Starting phenix.real_space_refine on Wed Jun 18 11:56:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5aco_3121/06_2025/5aco_3121.cif Found real_map, /net/cci-nas-00/data/ceres_data/5aco_3121/06_2025/5aco_3121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5aco_3121/06_2025/5aco_3121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5aco_3121/06_2025/5aco_3121.map" model { file = "/net/cci-nas-00/data/ceres_data/5aco_3121/06_2025/5aco_3121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5aco_3121/06_2025/5aco_3121.cif" } resolution = 4.36 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 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 120 5.16 5 C 13269 2.51 5 N 3390 2.21 5 O 4518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21297 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3453 Classifications: {'peptide': 438} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 413} Chain breaks: 4 Chain: "B" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1051 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "C" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3453 Classifications: {'peptide': 438} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 413} Chain breaks: 4 Chain: "D" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3453 Classifications: {'peptide': 438} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 413} Chain breaks: 4 Chain: "E" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1051 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "F" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1051 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "G" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1028 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "H" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1028 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "I" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1028 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "J" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 752 Classifications: {'peptide': 103} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain: "K" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 752 Classifications: {'peptide': 103} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain: "L" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 752 Classifications: {'peptide': 103} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 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: 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: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 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: "V" 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: "W" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: 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: "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: 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: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 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: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" 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: "m" 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: "n" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "w" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 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: "0" 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: "1" 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: "2" 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: "3" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 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: "6" 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: "7" 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: "8" 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: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "AA" Number of atoms: 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 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 Time building chain proxies: 12.61, per 1000 atoms: 0.59 Number of scatterers: 21297 At special positions: 0 Unit cell: (151.96, 154.58, 148.03, 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 120 16.00 O 4518 8.00 N 3390 7.00 C 13269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.10 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.11 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.11 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=1.62 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=2.11 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.09 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.22 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=2.10 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.11 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.11 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=1.62 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.11 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.09 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.22 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.10 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.11 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.11 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.04 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=1.62 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=2.11 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.09 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.22 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=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 32 " - pdb=" SG CYS G 52B" distance=2.14 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 32 " - pdb=" SG CYS H 52B" distance=2.14 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 32 " - pdb=" SG CYS I 52B" distance=2.14 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.05 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM19960 O5 NAG l 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19187 O5 NAG U 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM20705 O5 NAG 1 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM20527 O5 NAG x 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19009 O5 NAG Q 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19782 O5 NAG h 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19810 O5 NAG i 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19037 O5 NAG R 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM20555 O5 NAG y 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 3 4 " - " MAN 3 5 " " MAN 3 5 " - " MAN 3 6 " " MAN 3 8 " - " MAN 3 9 " " MAN S 4 " - " MAN S 5 " " MAN W 4 " - " MAN W 5 " " MAN W 5 " - " MAN W 6 " " MAN W 8 " - " MAN W 9 " " MAN j 4 " - " MAN j 5 " " MAN n 4 " - " MAN n 5 " " MAN n 5 " - " MAN n 6 " " MAN n 8 " - " MAN n 9 " " MAN z 4 " - " MAN z 5 " ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " BMA 2 3 " - " MAN 2 7 " " MAN 2 4 " - " MAN 2 5 " " BMA 3 3 " - " MAN 3 4 " " MAN 3 7 " - " MAN 3 10 " " BMA S 3 " - " MAN S 4 " " MAN S 6 " - " MAN S 7 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 7 " " MAN V 4 " - " MAN V 5 " " BMA W 3 " - " MAN W 4 " " MAN W 7 " - " MAN W 10 " " BMA j 3 " - " MAN j 4 " " MAN j 6 " - " MAN j 7 " " BMA l 3 " - " MAN l 4 " " BMA m 3 " - " MAN m 7 " " MAN m 4 " - " MAN m 5 " " BMA n 3 " - " MAN n 4 " " MAN n 7 " - " MAN n 10 " " BMA z 3 " - " MAN z 4 " " MAN z 6 " - " MAN z 7 " ALPHA1-6 " BMA 1 3 " - " MAN 1 5 " " BMA 2 3 " - " MAN 2 4 " " MAN 2 4 " - " MAN 2 6 " " BMA 3 3 " - " MAN 3 7 " " MAN 3 7 " - " MAN 3 8 " " BMA S 3 " - " MAN S 6 " " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 4 " " MAN V 4 " - " MAN V 6 " " BMA W 3 " - " MAN W 7 " " MAN W 7 " - " MAN W 8 " " BMA j 3 " - " MAN j 6 " " BMA l 3 " - " MAN l 5 " " BMA m 3 " - " MAN m 4 " " MAN m 4 " - " MAN m 6 " " BMA n 3 " - " MAN n 7 " " MAN n 7 " - " MAN n 8 " " BMA z 3 " - " MAN z 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 5 2 " - " BMA 5 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " 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 j 2 " - " BMA j 3 " " 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 m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " NAG-ASN " NAG 0 1 " - " ASN D 276 " " NAG 1 1 " - " ASN D 295 " " NAG 2 1 " - " ASN D 301 " " NAG 3 1 " - " ASN D 332 " " NAG 4 1 " - " ASN D 355 " " NAG 5 1 " - " ASN D 363 " " NAG 6 1 " - " ASN D 386 " " NAG 7 1 " - " ASN D 392 " " NAG 8 1 " - " ASN D 448 " " NAG 9 1 " - " ASN E 611 " " NAG A1343 " - " ASN A 339 " " NAG B1618 " - " ASN B 618 " " NAG B1637 " - " ASN B 637 " " NAG C1343 " - " ASN C 339 " " NAG D1343 " - " ASN D 339 " " NAG E1618 " - " ASN E 618 " " NAG E1637 " - " ASN E 637 " " NAG F1618 " - " ASN F 618 " " NAG F1637 " - " ASN F 637 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 133 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 160 " " NAG Q 1 " - " ASN A 197 " " NAG R 1 " - " ASN A 234 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 276 " " NAG U 1 " - " ASN A 295 " " NAG V 1 " - " ASN A 301 " " NAG W 1 " - " ASN A 332 " " NAG X 1 " - " ASN A 355 " " NAG Y 1 " - " ASN A 363 " " NAG Z 1 " - " ASN A 386 " " NAG a 1 " - " ASN A 392 " " NAG b 1 " - " ASN A 448 " " NAG c 1 " - " ASN B 611 " " NAG d 1 " - " ASN C 88 " " NAG e 1 " - " ASN C 133 " " NAG f 1 " - " ASN C 156 " " NAG g 1 " - " ASN C 160 " " NAG h 1 " - " ASN C 197 " " NAG i 1 " - " ASN C 234 " " NAG j 1 " - " ASN C 262 " " NAG k 1 " - " ASN C 276 " " NAG l 1 " - " ASN C 295 " " NAG m 1 " - " ASN C 301 " " NAG n 1 " - " ASN C 332 " " NAG o 1 " - " ASN C 355 " " NAG p 1 " - " ASN C 363 " " NAG q 1 " - " ASN C 386 " " NAG r 1 " - " ASN C 392 " " NAG s 1 " - " ASN C 448 " " NAG t 1 " - " ASN D 88 " " NAG u 1 " - " ASN D 133 " " NAG v 1 " - " ASN D 156 " " NAG w 1 " - " ASN D 160 " " NAG x 1 " - " ASN D 197 " " NAG y 1 " - " ASN D 234 " " NAG z 1 " - " ASN D 262 " " NAGAA 1 " - " ASN F 611 " Time building additional restraints: 7.11 Conformation dependent library (CDL) restraints added in 2.4 seconds 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4476 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 63 sheets defined 20.2% alpha, 41.