0.9101 (t0) cc_final: 0.8822 (p0) REVERT: C 150 MET cc_start: 0.9022 (mpp) cc_final: 0.8265 (mpp) REVERT: C 426 MET cc_start: 0.8864 (ttm) cc_final: 0.8648 (ttm) REVERT: D 95 MET cc_start: 0.8997 (tpp) cc_final: 0.8782 (tpp) REVERT: D 99 ASN cc_start: 0.8343 (m-40) cc_final: 0.8053 (m-40) REVERT: D 100 MET cc_start: 0.8871 (ttp) cc_final: 0.8612 (ttm) REVERT: D 102 GLU cc_start: 0.8404 (pm20) cc_final: 0.7847 (pm20) REVERT: D 492 GLU cc_start: 0.8714 (tt0) cc_final: 0.8029 (tm-30) REVERT: E 571 TRP cc_start: 0.6236 (m-10) cc_final: 0.5453 (m-10) REVERT: E 626 MET cc_start: 0.8166 (ttt) cc_final: 0.7521 (ttt) REVERT: E 634 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8390 (mt-10) REVERT: E 655 LYS cc_start: 0.9389 (mttp) cc_final: 0.8998 (mttm) REVERT: F 624 ASP cc_start: 0.8382 (m-30) cc_final: 0.8144 (m-30) REVERT: G 31 ASP cc_start: 0.8842 (p0) cc_final: 0.8603 (p0) REVERT: G 100 PHE cc_start: 0.9256 (m-80) cc_final: 0.8803 (m-80) REVERT: H 18 VAL cc_start: 0.9329 (p) cc_final: 0.9104 (t) REVERT: H 72 ASP cc_start: 0.8417 (p0) cc_final: 0.7894 (p0) REVERT: H 80 MET cc_start: 0.9400 (tmm) cc_final: 0.8710 (tmm) REVERT: I 23 GLU cc_start: 0.8474 (tp30) cc_final: 0.7913 (tp30) REVERT: I 28 ASN cc_start: 0.7916 (t0) cc_final: 0.7285 (t0) REVERT: I 62 GLN cc_start: 0.9294 (tt0) cc_final: 0.9068 (tt0) REVERT: J 4 LEU cc_start: 0.5322 (tp) cc_final: 0.4896 (tp) REVERT: J 48 MET cc_start: 0.7183 (mmp) cc_final: 0.6616 (mmm) REVERT: J 60 LYS cc_start: 0.7595 (pttm) cc_final: 0.7075 (pttm) REVERT: J 100 ARG cc_start: 0.8190 (ptm160) cc_final: 0.7690 (ptm160) REVERT: J 100 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7645 (mm-30) REVERT: K 2 ILE cc_start: 0.8443 (mp) cc_final: 0.7600 (mp) REVERT: K 26 ASN cc_start: 0.7927 (m110) cc_final: 0.7672 (p0) REVERT: K 36 TYR cc_start: 0.8630 (m-80) cc_final: 0.8046 (m-10) REVERT: K 37 GLN cc_start: 0.8385 (pp30) cc_final: 0.8057 (pp30) REVERT: K 46 LEU cc_start: 0.9095 (tp) cc_final: 0.8799 (tp) REVERT: K 55 GLU cc_start: 0.7816 (tt0) cc_final: 0.7323 (tt0) REVERT: K 58 VAL cc_start: 0.8268 (t) cc_final: 0.7826 (t) REVERT: K 65 ARG cc_start: 0.6533 (mtm110) cc_final: 0.6158 (mtm110) REVERT: L 5 THR cc_start: 0.7510 (t) cc_final: 0.7232 (t) REVERT: L 96 GLU cc_start: 0.8751 (pt0) cc_final: 0.8507 (pt0) REVERT: L 97 PHE cc_start: 0.8940 (m-80) cc_final: 0.8724 (m-80) REVERT: M 34 ASN cc_start: 0.9127 (m-40) cc_final: 0.8697 (m-40) REVERT: M 36 TYR cc_start: 0.8886 (m-10) cc_final: 0.8465 (m-10) REVERT: M 69 GLN cc_start: 0.8099 (pm20) cc_final: 0.7277 (mm110) REVERT: M 70 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7445 (tm-30) REVERT: N 21 LEU cc_start: 0.3801 (mt) cc_final: 0.3498 (mt) outliers start: 1 outliers final: 0 residues processed: 486 average time/residue: 0.3411 time to fit residues: 259.9321 Evaluate side-chains 374 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 0.9980 chunk 245 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 116 optimal weight: 0.0970 chunk 171 optimal weight: 0.6980 chunk 258 optimal weight: 20.0000 chunk 237 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 overall best weight: 1.