Starting phenix.real_space_refine (version: dev) on Wed Dec 14 15:46:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aco_3121/12_2022/5aco_3121.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aco_3121/12_2022/5aco_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aco_3121/12_2022/5aco_3121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aco_3121/12_2022/5aco_3121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aco_3121/12_2022/5aco_3121.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aco_3121/12_2022/5aco_3121.pdb" } resolution = 4.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 1 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 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: 1 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: 1 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 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 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: 5 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: 1 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: 3 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: 5 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: 8 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 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: 1 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: 1 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 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 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 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: 1 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 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: 1 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: 1 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 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 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: 5 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: 1 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: 3 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: 5 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: 8 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 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: 1 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: 1 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 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 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: 1 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 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: 1 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: 1 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 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 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: 5 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: 1 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: 3 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: 5 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: 8 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 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: 1 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: 1 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 11.50, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "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: 11.87 Conformation dependent library (CDL) restraints added in 2.6 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: 1.72 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: 9.31 Time building geometry restraints manager: 12.47 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: 93.55 - 104.69: 624 104.69 - 115.82: 15132 115.82 - 126.96: 13355 126.96 - 138.09: 402 138.09 - 149.23: 19 Bond angle restraints: 29532 Sorted by residual: angle pdb=" C2 NAG u 1 " pdb=" C1 NAG u 1 " pdb=" O5 NAG u 1 " ideal model delta sigma weight residual 109.64 99.60 10.04 5.38e-01 3.45e+00 3.48e+02 angle pdb=" C2 NAG C1343 " pdb=" C1 NAG C1343 " pdb=" O5 NAG C1343 " ideal model delta sigma weight residual 109.64 99.61 10.03 5.38e-01 3.45e+00 3.47e+02 angle pdb=" C2 NAG q 1 " pdb=" C1 NAG q 1 " pdb=" O5 NAG q 1 " ideal model delta sigma weight residual 109.64 99.62 10.02 5.38e-01 3.45e+00 3.47e+02 angle pdb=" C2 NAG B1618 " pdb=" C1 NAG B1618 " pdb=" O5 NAG B1618 " ideal model delta sigma weight residual 109.64 99.62 10.02 5.38e-01 3.45e+00 3.47e+02 angle pdb=" C2 NAG E1637 " pdb=" C1 NAG E1637 " pdb=" O5 NAG E1637 " ideal model delta sigma weight residual 109.64 99.63 10.01 5.38e-01 3.45e+00 3.46e+02 ... (remaining 29527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 12306 17.21 - 34.41: 567 34.41 - 51.62: 69 51.62 - 68.82: 54 68.82 - 86.03: 12 Dihedral angle restraints: 13008 sinusoidal: 6075 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 13005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.227: 3771 0.227 - 0.455: 132 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 2.520 nonbonded pdb=" ND2 ASN A 279 " pdb=" O6 NAG T 1 " model vdw 1.987 2.520 nonbonded pdb=" ND2 ASN C 279 " pdb=" O6 NAG k 1 " model vdw 1.987 2.520 nonbonded pdb=" O ALA I 52C" pdb=" N2 NAG 2 1 " model vdw 2.062 2.520 nonbonded pdb=" O ALA H 52C" pdb=" N2 NAG V 1 " model vdw 2.063 2.520 ... (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 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 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. 