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.679A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.272A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.904A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 546 removed outlier: 4.059A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 removed outlier: 4.140A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.726A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 648 removed outlier: 3.978A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 654 Processing helix chain 'B' and resid 656 through 662 Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 351 removed outlier: 3.679A pdb=" N GLN C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.272A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.905A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 115 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 335 through 351 removed outlier: 3.678A pdb=" N GLN D 348 " --> pdb=" O LYS D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 425 through 429 removed outlier: 4.272A pdb=" N GLN D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 484 removed outlier: 3.905A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 546 removed outlier: 4.059A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU E 545 " --> pdb=" O ALA E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 596 removed outlier: 4.141A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU E 592 " --> pdb=" O ARG E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 623 Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.727A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 648 removed outlier: 3.978A pdb=" N LEU E 645 " --> pdb=" O ILE E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 648 through 654 Processing helix chain 'E' and resid 656 through 662 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 546 removed outlier: 4.059A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 596 removed outlier: 4.140A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.727A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 648 removed outlier: 3.979A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 654 Processing helix chain 'F' and resid 656 through 662 Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 63 through 65 No H-bonds generated for 'chain 'I' and resid 63 through 65' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AB, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.044A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AD, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AE, first strand: chain 'A' and resid 129 through 131 Processing sheet with id=AF, first strand: chain 'A' and resid 154 through 161 Processing sheet with id=AG, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AH, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.503A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AI, first strand: chain 'A' and resid 271 through 273 Processing sheet with id=AJ, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.413A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.279A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.163A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing sheet with id=AK, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.413A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) Processing sheet with id=AL, first strand: chain 'A' and resid 306 through 307 Processing sheet with id=AM, first strand: chain 'A' and resid 324 through 325 Processing sheet with id=CA, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=CB, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.045A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=CC, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=CD, first strand: chain 'C' and resid 92 through 94 Processing sheet with id=CE, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=CF, first strand: chain 'C' and resid 154 through 161 Processing sheet with id=CG, first strand: chain 'C' and resid 201 through 203 Processing sheet with id=CH, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.503A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=CI, first strand: chain 'C' and resid 271 through 273 removed outlier: 12.783A pdb=" N MET C 271 " --> pdb=" O ASN C 283 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU C 285 " --> pdb=" O MET C 271 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLN C 287 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=CJ, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.414A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.279A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.163A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.769A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) Processing sheet with id=CK, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.414A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N MET C 271 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ARG C 273 " --> pdb=" O GLN C 287 " (cutoff:3.500A) removed outlier: 14.170A pdb=" N ASN C 289 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=CL, first strand: chain 'C' and resid 306 through 307 Processing sheet with id=CM, first strand: chain 'C' and resid 324 through 325 Processing sheet with id=DA, first strand: chain 'D' and resid 494 through 499 Processing sheet with id=DB, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.044A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing sheet with id=DC, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=DD, first strand: chain 'D' and resid 92 through 94 Processing sheet with id=DE, first strand: chain 'D' and resid 129 through 131 Processing sheet with id=DF, first strand: chain 'D' and resid 154 through 161 Processing sheet with id=DG, first strand: chain 'D' and resid 201 through 203 Processing sheet with id=DH, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.503A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) Processing sheet with id=DI, first strand: chain 'D' and resid 271 through 273 removed outlier: 12.784A pdb=" N MET D 271 " --> pdb=" O ASN D 283 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU D 285 " --> pdb=" O MET D 271 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLN D 287 " --> pdb=" O ARG D 273 " (cutoff:3.500A) Processing sheet with id=DJ, first strand: chain 'D' and resid 374 through 378 removed outlier: 4.414A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 12.280A pdb=" N PHE D 288 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 12.163A pdb=" N ILE D 453 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N THR D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLY D 451 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing sheet with id=DK, first strand: chain 'D' and resid 374 through 378 removed outlier: 4.414A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N MET D 271 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ARG D 273 " --> pdb=" O GLN D 287 " (cutoff:3.500A) removed outlier: 14.170A pdb=" N ASN D 289 " --> pdb=" O ARG D 273 " (cutoff:3.500A) Processing sheet with id=DL, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=DM, first strand: chain 'D' and resid 324 through 325 Processing sheet with id=GA, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=GB, first strand: chain 'G' and resid 56 through 59 removed outlier: 6.081A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS G 92 " --> pdb=" O LEU G 102 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU G 102 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ARG G 94 " --> pdb=" O VAL G 100K" (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL G 100K" --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY G 96 " --> pdb=" O ALA G 100I" (cutoff:3.500A) Processing sheet with id=GC, first strand: chain 'G' and resid 56 through 59 removed outlier: 6.081A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) Processing sheet with id=GD, first strand: chain 'G' and resid 100G through 103 removed outlier: 5.833A pdb=" N GLU G 98 " --> pdb=" O PRO G 100H" (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) Processing sheet with id=HA, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=HB, first strand: chain 'H' and resid 56 through 59 removed outlier: 6.081A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS H 92 