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 425 ASN C 66 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN K 26 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.6593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23404 Z= 0.208 Angle : 0.688 9.529 31789 Z= 0.336 Chirality : 0.046 0.414 3977 Planarity : 0.004 0.082 3838 Dihedral : 8.641 59.822 6038 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.04 % Allowed : 0.30 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.16), residues: 2589 helix: 1.01 (0.27), residues: 405 sheet: -0.16 (0.18), residues: 825 loop : 0.25 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I 50 HIS 0.011 0.001 HIS C 72 PHE 0.025 0.002 PHE N 98 TYR 0.018 0.001 TYR M 36 ARG 0.012 0.001 ARG G 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5178 Ramachandran restraints generated. 2589 Oldfield, 0 Emsley, 2589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 498 time to evaluate : 2.735 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: A 45 TRP cc_start: 0.8234 (m-90) cc_final: 0.7887 (m-90) REVERT: A 69 TRP cc_start: 0.8723 (m-90) cc_final: 0.8268 (m-90) REVERT: A 111 LEU cc_start: 0.9533 (mt) cc_final: 0.9181 (mt) REVERT: A 356 ASN cc_start: 0.7340 (m-40) cc_final: 0.6926 (p0) REVERT: A 377 ASN cc_start: 0.9255 (t0) cc_final: 0.9039 (t0) REVERT: A 395 TRP cc_start: 0.8678 (m100) cc_final: 0.8398 (m100) REVERT: A 426 MET cc_start: 0.8895 (tpt) cc_final: 0.8525 (tpp) REVERT: A 482 GLU cc_start: 0.8460 (mp0) cc_final: 0.8058 (mp0) REVERT: B 530 MET cc_start: 0.9060 (mtp) cc_final: 0.8715 (mtt) REVERT: B 588 ARG cc_start: 0.8927 (ttp-170) cc_final: 0.8709 (ttp-170) REVERT: B 630 GLN cc_start: 0.8361 (mp10) cc_final: 0.8008 (mp10) REVERT: B 634 GLU cc_start: 0.8452 (tt0) cc_final: 0.7424 (tp30) REVERT: B 648 GLU cc_start: 0.7398 (tp30) cc_final: 0.7153 (tp30) REVERT: C 80 ASN cc_start: 0.9049 (t0) cc_final: 0.8825 (p0) REVERT: C 150 MET cc_start: 0.9048 (mpp) cc_final: 0.8428 (mpp) REVERT: C 426 MET cc_start: 0.8768 (ttm) cc_final: 0.8537 (ttm) REVERT: D 95 MET cc_start: 0.8935 (tpp) cc_final: 0.8261 (tpp) REVERT: D 99 ASN cc_start: 0.8238 (m-40) cc_final: 0.7969 (m110) REVERT: D 102 GLU cc_start: 0.8318 (pm20) cc_final: 0.7768 (pm20) REVERT: D 107 ASP cc_start: 0.8841 (t0) cc_final: 0.8634 (t0) REVERT: D 492 GLU cc_start: 0.8712 (tt0) cc_final: 0.8073 (tm-30) REVERT: E 571 TRP cc_start: 0.6298 (m-10) cc_final: 0.5488 (m-10) REVERT: E 634 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8308 (mt-10) REVERT: E 655 LYS cc_start: 0.9357 (mttp) cc_final: 0.8987 (mttm) REVERT: F 624 ASP cc_start: 0.8334 (m-30) cc_final: 0.8105 (m-30) REVERT: G 95 GLN cc_start: 0.9296 (tt0) cc_final: 0.8975 (tt0) REVERT: G 100 PHE cc_start: 0.9282 (m-80) cc_final: 0.8796 (m-80) REVERT: H 18 VAL cc_start: 0.9304 (p) cc_final: 0.9089 (t) REVERT: H 72 ASP cc_start: 0.8422 (p0) cc_final: 0.8139 (p0) REVERT: H 80 MET cc_start: 0.9391 (tmm) cc_final: 0.8714 (tmm) REVERT: I 23 GLU cc_start: 0.8390 (tp30) cc_final: 0.7767 (tp30) REVERT: I 27 TYR cc_start: 0.8767 (p90) cc_final: 0.8509 (p90) REVERT: I 28 ASN cc_start: 0.7908 (t0) cc_final: 0.7254 (t0) REVERT: I 62 GLN cc_start: 0.9281 (tt0) cc_final: 0.8972 (tt0) REVERT: I 102 VAL cc_start: 0.9203 (m) cc_final: 0.8822 (p) REVERT: J 4 LEU cc_start: 0.5354 (tp) cc_final: 0.4984 (tp) REVERT: J 100 ARG cc_start: 0.8258 (ptm160) cc_final: 0.7769 (ptm160) REVERT: J 100 TYR cc_start: 0.8540 (m-10) cc_final: 0.8265 (m-10) REVERT: J 100 GLU cc_start: 0.8508 (mm-30) cc_final: 0.7666 (mm-30) REVERT: K 24 GLN cc_start: 0.7895 (pm20) cc_final: 0.7484 (pm20) REVERT: K 36 TYR cc_start: 0.8589 (m-80) cc_final: 0.8056 (m-10) REVERT: K 37 GLN cc_start: 0.8410 (pp30) cc_final: 0.8034 (pp30) REVERT: K 46 LEU cc_start: 0.9046 (tp) cc_final: 0.8763 (tp) REVERT: K 55 GLU cc_start: 0.7745 (tt0) cc_final: 0.7150 (tt0) REVERT: K 58 VAL cc_start: 0.8325 (t) cc_final: 0.7883 (t) REVERT: L 5 THR cc_start: 0.7416 (t) cc_final: 0.7191 (t) REVERT: L 96 GLU cc_start: 0.8750 (pt0) cc_final: 0.8442 (pt0) REVERT: M 4 MET cc_start: 0.8188 (ppp) cc_final: 0.7641 (tmm) REVERT: M 34 ASN cc_start: 0.9095 (m-40) cc_final: 0.8667 (m-40) REVERT: M 36 TYR cc_start: 0.8883 (m-10) cc_final: 0.8547 (m-10) REVERT: M 69 GLN cc_start: 0.8088 (pm20) cc_final: 0.7333 (mm110) REVERT: M 70 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7421 (tm-30) REVERT: N 47 LEU cc_start: 0.7220 (mp) cc_final: 0.6931 (mt) outliers start: 1 outliers final: 0 residues processed: 499 average time/residue: 0.3402 time to fit residues: 266.8540 Evaluate side-chains 374 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 62 optimal weight: 0.0020 chunk 189 optimal weight: 0.1980 chunk 30 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 211 optimal weight: 0.0040 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN C 66 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN H 108 GLN ** K 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.095097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.078382 restraints weight = 78630.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.080402 restraints weight = 45790.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.081713 restraints weight = 31210.124| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.6710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23404 Z= 0.172 Angle : 0.669 9.530 31789 Z= 0.328 Chirality : 0.046 0.408 3977 Planarity : 0.004 0.072 3838 Dihedral : 8.323 58.175 6038 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2589 helix: 1.10 (0.27), residues: 405 sheet: -0.04 (0.18), residues: 822 loop : 0.24 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I 50 HIS 0.012 0.001 HIS C 72 PHE 0.028 0.002 PHE N 98 TYR 0.020 0.001 TYR C 484 ARG 0.007 0.000 ARG G 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5626.21 seconds wall clock time: 103 minutes 19.39 seconds (6199.39 seconds total)