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.100 Check model and map are aligned: 0.340 Convert atoms to be neutral: 0.190 Process input model: 58.780 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 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 : 0.012 0.278 21711 Z= 0.783 Angle : 1.907 38.429 29532 Z= 1.490 Chirality : 0.107 1.137 3924 Planarity : 0.015 0.198 3450 Dihedral : 10.209 86.027 8406 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 1.91 % Allowed : 9.15 % Favored : 88.95 % Rotamer Outliers : 0.29 % 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 533 time to evaluate : 2.396 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 outliers start: 6 outliers final: 3 residues processed: 539 average time/residue: 0.3553 time to fit residues: 282.0882 Evaluate side-chains 263 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 260 time to evaluate : 2.615 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.1887 time to fit residues: 4.4233 ------------------------------------------------------------------------------- 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: 1.9990 chunk 179 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN A 300 ASN A 348 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN B 630 GLN C 136 ASN C 293 GLN C 300 ASN C 348 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 21711 Z= 0.327 Angle : 0.793 21.397 29532 Z= 0.427 Chirality : 0.056 0.869 3924 Planarity : 0.004 0.043 3450 Dihedral : 6.214 50.708 4038 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.69 % Favored : 92.80 % Rotamer Outliers : 0.00 % 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: -1.57 (0.16), residues: 2361 helix: -1.06 (0.24), residues: 411 sheet: -0.48 (0.20), residues: 669 loop : -1.32 (0.16), residues: 1281 *********************** 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 320 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 4.413 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 outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.3608 time to fit residues: 176.4031 Evaluate side-chains 225 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 2.160 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 179 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 192 optimal weight: 8.9990 chunk 213 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 172 optimal weight: 9.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 C 293 GLN C 422 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 GLN D 422 GLN G 3 GLN H 3 GLN I 3 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.073 21711 Z= 0.464 Angle : 0.850 21.341 29532 Z= 0.438 Chirality : 0.052 0.692 3924 Planarity : 0.005 0.082 3450 Dihedral : 6.530 53.374 4038 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.62 % Favored : 91.83 % Rotamer Outliers : 0.14 % 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: -1.48 (0.16), residues: 2361 helix: -0.69 (0.25), residues: 405 sheet: -0.23 (0.19), residues: 747 loop : -1.56 (0.16), residues: 1209 *********************** 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 272 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 269 time to evaluate : 2.591 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 outliers start: 3 outliers final: 0 residues processed: 272 average time/residue: 0.3432 time to fit residues: 141.9675 Evaluate side-chains 183 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 2.325 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 20.0000 chunk 162 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 229 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 chunk 205 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN B 650 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 653 GLN E 656 ASN ** G 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 21711 Z= 0.236 Angle : 0.673 21.350 29532 Z= 0.351 Chirality : 0.049 0.658 3924 Planarity : 0.004 0.037 3450 Dihedral : 6.036 48.729 4038 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.65 % Favored : 92.84 % Rotamer Outliers : 0.00 % 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: -1.09 (0.17), residues: 2361 helix: 0.35 (0.28), residues: 366 sheet: -0.07 (0.19), residues: 744 loop : -1.48 (0.17), residues: 1251 *********************** 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 273 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 2.466 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 outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.3384 time to fit residues: 142.6008 Evaluate side-chains 186 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.369 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 20.0000 chunk 130 optimal weight: 7.9990 chunk 3 optimal weight: 0.0060 chunk 170 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 158 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.1738 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN C 374 HIS ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 21711 Z= 0.192 Angle : 0.644 21.221 29532 Z= 0.332 Chirality : 0.048 0.620 3924 Planarity : 0.004 0.036 3450 Dihedral : 5.803 47.154 4038 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.82 % Favored : 92.67 % Rotamer Outliers : 0.00 % 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: -0.94 (0.17), residues: 2361 helix: 0.75 (0.29), residues: 360 sheet: 0.07 (0.19), residues: 678 loop : -1.43 (0.16), residues: 1323 *********************** 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 263 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 2.330 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 outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.3450 time to fit residues: 139.9544 Evaluate side-chains 185 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.378 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 190 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN K 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 21711 Z= 0.376 Angle : 0.735 20.817 29532 Z= 0.375 Chirality : 0.049 0.640 3924 Planarity : 0.004 0.042 3450 Dihedral : 6.136 53.239 4038 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.67 % Favored : 91.83 % Rotamer Outliers : 0.05 % 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: 0.34 (0.28), residues: 378 sheet: -0.13 (0.19), residues: 678 loop : -1.46 (0.17), residues: 1305 *********************** 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 229 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 2.346 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 outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.3302 time to fit residues: 119.3238 Evaluate side-chains 172 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 2.342 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 228 optimal weight: 20.0000 chunk 142 optimal weight: 0.0020 chunk 139 optimal weight: 8.