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU H 102 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ARG H 94 " --> pdb=" O VAL H 100K" (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL H 100K" --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY H 96 " --> pdb=" O ALA H 100I" (cutoff:3.500A) Processing sheet with id=HC, first strand: chain 'H' and resid 56 through 59 removed outlier: 6.081A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=HD, first strand: chain 'H' and resid 100G through 103 removed outlier: 5.832A pdb=" N GLU H 98 " --> pdb=" O PRO H 100H" (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) Processing sheet with id=IA, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=IB, first strand: chain 'I' and resid 56 through 59 removed outlier: 6.080A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS I 92 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU I 102 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG I 94 " --> pdb=" O VAL I 100K" (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL I 100K" --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY I 96 " --> pdb=" O ALA I 100I" (cutoff:3.500A) Processing sheet with id=IC, first strand: chain 'I' and resid 56 through 59 removed outlier: 6.080A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) Processing sheet with id=ID, first strand: chain 'I' and resid 100G through 103 removed outlier: 5.833A pdb=" N GLU I 98 " --> pdb=" O PRO I 100H" (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG I 94 " --> pdb=" O ASP I 101 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) Processing sheet with id=JA, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.169A pdb=" N ASP J 95A" --> pdb=" O SER J 90 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE J 97 " --> pdb=" O VAL J 92 " (cutoff:3.500A) Processing sheet with id=JB, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.592A pdb=" N TRP J 35 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=JC, first strand: chain 'J' and resid 95A through 98 removed outlier: 12.853A pdb=" N ASP J 95A" --> pdb=" O CYS J 88 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER J 90 " --> pdb=" O ASP J 95A" (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL J 92 " --> pdb=" O ILE J 97 " (cutoff:3.500A) Processing sheet with id=JD, first strand: chain 'J' and resid 18 through 24 Processing sheet with id=KA, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.169A pdb=" N ASP K 95A" --> pdb=" O SER K 90 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE K 97 " --> pdb=" O VAL K 92 " (cutoff:3.500A) Processing sheet with id=KB, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.592A pdb=" N TRP K 35 " --> pdb=" O VAL K 47 " (cutoff:3.500A) Processing sheet with id=KC, first strand: chain 'K' and resid 95A through 98 removed outlier: 12.852A pdb=" N ASP K 95A" --> pdb=" O CYS K 88 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER K 90 " --> pdb=" O ASP K 95A" (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL K 92 " --> pdb=" O ILE K 97 " (cutoff:3.500A) Processing sheet with id=KD, first strand: chain 'K' and resid 18 through 24 Processing sheet with id=LA, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.169A pdb=" N ASP L 95A" --> pdb=" O SER L 90 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE L 97 " --> pdb=" O VAL L 92 " (cutoff:3.500A) Processing sheet with id=LB, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.592A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=LC, first strand: chain 'L' and resid 95A through 98 removed outlier: 12.853A pdb=" N ASP L 95A" --> pdb=" O CYS L 88 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER L 90 " --> pdb=" O ASP L 95A" (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL L 92 " --> pdb=" O ILE L 97 " (cutoff:3.500A) Processing sheet with id=LD, first strand: chain 'L' and resid 18 through 24 825 hydrogen bonds defined for protein. 2118 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: 8.25 Time building geometry restraints manager: 7.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3384 1.31 - 1.44: 6086 1.44 - 1.56: 12064 1.56 - 1.69: 21 1.69 - 1.81: 156 Bond restraints: 21711 Sorted by residual: bond pdb=" C PRO L 8 " pdb=" N SER L 9 " ideal model delta sigma weight residual 1.331 1.584 -0.253 1.23e-02 6.61e+03 4.25e+02 bond pdb=" C PRO J 8 " pdb=" N SER J 9 " ideal model delta sigma weight residual 1.331 1.584 -0.253 1.23e-02 6.61e+03 4.24e+02 bond pdb=" C PRO K 8 " pdb=" N SER K 9 " ideal model delta sigma weight residual 1.331 1.584 -0.253 1.23e-02 6.61e+03 4.23e+02 bond pdb=" C GLN F 658 " pdb=" N ASP F 659 " ideal model delta sigma weight residual 1.335 1.613 -0.278 1.36e-02 5.41e+03 4.18e+02 bond pdb=" C GLN B 658 " pdb=" N ASP B 659 " ideal model delta sigma weight residual 1.335 1.613 -0.278 1.36e-02 5.41e+03 4.18e+02 ... (remaining 21706 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.69: 29287 7.69 - 15.37: 194 15.37 - 23.06: 48 23.06 - 30.74: 0 30.74 - 38.43: 3 Bond angle restraints: 29532 Sorted by residual: angle pdb=" N GLU E 648 " pdb=" CA GLU E 648 " pdb=" C GLU E 648 " ideal model delta sigma weight residual 110.80 149.23 -38.43 2.13e+00 2.20e-01 3.26e+02 angle pdb=" N GLU B 648 " pdb=" CA GLU B 648 " pdb=" C GLU B 648 " ideal model delta sigma weight residual 110.80 149.22 -38.42 2.13e+00 2.20e-01 3.25e+02 angle pdb=" N GLU F 648 " pdb=" CA GLU F 648 " pdb=" C GLU F 648 " ideal model delta sigma weight residual 110.80 149.17 -38.37 2.13e+00 2.20e-01 3.25e+02 angle pdb=" O LEU D 86 " pdb=" C LEU D 86 " pdb=" N GLU D 87 " ideal model delta sigma weight residual 122.87 102.49 20.38 1.23e+00 6.61e-01 2.74e+02 angle pdb=" O LEU A 86 " pdb=" C LEU A 86 " pdb=" N GLU A 87 " ideal model delta sigma weight residual 122.87 102.49 20.38 1.23e+00 6.61e-01 2.74e+02 ... (remaining 29527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.93: 14559 21.93 - 43.86: 438 43.86 - 65.79: 102 65.79 - 87.72: 177 87.72 - 109.65: 126 Dihedral angle restraints: 15402 sinusoidal: 8469 harmonic: 6933 Sorted by residual: dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -162.25 76.25 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS D 378 " pdb=" SG CYS D 378 " pdb=" SG CYS D 445 " pdb=" CB CYS D 445 " ideal model delta sinusoidal sigma weight residual -86.00 -162.24 76.24 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -162.24 76.24 1 1.00e+01 1.00e-02 7.32e+01 ... (remaining 15399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.227: 3774 0.227 - 0.455: 129 0.455 - 0.682: 15 0.682 - 0.909: 3 0.909 - 1.137: 3 Chirality restraints: 3924 Sorted by residual: chirality pdb=" C1 MAN S 7 " pdb=" O3 MAN S 6 " pdb=" C2 MAN S 7 " pdb=" O5 MAN S 7 " both_signs ideal model delta sigma weight residual False 2.40 1.62 0.78 2.00e-02 2.50e+03 1.53e+03 chirality pdb=" C1 MAN j 7 " pdb=" O3 MAN j 6 " pdb=" C2 MAN j 7 " pdb=" O5 MAN j 7 " both_signs ideal model delta sigma weight residual False 2.40 1.62 0.78 2.00e-02 2.50e+03 1.52e+03 chirality pdb=" C1 MAN z 7 " pdb=" O3 MAN z 6 " pdb=" C2 MAN z 7 " pdb=" O5 MAN z 7 " both_signs ideal model delta sigma weight residual False 2.40 1.62 0.78 2.00e-02 2.50e+03 1.51e+03 ... (remaining 3921 not shown) Planarity restraints: 3510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 637 " -0.193 2.00e-02 2.50e+03 2.16e-01 5.85e+02 pdb=" CG ASN E 637 " 0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN E 637 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN E 637 " 0.351 2.00e-02 2.50e+03 pdb=" C1 NAG E1637 " -0.259 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 637 " 0.193 2.00e-02 2.50e+03 2.16e-01 5.84e+02 pdb=" CG ASN B 637 " -0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN B 637 " -0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN B 637 " -0.351 2.00e-02 2.50e+03 pdb=" C1 NAG B1637 " 0.259 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 637 " -0.193 2.00e-02 2.50e+03 2.16e-01 5.84e+02 pdb=" CG ASN F 637 " 0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN F 637 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN F 637 " 0.351 2.00e-02 2.50e+03 pdb=" C1 NAG F1637 " -0.259 2.00e-02 2.50e+03 ... (remaining 3507 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 209 2.57 - 3.15: 17972 3.15 - 3.73: 29769 3.73 - 4.32: 45133 4.32 - 4.90: 69912 Nonbonded interactions: 162995 Sorted by model distance: nonbonded pdb=" ND2 ASN D 279 " pdb=" O6 NAG 0 1 " model vdw 1.986 3.120 nonbonded pdb=" ND2 ASN A 279 " pdb=" O6 NAG T 1 " model vdw 1.987 3.120 nonbonded pdb=" ND2 ASN C 279 " pdb=" O6 NAG k 1 " model vdw 1.987 3.120 nonbonded pdb=" O ALA I 52C" pdb=" N2 NAG 2 1 " model vdw 2.062 3.120 nonbonded pdb=" O ALA H 52C" pdb=" N2 NAG V 1 " model vdw 2.063 3.120 ... (remaining 162990 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain '0' selection = chain '5' selection = chain '6' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'T' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'k' selection = chain 'p' selection = chain 'q' selection = chain 't' selection = chain 'v' selection = chain 'w' } ncs_group { reference = chain '1' selection = chain 'U' selection = chain 'l' } ncs_group { reference = chain '2' selection = chain 'S' selection = chain 'V' selection = chain 'j' selection = chain 'm' selection = chain 'z' } ncs_group { reference = chain '3' selection = chain 'W' selection = chain 'n' } ncs_group { reference = chain '4' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'AA' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'X' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'h' selection = chain 'i' selection = chain 'o' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 50.410 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 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 : 0.016 0.413 21945 Z= 0.945 Angle : 2.296 38.429 30192 Z= 1.230 Chirality : 0.109 1.137 3924 Planarity : 0.015 0.198 3450 Dihedral : 17.674 109.654 10800 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 1.91 % Allowed : 9.15 % Favored : 88.95 % Rotamer: Outliers : 0.29 % Allowed : 0.71 % Favored : 99.00 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % 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: -2.40 (0.15), residues: 2361 helix: -2.40 (0.20), residues: 417 sheet: -0.63 (0.20), residues: 639 loop : -1.83 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP G 100J HIS 0.001 0.000 HIS H 59 PHE 0.003 0.000 PHE D 382 TYR 0.020 0.001 TYR J 87 ARG 0.002 0.000 ARG C 360 Details of bonding type rmsd link_NAG-ASN : bond 0.14324 ( 60) link_NAG-ASN : angle 11.49146 ( 180) link_ALPHA1-6 : bond 0.03748 ( 18) link_ALPHA1-6 : angle 5.29164 ( 54) link_BETA1-4 : bond 0.04228 ( 81) link_BETA1-4 : angle 6.03626 ( 243) link_ALPHA1-2 : bond 0.01962 ( 12) link_ALPHA1-2 : angle 4.77549 ( 36) link_ALPHA1-3 : bond 0.04462 ( 21) link_ALPHA1-3 : angle 7.38689 ( 63) hydrogen bonds : bond 0.20828 ( 704) hydrogen bonds : angle 8.97476 ( 2118) SS BOND : bond 0.13212 ( 42) SS BOND : angle 7.57399 ( 84) covalent geometry : bond 0.01232 (21711) covalent geometry : angle 1.98087 (29532) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 533 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8071 (ptm) cc_final: 0.7855 (ptp) REVERT: A 195 ASN cc_start: 0.8943 (p0) cc_final: 0.8520 (t0) REVERT: A 377 ASN cc_start: 0.9037 (t0) cc_final: 0.8638 (t0) REVERT: A 423 ILE cc_start: 0.9434 (mt) cc_final: 0.9179 (mt) REVERT: B 546 SER cc_start: 0.6668 (t) cc_final: 0.6463 (t) REVERT: B 571 TRP cc_start: 0.7966 (m-10) cc_final: 0.7323 (m-10) REVERT: B 576 LEU cc_start: 0.7974 (tp) cc_final: 0.7682 (tp) REVERT: B 642 ILE cc_start: 0.8771 (mt) cc_final: 0.8530 (tp) REVERT: C 95 MET cc_start: 0.7875 (ptm) cc_final: 0.7564 (ptp) REVERT: C 100 MET cc_start: 0.7004 (mtp) cc_final: 0.6569 (ttt) REVERT: C 201 ILE cc_start: 0.9223 (tt) cc_final: 0.8834 (tt) REVERT: C 377 ASN cc_start: 0.8989 (t0) cc_final: 0.8646 (t0) REVERT: D 95 MET cc_start: 0.8040 (ptm) cc_final: 0.7644 (ptp) REVERT: D 201 ILE cc_start: 0.9262 (tt) cc_final: 0.9040 (tt) REVERT: D 377 ASN cc_start: 0.8977 (t0) cc_final: 0.8598 (t0) REVERT: D 423 ILE cc_start: 0.9430 (mt) cc_final: 0.9224 (mt) REVERT: E 571 TRP cc_start: 0.7542 (m-10) cc_final: 0.7186 (m-10) REVERT: E 576 LEU cc_start: 0.8151 (tp) cc_final: 0.7763 (tt) REVERT: E 642 ILE cc_start: 0.8835 (mt) cc_final: 0.8575 (tp) REVERT: F 571 TRP cc_start: 0.7883 (m-10) cc_final: 0.7285 (m-10) REVERT: F 576 LEU cc_start: 0.8357 (tp) cc_final: 0.8076 (tt) REVERT: G 24 VAL cc_start: 0.7870 (t) cc_final: 0.7585 (t) REVERT: J 46 LEU cc_start: 0.8387 (tp) cc_final: 0.8160 (tt) REVERT: J 86 TYR cc_start: 0.5311 (m-80) cc_final: 0.5002 (m-10) REVERT: K 46 LEU cc_start: 0.8407 (tp) cc_final: 0.8074 (tt) REVERT: K 91 LEU cc_start: 0.7821 (tp) cc_final: 0.7581 (tp) outliers start: 6 outliers final: 3 residues processed: 539 average time/residue: 0.3624 time to fit residues: 286.7783 Evaluate side-chains 269 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 266 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 112 optimal weight: 0.3980 chunk 138 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN A 300 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN B 630 GLN C 136 ASN C 293 GLN C 300 ASN D 293 GLN D 300 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN F 607 ASN G 3 GLN H 3 GLN I 3 GLN K 94 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.058180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.044739 restraints weight = 105816.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.046273 restraints weight = 58767.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.047300 restraints weight = 40518.302| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21945 Z= 0.186 Angle : 1.025 14.821 30192 Z= 0.463 Chirality : 0.051 0.544 3924 Planarity : 0.004 0.036 3450 Dihedral : 16.254 93.416 6432 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.27 % Favored : 93.22 % Rotamer: Outliers : 0.14 % Allowed : 1.76 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % 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: -1.52 (0.16), residues: 2361 helix: -1.04 (0.24), residues: 411 sheet: -0.46 (0.20), residues: 669 loop : -1.26 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 100E HIS 0.004 0.001 HIS L 39 PHE 0.016 0.002 PHE A 382 TYR 0.032 0.002 TYR I 58 ARG 0.008 0.001 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00643 ( 60) link_NAG-ASN : angle 4.73166 ( 180) link_ALPHA1-6 : bond 0.00408 ( 18) link_ALPHA1-6 : angle 1.95119 ( 54) link_BETA1-4 : bond 0.00491 ( 81) link_BETA1-4 : angle 3.15257 ( 243) link_ALPHA1-2 : bond 0.00504 ( 12) link_ALPHA1-2 : angle 1.72462 ( 36) link_ALPHA1-3 : bond 0.01051 ( 21) link_ALPHA1-3 : angle 1.73266 ( 63) hydrogen bonds : bond 0.05724 ( 704) hydrogen bonds : angle 6.57452 ( 2118) SS BOND : bond 0.00308 ( 42) SS BOND : angle 1.14944 ( 84) covalent geometry : bond 0.00392 (21711) covalent geometry : angle 0.91402 (29532) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 342 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9119 (tpp) cc_final: 0.8746 (tpp) REVERT: A 434 MET cc_start: 0.9128 (tmm) cc_final: 0.8682 (tmm) REVERT: B 530 MET cc_start: 0.8519 (mtt) cc_final: 0.8171 (mtt) REVERT: B 543 ASN cc_start: 0.8686 (t0) cc_final: 0.8200 (t0) REVERT: B 544 LEU cc_start: 0.8100 (mt) cc_final: 0.7864 (mt) REVERT: B 546 SER cc_start: 0.7804 (t) cc_final: 0.7599 (p) REVERT: B 584 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8220 (tm-30) REVERT: B 631 TRP cc_start: 0.9486 (t-100) cc_final: 0.8685 (t-100) REVERT: B 634 GLU cc_start: 0.8606 (pm20) cc_final: 0.8400 (pm20) REVERT: B 650 GLN cc_start: 0.8394 (tt0) cc_final: 0.7842 (tt0) REVERT: C 150 MET cc_start: 0.5838 (tpt) cc_final: 0.4983 (tpp) REVERT: C 180 ASP cc_start: 0.8766 (m-30) cc_final: 0.8535 (m-30) REVERT: C 434 MET cc_start: 0.8971 (tmm) cc_final: 0.8156 (tmm) REVERT: D 434 MET cc_start: 0.9047 (tmm) cc_final: 0.8263 (tmm) REVERT: D 475 MET cc_start: 0.8630 (mmm) cc_final: 0.8339 (mmm) REVERT: E 530 MET cc_start: 0.8566 (mtt) cc_final: 0.8191 (mtt) REVERT: E 543 ASN cc_start: 0.8616 (t0) cc_final: 0.8118 (t0) REVERT: E 544 LEU cc_start: 0.8285 (mt) cc_final: 0.8009 (mt) REVERT: E 631 TRP cc_start: 0.9465 (t-100) cc_final: 0.9089 (t-100) REVERT: E 646 LEU cc_start: 0.9340 (mt) cc_final: 0.9136 (mt) REVERT: E 650 GLN cc_start: 0.8445 (tt0) cc_final: 0.7942 (tt0) REVERT: F 530 MET cc_start: 0.8360 (mtt) cc_final: 0.7873 (mtt) REVERT: F 543 ASN cc_start: 0.8732 (t0) cc_final: 0.8299 (t0) REVERT: F 544 LEU cc_start: 0.8199 (mt) cc_final: 0.7963 (mt) REVERT: F 571 TRP cc_start: 0.8249 (m-10) cc_final: 0.7831 (m-90) REVERT: F 631 TRP cc_start: 0.9531 (t-100) cc_final: 0.9101 (t-100) REVERT: F 654 GLU cc_start: 0.8218 (pt0) cc_final: 0.7800 (pt0) REVERT: G 22 CYS cc_start: 0.1495 (t) cc_final: 0.0474 (t) REVERT: G 58 TYR cc_start: 0.9081 (m-80) cc_final: 0.8739 (m-80) REVERT: G 72 ASP cc_start: 0.8199 (t0) cc_final: 0.6158 (t0) REVERT: G 75 LYS cc_start: 0.9333 (mttt) cc_final: 0.9047 (mttp) REVERT: G 100 LYS cc_start: 0.8921 (mttp) cc_final: 0.8496 (mmtm) REVERT: H 72 ASP cc_start: 0.8213 (t0) cc_final: 0.6772 (t0) REVERT: I 52 TYR cc_start: 0.8585 (t80) cc_final: 0.8040 (t80) REVERT: I 72 ASP cc_start: 0.8264 (t0) cc_final: 0.5993 (t0) REVERT: I 95 PHE cc_start: 0.8301 (m-80) cc_final: 0.7871 (m-80) REVERT: I 98 GLU cc_start: 0.8546 (tp30) cc_final: 0.8009 (tm-30) REVERT: J 24 THR cc_start: 0.8899 (m) cc_final: 0.8437 (m) REVERT: J 87 TYR cc_start: 0.8495 (m-80) cc_final: 0.8236 (m-80) REVERT: J 104 LEU cc_start: 0.9467 (tp) cc_final: 0.9189 (tp) REVERT: K 24 THR cc_start: 0.9075 (m) cc_final: 0.8752 (m) REVERT: L 24 THR cc_start: 0.9024 (m) cc_final: 0.8766 (m) REVERT: L 45 LYS cc_start: 0.9439 (mtmm) cc_final: 0.9014 (mtmm) REVERT: L 53 LYS cc_start: 0.8241 (mppt) cc_final: 0.7906 (mmtt) outliers start: 3 outliers final: 0 residues processed: 343 average time/residue: 0.3516 time to fit residues: 181.4396 Evaluate side-chains 250 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 234 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 126 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 202 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN C 293 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN F 591 GLN G 5 GLN ** J 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.056799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.043448 restraints weight = 105153.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.044867 restraints weight = 59399.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.045814 restraints weight = 41386.646| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21945 Z= 0.188 Angle : 0.892 13.795 30192 Z= 0.406 Chirality : 0.048 0.402 3924 Planarity : 0.004 0.036 3450 Dihedral : 13.179 89.518 6432 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.52 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % 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: -1.15 (0.17), residues: 2361 helix: -0.46 (0.26), residues: 393 sheet: -0.10 (0.20), residues: 690 loop : -1.22 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 571 HIS 0.007 0.001 HIS L 39 PHE 0.028 0.002 PHE C 53 TYR 0.022 0.002 TYR H 58 ARG 0.005 0.001 ARG G 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 60) link_NAG-ASN : angle 2.97196 ( 180) link_ALPHA1-6 : bond 0.00540 ( 18) link_ALPHA1-6 : angle 1.93085 ( 54) link_BETA1-4 : bond 0.00400 ( 81) link_BETA1-4 : angle 2.79104 ( 243) link_ALPHA1-2 : bond 0.00343 ( 12) link_ALPHA1-2 : angle 1.66312 ( 36) link_ALPHA1-3 : bond 0.00632 ( 21) link_ALPHA1-3 : angle 1.78689 ( 63) hydrogen bonds : bond 0.04695 ( 704) hydrogen bonds : angle 5.90016 ( 2118) SS BOND : bond 0.00301 ( 42) SS BOND : angle 0.89817 ( 84) covalent geometry : bond 0.00403 (21711) covalent geometry : angle 0.82188 (29532) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 2.092 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: A 161 MET cc_start: 0.9114 (tpp) cc_final: 0.8730 (tpp) REVERT: A 271 MET cc_start: 0.8033 (mmm) cc_final: 0.7648 (mmm) REVERT: A 434 MET cc_start: 0.9120 (tmm) cc_final: 0.8620 (tmm) REVERT: B 543 ASN cc_start: 0.8909 (t0) cc_final: 0.8479 (t0) REVERT: B 584 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8250 (tm-30) REVERT: B 631 TRP cc_start: 0.9493 (t-100) cc_final: 0.8559 (t-100) REVERT: B 635 ILE cc_start: 0.9666 (tp) cc_final: 0.9320 (tp) REVERT: C 150 MET cc_start: 0.6345 (tpt) cc_final: 0.5399 (tpp) REVERT: C 180 ASP cc_start: 0.8680 (m-30) cc_final: 0.8282 (m-30) REVERT: C 424 ILE cc_start: 0.9236 (pt) cc_final: 0.8892 (pt) REVERT: C 434 MET cc_start: 0.8867 (tmm) cc_final: 0.8067 (tmm) REVERT: D 180 ASP cc_start: 0.8856 (m-30) cc_final: 0.8635 (m-30) REVERT: D 188 ASN cc_start: 0.6944 (p0) cc_final: 0.6706 (p0) REVERT: D 270 VAL cc_start: 0.8797 (t) cc_final: 0.8541 (t) REVERT: D 271 MET cc_start: 0.8286 (mmm) cc_final: 0.7958 (mmm) REVERT: D 434 MET cc_start: 0.9039 (tmm) cc_final: 0.8785 (tmm) REVERT: E 543 ASN cc_start: 0.8812 (t0) cc_final: 0.8290 (t0) REVERT: E 622 ILE cc_start: 0.9184 (mt) cc_final: 0.8477 (mt) REVERT: E 631 TRP cc_start: 0.9531 (t-100) cc_final: 0.9185 (t-100) REVERT: F 543 ASN cc_start: 0.8962 (t0) cc_final: 0.8571 (t0) REVERT: F 584 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8199 (tm-30) REVERT: F 631 TRP cc_start: 0.9568 (t-100) cc_final: 0.8819 (t-100) REVERT: F 634 GLU cc_start: 0.8692 (pm20) cc_final: 0.8223 (pm20) REVERT: F 635 ILE cc_start: 0.9578 (tp) cc_final: 0.9238 (tt) REVERT: F 654 GLU cc_start: 0.8290 (pt0) cc_final: 0.7550 (pt0) REVERT: G 22 CYS cc_start: 0.0970 (t) cc_final: 0.0335 (t) REVERT: G 58 TYR cc_start: 0.9173 (m-80) cc_final: 0.8674 (m-80) REVERT: G 72 ASP cc_start: 0.8209 (t0) cc_final: 0.5938 (t0) REVERT: G 75 LYS cc_start: 0.9383 (mttt) cc_final: 0.9113 (mttp) REVERT: G 98 GLU cc_start: 0.8607 (tp30) cc_final: 0.8388 (tp30) REVERT: H 13 GLU cc_start: 0.7582 (pp20) cc_final: 0.7296 (pp20) REVERT: H 72 ASP cc_start: 0.8377 (t0) cc_final: 0.7314 (t0) REVERT: H 75 LYS cc_start: 0.9021 (mtmm) cc_final: 0.8697 (mttp) REVERT: I 13 GLU cc_start: 0.7866 (pp20) cc_final: 0.7623 (pp20) REVERT: I 33 ASN cc_start: 0.9431 (m-40) cc_final: 0.8958 (p0) REVERT: I 58 TYR cc_start: 0.8806 (m-10) cc_final: 0.8499 (m-10) REVERT: I 100 ASP cc_start: 0.9206 (m-30) cc_final: 0.8931 (m-30) REVERT: J 33 VAL cc_start: 0.9181 (t) cc_final: 0.8766 (p) REVERT: J 87 TYR cc_start: 0.8414 (m-80) cc_final: 0.8173 (m-80) REVERT: K 24 THR cc_start: 0.9001 (m) cc_final: 0.8395 (m) REVERT: K 33 VAL cc_start: 0.9209 (t) cc_final: 0.8861 (p) REVERT: K 53 LYS cc_start: 0.8909 (mptt) cc_final: 0.8651 (mmtt) REVERT: K 91 LEU cc_start: 0.9349 (tp) cc_final: 0.8947 (mt) REVERT: L 45 LYS cc_start: 0.9374 (mtmm) cc_final: 0.9013 (mtmm) REVERT: L 87 TYR cc_start: 0.8563 (m-80) cc_final: 0.8186 (m-80) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.3416 time to fit residues: 158.8303 Evaluate side-chains 230 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 233 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 630 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.056619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.043161 restraints weight = 106977.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.044570 restraints weight = 61228.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.045520 restraints weight = 43064.193| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21945 Z= 0.154 Angle : 0.801 13.491 30192 Z= 0.366 Chirality : 0.047 0.523 3924 Planarity : 0.004 0.034 3450 Dihedral : 11.111 84.697 6432 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.10 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % 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: -0.97 (0.17), residues: 2361 helix: 0.09 (0.27), residues: 387 sheet: 0.01 (0.19), residues: 735 loop : -1.28 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 571 HIS 0.005 0.001 HIS J 39 PHE 0.011 0.001 PHE C 382 TYR 0.024 0.002 TYR H 58 ARG 0.010 0.001 ARG F 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 60) link_NAG-ASN : angle 2.58313 ( 180) link_ALPHA1-6 : bond 0.00611 ( 18) link_ALPHA1-6 : angle 1.94251 ( 54) link_BETA1-4 : bond 0.00355 ( 81) link_BETA1-4 : angle 2.51139 ( 243) link_ALPHA1-2 : bond 0.00354 ( 12) link_ALPHA1-2 : angle 1.54812 ( 36) link_ALPHA1-3 : bond 0.00757 ( 21) link_ALPHA1-3 : angle 1.71581 ( 63) hydrogen bonds : bond 0.04100 ( 704) hydrogen bonds : angle 5.52614 ( 2118) SS BOND : bond 0.00161 ( 42) SS BOND : angle 0.67147 ( 84) covalent geometry : bond 0.00334 (21711) covalent geometry : angle 0.73848 (29532) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 2.176 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: A 161 MET cc_start: 0.9129 (tpp) cc_final: 0.8659 (tpp) REVERT: A 434 MET cc_start: 0.9054 (tmm) cc_final: 0.8642 (tmm) REVERT: B 543 ASN cc_start: 0.9043 (t0) cc_final: 0.8484 (t0) REVERT: B 584 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8359 (tm-30) REVERT: B 631 TRP cc_start: 0.9468 (t-100) cc_final: 0.9049 (t-100) REVERT: B 634 GLU cc_start: 0.8441 (pm20) cc_final: 0.7901 (pm20) REVERT: C 150 MET cc_start: 0.6205 (tpt) cc_final: 0.5347 (tpp) REVERT: C 180 ASP cc_start: 0.8524 (m-30) cc_final: 0.8253 (m-30) REVERT: C 271 MET cc_start: 0.8161 (mmp) cc_final: 0.7908 (mmm) REVERT: C 424 ILE cc_start: 0.9072 (pt) cc_final: 0.8841 (pt) REVERT: C 434 MET cc_start: 0.8792 (tmm) cc_final: 0.8091 (tmm) REVERT: D 69 TRP cc_start: 0.7399 (t60) cc_final: 0.7183 (t60) REVERT: D 109 ILE cc_start: 0.9430 (mt) cc_final: 0.9213 (tt) REVERT: D 270 VAL cc_start: 0.8690 (t) cc_final: 0.8434 (t) REVERT: D 271 MET cc_start: 0.8160 (mmm) cc_final: 0.7820 (mmm) REVERT: D 424 ILE cc_start: 0.9144 (pt) cc_final: 0.8909 (pt) REVERT: D 434 MET cc_start: 0.9016 (tmm) cc_final: 0.8321 (tmm) REVERT: E 543 ASN cc_start: 0.8913 (t0) cc_final: 0.8365 (t0) REVERT: E 584 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8181 (tm-30) REVERT: E 588 ARG cc_start: 0.8216 (tpp-160) cc_final: 0.7838 (tpp-160) REVERT: E 631 TRP cc_start: 0.9395 (t-100) cc_final: 0.9166 (t-100) REVERT: E 651 ASN cc_start: 0.8359 (t0) cc_final: 0.7999 (t0) REVERT: F 543 ASN cc_start: 0.9042 (t0) cc_final: 0.8540 (t0) REVERT: F 631 TRP cc_start: 0.9439 (t-100) cc_final: 0.8514 (t-100) REVERT: F 635 ILE cc_start: 0.9552 (tp) cc_final: 0.9044 (tt) REVERT: G 33 ASN cc_start: 0.9357 (m-40) cc_final: 0.8968 (p0) REVERT: G 72 ASP cc_start: 0.8227 (t0) cc_final: 0.5869 (t0) REVERT: G 75 LYS cc_start: 0.9396 (mttt) cc_final: 0.9064 (mttp) REVERT: H 33 ASN cc_start: 0.9332 (m-40) cc_final: 0.8876 (p0) REVERT: H 72 ASP cc_start: 0.8323 (t0) cc_final: 0.6774 (t0) REVERT: H 75 LYS cc_start: 0.9014 (mtmm) cc_final: 0.8658 (mttp) REVERT: H 100 ASP cc_start: 0.9149 (m-30) cc_final: 0.8914 (m-30) REVERT: I 33 ASN cc_start: 0.9429 (m-40) cc_final: 0.8931 (p0) REVERT: I 100 ASP cc_start: 0.9235 (m-30) cc_final: 0.8936 (m-30) REVERT: J 33 VAL cc_start: 0.9120 (t) cc_final: 0.8696 (p) REVERT: J 87 TYR cc_start: 0.8382 (m-80) cc_final: 0.8179 (m-80) REVERT: K 24 THR cc_start: 0.8941 (m) cc_final: 0.8375 (m) REVERT: K 33 VAL cc_start: 0.9136 (t) cc_final: 0.8772 (p) REVERT: K 91 LEU cc_start: 0.9282 (tp) cc_final: 0.9009 (mt) REVERT: K 104 LEU cc_start: 0.9458 (tp) cc_final: 0.9093 (tp) REVERT: L 45 LYS cc_start: 0.9394 (mtmm) cc_final: 0.9097 (mtmm) REVERT: L 104 LEU cc_start: 0.9124 (tp) cc_final: 0.8870 (tp) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.3535 time to fit residues: 159.8516 Evaluate side-chains 220 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 155 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 220 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 170 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN C 422 GLN D 99 ASN D 136 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN H 59 HIS I 59 HIS ** J 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.053182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.039656 restraints weight = 110961.