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 653 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 GLN ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 21711 Z= 0.211 Angle : 0.630 20.769 29532 Z= 0.324 Chirality : 0.047 0.591 3924 Planarity : 0.003 0.035 3450 Dihedral : 5.794 48.514 4038 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.90 % Favored : 92.59 % Rotamer Outliers : 0.00 % 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: -0.98 (0.17), residues: 2361 helix: 0.58 (0.29), residues: 375 sheet: -0.03 (0.19), residues: 678 loop : -1.40 (0.17), residues: 1308 *********************** 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 235 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 2.391 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 outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.3235 time to fit residues: 120.1479 Evaluate side-chains 180 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.372 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 145 optimal weight: 0.4980 chunk 155 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 179 optimal weight: 0.5980 chunk 207 optimal weight: 20.0000 overall best weight: 1.4182 ------------------------------------------------------------------------------- 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** B 607 ASN B 650 GLN C 99 ASN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 21711 Z= 0.195 Angle : 0.624 20.522 29532 Z= 0.319 Chirality : 0.047 0.627 3924 Planarity : 0.003 0.036 3450 Dihedral : 5.655 47.094 4038 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.99 % Favored : 92.50 % Rotamer Outliers : 0.00 % 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: -0.91 (0.17), residues: 2361 helix: 0.70 (0.29), residues: 375 sheet: 0.02 (0.19), residues: 678 loop : -1.37 (0.17), residues: 1308 *********************** 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 233 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.575 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 outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.3284 time to fit residues: 121.1206 Evaluate side-chains 174 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.525 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 40.0000 chunk 199 optimal weight: 10.0000 chunk 212 optimal weight: 0.0870 chunk 128 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 192 optimal weight: 0.6980 chunk 201 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 225 optimal weight: 9.9990 overall best weight: 2.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 21711 Z= 0.261 Angle : 0.650 20.538 29532 Z= 0.331 Chirality : 0.047 0.643 3924 Planarity : 0.004 0.037 3450 Dihedral : 5.739 49.101 4038 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.24 % Favored : 92.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.93 (0.17), residues: 2361 helix: 0.74 (0.29), residues: 375 sheet: 0.02 (0.20), residues: 675 loop : -1.40 (0.17), residues: 1311 *********************** 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 226 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 2.656 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 outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.3226 time to fit residues: 114.7793 Evaluate side-chains 167 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 156 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 217 optimal weight: 20.0000 chunk 188 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 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 99 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.5847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.092 21711 Z= 0.262 Angle : 0.664 20.284 29532 Z= 0.339 Chirality : 0.047 0.639 3924 Planarity : 0.004 0.036 3450 Dihedral : 5.738 48.775 4038 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.33 % Favored : 92.12 % Rotamer Outliers : 0.00 % 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: -0.99 (0.17), residues: 2361 helix: 0.67 (0.29), residues: 375 sheet: -0.05 (0.20), residues: 663 loop : -1.41 (0.17), residues: 1323 ********************** 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 217 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 2.499 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 outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.3123 time to fit residues: 108.9712 Evaluate side-chains 164 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 2.399 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 0.6980 chunk 173 optimal weight: 5.9990 chunk 27 optimal weight: 0.0370 chunk 52 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 overall best weight: 3.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 607 ASN B 650 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.053460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.040387 restraints weight = 108930.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.041699 restraints weight = 62575.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.042568 restraints weight = 44281.951| |-----------------------------------------------------------------------------| r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.6114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.085 21711 Z= 0.338 Angle : 0.705 19.802 29532 Z= 0.361 Chirality : 0.048 0.661 3924 Planarity : 0.004 0.038 3450 Dihedral : 6.000 51.198 4038 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.01 % Favored : 91.44 % Rotamer Outliers : 0.00 % 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: -1.09 (0.17), residues: 2361 helix: 0.81 (0.29), residues: 357 sheet: -0.11 (0.20), residues: 663 loop : -1.52 (0.17), residues: 1341 =============================================================================== Job complete usr+sys time: 3551.08 seconds wall clock time: 67 minutes 4.07 seconds (4024.07 seconds total)