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.040946 restraints weight = 64816.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.041791 restraints weight = 46448.034| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 21945 Z= 0.334 Angle : 1.006 12.940 30192 Z= 0.459 Chirality : 0.050 0.424 3924 Planarity : 0.005 0.050 3450 Dihedral : 10.940 87.330 6432 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.75 % Favored : 91.74 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % 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: -1.35 (0.17), residues: 2361 helix: -0.37 (0.27), residues: 384 sheet: -0.28 (0.19), residues: 672 loop : -1.41 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E 623 HIS 0.005 0.002 HIS H 52A PHE 0.024 0.003 PHE L 98 TYR 0.027 0.003 TYR H 58 ARG 0.010 0.001 ARG F 617 Details of bonding type rmsd link_NAG-ASN : bond 0.01034 ( 60) link_NAG-ASN : angle 3.14092 ( 180) link_ALPHA1-6 : bond 0.00435 ( 18) link_ALPHA1-6 : angle 2.18432 ( 54) link_BETA1-4 : bond 0.00573 ( 81) link_BETA1-4 : angle 2.30116 ( 243) link_ALPHA1-2 : bond 0.00583 ( 12) link_ALPHA1-2 : angle 2.26088 ( 36) link_ALPHA1-3 : bond 0.00314 ( 21) link_ALPHA1-3 : angle 2.32016 ( 63) hydrogen bonds : bond 0.05148 ( 704) hydrogen bonds : angle 6.03256 ( 2118) SS BOND : bond 0.00738 ( 42) SS BOND : angle 1.13858 ( 84) covalent geometry : bond 0.00718 (21711) covalent geometry : angle 0.94965 (29532) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9245 (tpp) cc_final: 0.8749 (tpp) REVERT: A 180 ASP cc_start: 0.8646 (m-30) cc_final: 0.8426 (m-30) REVERT: A 309 ILE cc_start: 0.9129 (mp) cc_final: 0.8860 (mp) REVERT: A 434 MET cc_start: 0.9004 (tmm) cc_final: 0.8619 (tmm) REVERT: B 631 TRP cc_start: 0.9399 (t-100) cc_final: 0.9174 (t-100) REVERT: B 638 TYR cc_start: 0.8600 (m-80) cc_final: 0.8083 (m-80) REVERT: B 650 GLN cc_start: 0.8483 (tt0) cc_final: 0.7710 (tt0) REVERT: C 95 MET cc_start: 0.8923 (ptp) cc_final: 0.8597 (ptp) REVERT: C 150 MET cc_start: 0.6899 (tpt) cc_final: 0.6427 (tpp) REVERT: C 180 ASP cc_start: 0.8801 (m-30) cc_final: 0.8468 (m-30) REVERT: C 434 MET cc_start: 0.8714 (tmm) cc_final: 0.8397 (ttm) REVERT: D 180 ASP cc_start: 0.8766 (m-30) cc_final: 0.8503 (m-30) REVERT: D 424 ILE cc_start: 0.9348 (pt) cc_final: 0.9036 (pt) REVERT: D 434 MET cc_start: 0.8908 (tmm) cc_final: 0.8270 (tmm) REVERT: E 543 ASN cc_start: 0.8988 (t0) cc_final: 0.8427 (t0) REVERT: E 584 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8653 (tm-30) REVERT: E 601 LYS cc_start: 0.8633 (pttt) cc_final: 0.8293 (ptmt) REVERT: E 650 GLN cc_start: 0.8494 (tt0) cc_final: 0.7961 (mt0) REVERT: F 651 ASN cc_start: 0.8457 (t0) cc_final: 0.8046 (t0) REVERT: F 654 GLU cc_start: 0.8284 (pt0) cc_final: 0.7970 (mm-30) REVERT: G 33 ASN cc_start: 0.9341 (m-40) cc_final: 0.8853 (p0) REVERT: G 58 TYR cc_start: 0.8956 (m-80) cc_final: 0.8452 (m-80) REVERT: G 72 ASP cc_start: 0.8178 (t0) cc_final: 0.6018 (t0) REVERT: G 75 LYS cc_start: 0.9405 (mttt) cc_final: 0.9087 (mttp) REVERT: H 33 ASN cc_start: 0.9341 (m-40) cc_final: 0.8841 (p0) REVERT: H 58 TYR cc_start: 0.9154 (m-10) cc_final: 0.8953 (m-80) REVERT: H 72 ASP cc_start: 0.8304 (t0) cc_final: 0.6864 (t0) REVERT: H 75 LYS cc_start: 0.8985 (mtmm) cc_final: 0.8644 (mttp) REVERT: H 100 LYS cc_start: 0.9348 (mttt) cc_final: 0.9088 (mttp) REVERT: I 13 GLU cc_start: 0.8042 (pp20) cc_final: 0.7782 (pp20) REVERT: I 33 ASN cc_start: 0.9435 (m-40) cc_final: 0.9054 (p0) REVERT: I 58 TYR cc_start: 0.9158 (m-10) cc_final: 0.8262 (m-10) REVERT: I 98 GLU cc_start: 0.8633 (tp30) cc_final: 0.8293 (tp30) REVERT: J 87 TYR cc_start: 0.8412 (m-80) cc_final: 0.8197 (m-80) REVERT: J 91 LEU cc_start: 0.9211 (tp) cc_final: 0.8999 (mt) REVERT: J 104 LEU cc_start: 0.9253 (tp) cc_final: 0.9028 (tp) REVERT: K 24 THR cc_start: 0.9075 (m) cc_final: 0.8857 (p) REVERT: K 33 VAL cc_start: 0.9167 (t) cc_final: 0.8805 (p) REVERT: L 45 LYS cc_start: 0.9434 (mtmm) cc_final: 0.9102 (mtmm) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.3385 time to fit residues: 130.8742 Evaluate side-chains 192 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 159 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 217 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 B 630 GLN B 650 GLN C 99 ASN C 374 HIS ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS G 5 GLN G 59 HIS ** J 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 ASN L 94 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.054299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.040855 restraints weight = 108290.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.042199 restraints weight = 62547.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.043073 restraints weight = 44565.002| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21945 Z= 0.170 Angle : 0.789 12.620 30192 Z= 0.366 Chirality : 0.047 0.394 3924 Planarity : 0.004 0.033 3450 Dihedral : 10.007 82.611 6432 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.18 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % 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: -1.10 (0.17), residues: 2361 helix: 0.45 (0.29), residues: 357 sheet: -0.08 (0.20), residues: 675 loop : -1.45 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP F 571 HIS 0.007 0.001 HIS D 374 PHE 0.014 0.001 PHE D 53 TYR 0.020 0.002 TYR A 217 ARG 0.004 0.000 ARG F 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 60) link_NAG-ASN : angle 2.38920 ( 180) link_ALPHA1-6 : bond 0.00620 ( 18) link_ALPHA1-6 : angle 1.89246 ( 54) link_BETA1-4 : bond 0.00347 ( 81) link_BETA1-4 : angle 2.10305 ( 243) link_ALPHA1-2 : bond 0.00466 ( 12) link_ALPHA1-2 : angle 1.58306 ( 36) link_ALPHA1-3 : bond 0.00760 ( 21) link_ALPHA1-3 : angle 1.74716 ( 63) hydrogen bonds : bond 0.04243 ( 704) hydrogen bonds : angle 5.56356 ( 2118) SS BOND : bond 0.00310 ( 42) SS BOND : angle 0.86059 ( 84) covalent geometry : bond 0.00367 (21711) covalent geometry : angle 0.73907 (29532) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9226 (tpp) cc_final: 0.8713 (tpp) REVERT: A 309 ILE cc_start: 0.9141 (mp) cc_final: 0.8816 (mp) REVERT: A 424 ILE cc_start: 0.9228 (pt) cc_final: 0.9007 (pt) REVERT: A 434 MET cc_start: 0.8976 (tmm) cc_final: 0.8448 (tmm) REVERT: B 631 TRP cc_start: 0.9442 (t-100) cc_final: 0.9233 (t-100) REVERT: B 638 TYR cc_start: 0.8505 (m-80) cc_final: 0.7955 (m-80) REVERT: B 650 GLN cc_start: 0.8557 (tt0) cc_final: 0.7914 (mt0) REVERT: C 104 MET cc_start: 0.9442 (mmm) cc_final: 0.9217 (mmm) REVERT: C 150 MET cc_start: 0.6788 (tpt) cc_final: 0.6414 (tpp) REVERT: C 180 ASP cc_start: 0.8693 (m-30) cc_final: 0.8307 (m-30) REVERT: C 424 ILE cc_start: 0.9133 (pt) cc_final: 0.8837 (pt) REVERT: C 434 MET cc_start: 0.8571 (tmm) cc_final: 0.7936 (tmm) REVERT: D 102 GLU cc_start: 0.9150 (mp0) cc_final: 0.8931 (mp0) REVERT: E 543 ASN cc_start: 0.8967 (t0) cc_final: 0.8416 (t0) REVERT: E 601 LYS cc_start: 0.8538 (pttt) cc_final: 0.8213 (ptmt) REVERT: E 650 GLN cc_start: 0.8472 (tt0) cc_final: 0.7977 (mt0) REVERT: F 651 ASN cc_start: 0.8403 (t0) cc_final: 0.7944 (t0) REVERT: G 33 ASN cc_start: 0.9329 (m-40) cc_final: 0.8935 (p0) REVERT: G 58 TYR cc_start: 0.9001 (m-80) cc_final: 0.8630 (m-80) REVERT: G 72 ASP cc_start: 0.8202 (t0) cc_final: 0.5970 (t0) REVERT: G 75 LYS cc_start: 0.9404 (mttt) cc_final: 0.9046 (mttp) REVERT: H 33 ASN cc_start: 0.9332 (m-40) cc_final: 0.8894 (p0) REVERT: H 58 TYR cc_start: 0.9023 (m-10) cc_final: 0.8786 (m-10) REVERT: H 72 ASP cc_start: 0.8401 (t0) cc_final: 0.6867 (t0) REVERT: H 75 LYS cc_start: 0.9112 (mtmm) cc_final: 0.8856 (mttp) REVERT: H 100 LYS cc_start: 0.9218 (mttt) cc_final: 0.9002 (mttp) REVERT: I 33 ASN cc_start: 0.9376 (m-40) cc_final: 0.9014 (p0) REVERT: I 58 TYR cc_start: 0.9165 (m-10) cc_final: 0.8283 (m-10) REVERT: I 98 GLU cc_start: 0.8668 (tp30) cc_final: 0.8249 (tp30) REVERT: J 87 TYR cc_start: 0.8511 (m-80) cc_final: 0.8213 (m-80) REVERT: K 33 VAL cc_start: 0.9224 (t) cc_final: 0.8876 (p) REVERT: K 50 ASP cc_start: 0.9186 (t0) cc_final: 0.8758 (t0) REVERT: K 53 LYS cc_start: 0.8789 (mptt) cc_final: 0.8559 (mmtm) REVERT: L 104 LEU cc_start: 0.9159 (tp) cc_final: 0.8864 (tp) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.3240 time to fit residues: 128.6834 Evaluate side-chains 190 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 215 optimal weight: 7.9990 chunk 236 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 146 optimal weight: 0.8980 chunk 211 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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** B 630 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.054288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.040829 restraints weight = 108828.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.042118 restraints weight = 64445.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.042957 restraints weight = 46709.115| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 21945 Z= 0.185 Angle : 0.781 12.311 30192 Z= 0.360 Chirality : 0.046 0.392 3924 Planarity : 0.004 0.038 3450 Dihedral : 9.468 80.633 6432 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.16 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % 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: -1.13 (0.17), residues: 2361 helix: 0.46 (0.29), residues: 363 sheet: -0.13 (0.20), residues: 654 loop : -1.46 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 571 HIS 0.005 0.001 HIS C 105 PHE 0.019 0.002 PHE B 519 TYR 0.016 0.002 TYR H 58 ARG 0.008 0.001 ARG G 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 60) link_NAG-ASN : angle 2.26514 ( 180) link_ALPHA1-6 : bond 0.00648 ( 18) link_ALPHA1-6 : angle 1.83014 ( 54) link_BETA1-4 : bond 0.00361 ( 81) link_BETA1-4 : angle 2.03758 ( 243) link_ALPHA1-2 : bond 0.00376 ( 12) link_ALPHA1-2 : angle 1.72996 ( 36) link_ALPHA1-3 : bond 0.00639 ( 21) link_ALPHA1-3 : angle 1.84068 ( 63) hydrogen bonds : bond 0.04120 ( 704) hydrogen bonds : angle 5.46394 ( 2118) SS BOND : bond 0.00210 ( 42) SS BOND : angle 0.79843 ( 84) covalent geometry : bond 0.00403 (21711) covalent geometry : angle 0.73450 (29532) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 2.338 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: A 161 MET cc_start: 0.9260 (tpp) cc_final: 0.8759 (tpp) REVERT: A 195 ASN cc_start: 0.9534 (p0) cc_final: 0.9248 (p0) REVERT: A 309 ILE cc_start: 0.9188 (mp) cc_final: 0.8866 (mp) REVERT: A 434 MET cc_start: 0.8875 (tmm) cc_final: 0.8483 (tmm) REVERT: B 571 TRP cc_start: 0.8167 (m-10) cc_final: 0.7967 (m-10) REVERT: B 631 TRP cc_start: 0.9410 (t-100) cc_final: 0.9042 (t-100) REVERT: B 638 TYR cc_start: 0.8553 (m-80) cc_final: 0.7974 (m-80) REVERT: B 650 GLN cc_start: 0.8516 (tt0) cc_final: 0.8004 (tt0) REVERT: C 150 MET cc_start: 0.6756 (tpt) cc_final: 0.6413 (tpp) REVERT: C 180 ASP cc_start: 0.8710 (m-30) cc_final: 0.8379 (m-30) REVERT: C 271 MET cc_start: 0.7958 (mmt) cc_final: 0.7750 (mmt) REVERT: D 195 ASN cc_start: 0.9435 (p0) cc_final: 0.9166 (p0) REVERT: D 271 MET cc_start: 0.8370 (mmm) cc_final: 0.8062 (mmm) REVERT: D 434 MET cc_start: 0.8857 (tmm) cc_final: 0.8311 (tmm) REVERT: E 543 ASN cc_start: 0.8990 (t0) cc_final: 0.8450 (t0) REVERT: E 546 SER cc_start: 0.8078 (t) cc_final: 0.7696 (t) REVERT: E 601 LYS cc_start: 0.8729 (pttt) cc_final: 0.8431 (ptmt) REVERT: E 650 GLN cc_start: 0.8557 (tt0) cc_final: 0.7897 (tt0) REVERT: G 33 ASN cc_start: 0.9380 (m-40) cc_final: 0.9049 (p0) REVERT: G 58 TYR cc_start: 0.8998 (m-80) cc_final: 0.8663 (m-80) REVERT: G 72 ASP cc_start: 0.8195 (t0) cc_final: 0.5997 (t0) REVERT: G 75 LYS cc_start: 0.9411 (mttt) cc_final: 0.9034 (mttp) REVERT: G 98 GLU cc_start: 0.8859 (tp30) cc_final: 0.8595 (tp30) REVERT: H 33 ASN cc_start: 0.9347 (m-40) cc_final: 0.8917 (p0) REVERT: H 58 TYR cc_start: 0.9010 (m-10) cc_final: 0.8701 (m-10) REVERT: H 72 ASP cc_start: 0.8371 (t0) cc_final: 0.6869 (t0) REVERT: H 75 LYS cc_start: 0.9118 (mtmm) cc_final: 0.8864 (mttp) REVERT: H 100 LYS cc_start: 0.9149 (mttt) cc_final: 0.8895 (mttp) REVERT: I 22 CYS cc_start: 0.3433 (t) cc_final: 0.3103 (t) REVERT: I 33 ASN cc_start: 0.9368 (m-40) cc_final: 0.9018 (p0) REVERT: I 58 TYR cc_start: 0.9232 (m-10) cc_final: 0.8305 (m-10) REVERT: I 98 GLU cc_start: 0.8669 (tp30) cc_final: 0.8204 (tp30) REVERT: J 87 TYR cc_start: 0.8518 (m-80) cc_final: 0.8243 (m-80) REVERT: K 53 LYS cc_start: 0.8845 (mptt) cc_final: 0.8555 (mmtm) REVERT: K 104 LEU cc_start: 0.9362 (tp) cc_final: 0.9039 (tp) REVERT: L 45 LYS cc_start: 0.9428 (mtmm) cc_final: 0.9188 (mtmm) REVERT: L 104 LEU cc_start: 0.9123 (tp) cc_final: 0.8858 (tp) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.3191 time to fit residues: 125.3359 Evaluate side-chains 186 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 13 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 234 optimal weight: 0.0470 chunk 166 optimal weight: 0.7980 chunk 198 optimal weight: 6.9990 chunk 150 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.9684 ------------------------------------------------------------------------------- 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** B 630 GLN D 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.054408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.040837 restraints weight = 108832.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.042209 restraints weight = 62111.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.043102 restraints weight = 44095.392| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21945 Z= 0.156 Angle : 0.750 12.207 30192 Z= 0.348 Chirality : 0.045 0.371 3924 Planarity : 0.003 0.034 3450 Dihedral : 9.099 77.624 6432 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.10 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % 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: -1.14 (0.17), residues: 2361 helix: 0.46 (0.29), residues: 363 sheet: -0.11 (0.20), residues: 654 loop : -1.48 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 571 HIS 0.003 0.001 HIS H 52A PHE 0.018 0.001 PHE B 519 TYR 0.025 0.001 TYR D 217 ARG 0.005 0.000 ARG B 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 60) link_NAG-ASN : angle 2.08872 ( 180) link_ALPHA1-6 : bond 0.00708 ( 18) link_ALPHA1-6 : angle 1.74994 ( 54) link_BETA1-4 : bond 0.00354 ( 81) link_BETA1-4 : angle 1.99259 ( 243) link_ALPHA1-2 : bond 0.00421 ( 12) link_ALPHA1-2 : angle 1.57349 ( 36) link_ALPHA1-3 : bond 0.00751 ( 21) link_ALPHA1-3 : angle 1.72925 ( 63) hydrogen bonds : bond 0.03988 ( 704) hydrogen bonds : angle 5.36442 ( 2118) SS BOND : bond 0.00186 ( 42) SS BOND : angle 0.82433 ( 84) covalent geometry : bond 0.00341 (21711) covalent geometry : angle 0.70626 (29532) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 2.457 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: 0.7423 (t60) cc_final: 0.7151 (t60) REVERT: A 161 MET cc_start: 0.9235 (tpp) cc_final: 0.8721 (tpp) REVERT: A 180 ASP cc_start: 0.8869 (m-30) cc_final: 0.8633 (m-30) REVERT: A 195 ASN cc_start: 0.9546 (p0) cc_final: 0.9239 (p0) REVERT: A 309 ILE cc_start: 0.9159 (mp) cc_final: 0.8854 (mp) REVERT: A 434 MET cc_start: 0.8877 (tmm) cc_final: 0.8516 (tmm) REVERT: B 571 TRP cc_start: 0.8211 (m-10) cc_final: 0.8000 (m-10) REVERT: B 631 TRP cc_start: 0.9343 (t-100) cc_final: 0.9093 (t-100) REVERT: B 638 TYR cc_start: 0.8421 (m-80) cc_final: 0.7854 (m-80) REVERT: B 650 GLN cc_start: 0.8206 (tt0) cc_final: 0.7896 (pp30) REVERT: C 180 ASP cc_start: 0.8654 (m-30) cc_final: 0.8263 (m-30) REVERT: C 195 ASN cc_start: 0.9380 (p0) cc_final: 0.9171 (p0) REVERT: D 104 MET cc_start: 0.9200 (mmm) cc_final: 0.8959 (tpp) REVERT: D 180 ASP cc_start: 0.8801 (m-30) cc_final: 0.8589 (m-30) REVERT: D 195 ASN cc_start: 0.9236 (p0) cc_final: 0.9022 (p0) REVERT: E 543 ASN cc_start: 0.8976 (t0) cc_final: 0.8449 (t0) REVERT: E 601 LYS cc_start: 0.8582 (pttt) cc_final: 0.8318 (ptmt) REVERT: E 626 MET cc_start: 0.8301 (tpp) cc_final: 0.7897 (tpp) REVERT: E 650 GLN cc_start: 0.8433 (tt0) cc_final: 0.7791 (tt0) REVERT: F 601 LYS cc_start: 0.8599 (pttt) cc_final: 0.8327 (ptmt) REVERT: G 33 ASN cc_start: 0.9347 (m-40) cc_final: 0.9018 (p0) REVERT: G 98 GLU cc_start: 0.8809 (tp30) cc_final: 0.8545 (tp30) REVERT: H 33 ASN cc_start: 0.9282 (m-40) cc_final: 0.8913 (p0) REVERT: H 58 TYR cc_start: 0.8902 (m-10) cc_final: 0.8556 (m-10) REVERT: H 72 ASP cc_start: 0.8385 (t0) cc_final: 0.6858 (t0) REVERT: H 75 LYS cc_start: 0.9123 (mtmm) cc_final: 0.8859 (mttp) REVERT: H 100 LYS cc_start: 0.9165 (mttt) cc_final: 0.8840 (mttm) REVERT: I 22 CYS cc_start: 0.4059 (t) cc_final: 0.3745 (t) REVERT: I 33 ASN cc_start: 0.9321 (m-40) cc_final: 0.9002 (p0) REVERT: I 58 TYR cc_start: 0.9110 (m-10) cc_final: 0.8253 (m-10) REVERT: I 98 GLU cc_start: 0.8646 (tp30) cc_final: 0.8425 (tp30) REVERT: I 105 ARG cc_start: 0.8361 (ptp90) cc_final: 0.8102 (ptp90) REVERT: J 87 TYR cc_start: 0.8441 (m-80) cc_final: 0.8193 (m-80) REVERT: J 104 LEU cc_start: 0.9301 (tp) cc_final: 0.9033 (tp) REVERT: K 31 ASN cc_start: 0.8164 (p0) cc_final: 0.7286 (t0) REVERT: K 53 LYS cc_start: 0.8780 (mptt) cc_final: 0.8554 (mmtm) REVERT: L 31 ASN cc_start: 0.8184 (p0) cc_final: 0.7396 (t0) REVERT: L 45 LYS cc_start: 0.9380 (mtmm) cc_final: 0.9130 (mtmm) REVERT: L 104 LEU cc_start: 0.9115 (tp) cc_final: 0.8832 (tp) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.3466 time to fit residues: 132.3261 Evaluate side-chains 193 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 23 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 215 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 203 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 117 optimal weight: 0.4980 chunk 51 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 630 GLN F 652 GLN I 82AASN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.052873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.039521 restraints weight = 109692.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.040812 restraints weight = 63296.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.041661 restraints weight = 45166.500| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.5933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 21945 Z= 0.295 Angle : 0.885 11.671 30192 Z= 0.408 Chirality : 0.047 0.401 3924 Planarity : 0.004 0.041 3450 Dihedral : 9.517 79.894 6432 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.75 % Favored : 91.74 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % 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: -1.46 (0.17), residues: 2361 helix: -0.04 (0.28), residues: 372 sheet: -0.38 (0.19), residues: 672 loop : -1.59 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP J 95 HIS 0.005 0.001 HIS K 39 PHE 0.017 0.002 PHE B 519 TYR 0.023 0.002 TYR D 217 ARG 0.004 0.001 ARG C 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00825 ( 60) link_NAG-ASN : angle 2.54476 ( 180) link_ALPHA1-6 : bond 0.00576 ( 18) link_ALPHA1-6 : angle 1.87762 ( 54) link_BETA1-4 : bond 0.00473 ( 81) link_BETA1-4 : angle 2.06230 ( 243) link_ALPHA1-2 : bond 0.00559 ( 12) link_ALPHA1-2 : angle 2.01044 ( 36) link_ALPHA1-3 : bond 0.00495 ( 21) link_ALPHA1-3 : angle 2.14273 ( 63) hydrogen bonds : bond 0.04661 ( 704) hydrogen bonds : angle 5.72502 ( 2118) SS BOND : bond 0.00245 ( 42) SS BOND : angle 1.00556 ( 84) covalent geometry : bond 0.00640 (21711) covalent geometry : angle 0.83766 (29532) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 2.168 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: 0.7564 (t60) cc_final: 0.7293 (t60) REVERT: A 161 MET cc_start: 0.9295 (tpp) cc_final: 0.8791 (tpp) REVERT: A 180 ASP cc_start: 0.8854 (m-30) cc_final: 0.8510 (m-30) REVERT: A 195 ASN cc_start: 0.9483 (p0) cc_final: 0.9077 (p0) REVERT: A 309 ILE cc_start: 0.9214 (mp) cc_final: 0.8857 (mp) REVERT: A 424 ILE cc_start: 0.9348 (pt) cc_final: 0.9126 (pt) REVERT: A 434 MET cc_start: 0.8977 (tmm) cc_final: 0.8516 (tmm) REVERT: B 571 TRP cc_start: 0.8198 (m-10) cc_final: 0.7917 (m-10) REVERT: B 631 TRP cc_start: 0.9371 (t-100) cc_final: 0.9113 (t-100) REVERT: B 638 TYR cc_start: 0.8537 (m-80) cc_final: 0.7962 (m-80) REVERT: B 650 GLN cc_start: 0.8557 (tt0) cc_final: 0.8099 (pp30) REVERT: C 104 MET cc_start: 0.9299 (tpp) cc_final: 0.9049 (mmt) REVERT: C 180 ASP cc_start: 0.8778 (m-30) cc_final: 0.8409 (m-30) REVERT: C 195 ASN cc_start: 0.9423 (p0) cc_final: 0.9135 (p0) REVERT: D 195 ASN cc_start: 0.9361 (p0) cc_final: 0.8988 (p0) REVERT: D 434 MET cc_start: 0.8889 (tmm) cc_final: 0.8586 (ttp) REVERT: E 543 ASN cc_start: 0.8974 (t0) cc_final: 0.8571 (t0) REVERT: E 601 LYS cc_start: 0.8817 (pttt) cc_final: 0.8490 (ptmt) REVERT: E 638 TYR cc_start: 0.8595 (m-80) cc_final: 0.8314 (m-80) REVERT: E 650 GLN cc_start: 0.8553 (tt0) cc_final: 0.8265 (tt0) REVERT: G 33 ASN cc_start: 0.9362 (m-40) cc_final: 0.9049 (p0) REVERT: G 98 GLU cc_start: 0.8919 (tp30) cc_final: 0.8642 (tp30) REVERT: H 33 ASN cc_start: 0.9238 (m-40) cc_final: 0.8812 (p0) REVERT: H 58 TYR cc_start: 0.8909 (m-10) cc_final: 0.8523 (m-10) REVERT: H 72 ASP cc_start: 0.8297 (t0) cc_final: 0.6851 (t0) REVERT: H 75 LYS cc_start: 0.9124 (mtmm) cc_final: 0.8875 (mttp) REVERT: H 100 LYS cc_start: 0.9217 (mttt) cc_final: 0.9008 (mttm) REVERT: I 33 ASN cc_start: 0.9377 (m-40) cc_final: 0.9096 (p0) REVERT: I 58 TYR cc_start: 0.9096 (m-10) cc_final: 0.8524 (m-80) REVERT: I 98 GLU cc_start: 0.8690 (tp30) cc_final: 0.8481 (tp30) REVERT: J 87 TYR cc_start: 0.8319 (m-80) cc_final: 0.8048 (m-80) REVERT: K 31 ASN cc_start: 0.8132 (p0) cc_final: 0.7393 (t0) REVERT: K 104 LEU cc_start: 0.9323 (tp) cc_final: 0.9008 (tp) REVERT: L 31 ASN cc_start: 0.8311 (p0) cc_final: 0.7235 (t0) REVERT: L 45 LYS cc_start: 0.9373 (mtmm) cc_final: 0.8650 (mmmt) REVERT: L 104 LEU cc_start: 0.9158 (tp) cc_final: 0.8853 (tp) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.3368 time to fit residues: 119.9026 Evaluate side-chains 182 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 15 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 chunk 214 optimal weight: 20.0000 chunk 115 optimal weight: 0.7980 chunk 180 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 72 optimal weight: 0.0980 chunk 215 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 184 optimal weight: 6.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN B 630 GLN J 17 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.054195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.040497 restraints weight = 109005.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.041900 restraints weight = 61523.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.042832 restraints weight = 43262.942| |-----------------------------------------------------------------------------| r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.5962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21945 Z= 0.147 Angle : 0.763 11.761 30192 Z= 0.355 Chirality : 0.046 0.367 3924 Planarity : 0.004 0.034 3450 Dihedral : 8.895 75.525 6432 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.06 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % 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: -1.23 (0.17), residues: 2361 helix: 0.40 (0.29), residues: 363 sheet: -0.20 (0.20), residues: 654 loop : -1.51 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 571 HIS 0.004 0.001 HIS K 39 PHE 0.019 0.001 PHE B 519 TYR 0.034 0.002 TYR A 217 ARG 0.003 0.000 ARG E 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 60) link_NAG-ASN : angle 2.21475 ( 180) link_ALPHA1-6 : bond 0.00744 ( 18) link_ALPHA1-6 : angle 1.66234 ( 54) link_BETA1-4 : bond 0.00353 ( 81) link_BETA1-4 : angle 1.98381 ( 243) link_ALPHA1-2 : bond 0.00443 ( 12) link_ALPHA1-2 : angle 1.49531 ( 36) link_ALPHA1-3 : bond 0.00784 ( 21) link_ALPHA1-3 : angle 1.71600 ( 63) hydrogen bonds : bond 0.04041 ( 704) hydrogen bonds : angle 5.40596 ( 2118) SS BOND : bond 0.00239 ( 42) SS BOND : angle 0.86067 ( 84) covalent geometry : bond 0.00318 (21711) covalent geometry : angle 0.71845 (29532) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.7480 (t60) cc_final: 0.7218 (t60) REVERT: A 180 ASP cc_start: 0.8858 (m-30) cc_final: 0.8577 (m-30) REVERT: A 195 ASN cc_start: 0.9568 (p0) cc_final: 0.9257 (p0) REVERT: A 434 MET cc_start: 0.8907 (tmm) cc_final: 0.8423 (tmm) REVERT: B 571 TRP cc_start: 0.8047 (m-10) cc_final: 0.7796 (m-10) REVERT: B 638 TYR cc_start: 0.8462 (m-80) cc_final: 0.7903 (m-80) REVERT: B 650 GLN cc_start: 0.8466 (tt0) cc_final: 0.8064 (pp30) REVERT: C 180 ASP cc_start: 0.8740 (m-30) cc_final: 0.8341 (m-30) REVERT: C 195 ASN cc_start: 0.9522 (p0) cc_final: 0.9229 (p0) REVERT: D 180 ASP cc_start: 0.8783 (m-30) cc_final: 0.8524 (m-30) REVERT: D 195 ASN cc_start: 0.9382 (p0) cc_final: 0.9097 (p0) REVERT: D 434 MET cc_start: 0.8831 (tmm) cc_final: 0.8309 (tmm) REVERT: E 543 ASN cc_start: 0.8975 (t0) cc_final: 0.8436 (t0) REVERT: E 650 GLN cc_start: 0.8582 (tt0) cc_final: 0.7907 (tt0) REVERT: G 33 ASN cc_start: 0.9331 (m-40) cc_final: 0.9025 (p0) REVERT: G 98 GLU cc_start: 0.8919 (tp30) cc_final: 0.8593 (tp30) REVERT: H 33 ASN cc_start: 0.9267 (m-40) cc_final: 0.8931 (p0) REVERT: H 58 TYR cc_start: 0.8835 (m-10) cc_final: 0.8408 (m-10) REVERT: H 72 ASP cc_start: 0.8307 (t0) cc_final: 0.6879 (t0) REVERT: H 75 LYS cc_start: 0.9126 (mtmm) cc_final: 0.8875 (mttp) REVERT: H 100 LYS cc_start: 0.9186 (mttt) cc_final: 0.8967 (mttm) REVERT: I 33 ASN cc_start: 0.9327 (m-40) cc_final: 0.9014 (p0) REVERT: I 98 GLU cc_start: 0.8712 (tp30) cc_final: 0.8490 (tp30) REVERT: J 31 ASN cc_start: 0.7720 (p0) cc_final: 0.7190 (t0) REVERT: J 87 TYR cc_start: 0.8470 (m-80) cc_final: 0.8199 (m-80) REVERT: K 104 LEU cc_start: 0.9326 (tp) cc_final: 0.9027 (tp) REVERT: L 31 ASN cc_start: 0.8136 (p0) cc_final: 0.7354 (t0) REVERT: L 45 LYS cc_start: 0.9363 (mtmm) cc_final: 0.8661 (mmmt) REVERT: L 104 LEU cc_start: 0.9144 (tp) cc_final: 0.8837 (tp) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.3421 time to fit residues: 127.7673 Evaluate side-chains 180 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 191 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 208 optimal weight: 8.9990 chunk 173 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 607 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 550 GLN F 550 GLN J 17 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.052324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.038617 restraints weight = 113306.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.039932 restraints weight = 65270.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.040795 restraints weight = 46605.878| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.6254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 21945 Z= 0.337 Angle : 0.942 11.446 30192 Z= 0.433 Chirality : 0.048 0.437 3924 Planarity : 0.005 0.043 3450 Dihedral : 9.513 78.709 6432 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.22 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % 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: -1.61 (0.17), residues: 2361 helix: -0.40 (0.27), residues: 372 sheet: -0.55 (0.19), residues: 687 loop : -1.57 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 35 HIS 0.005 0.002 HIS D 85 PHE 0.019 0.003 PHE D 361 TYR 0.032 0.003 TYR D 217 ARG 0.005 0.001 ARG A 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00938 ( 60) link_NAG-ASN : angle 2.74535 ( 180) link_ALPHA1-6 : bond 0.00552 ( 18) link_ALPHA1-6 : angle 1.91550 ( 54) link_BETA1-4 : bond 0.00530 ( 81) link_BETA1-4 : angle 2.07857 ( 243) link_ALPHA1-2 : bond 0.00499 ( 12) link_ALPHA1-2 : angle 2.09925 ( 36) link_ALPHA1-3 : bond 0.00412 ( 21) link_ALPHA1-3 : angle 2.26460 ( 63) hydrogen bonds : bond 0.04886 ( 704) hydrogen bonds : angle 5.80486 ( 2118) SS BOND : bond 0.00251 ( 42) SS BOND : angle 1.01030 ( 84) covalent geometry : bond 0.00730 (21711) covalent geometry : angle 0.89441 (29532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6075.17 seconds wall clock time: 107 minutes 57.84 seconds (6477.84 seconds total)