Starting phenix.real_space_refine (version: dev) on Thu Feb 23 22:53:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mn7_9166/02_2023/6mn7_9166.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mn7_9166/02_2023/6mn7_9166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mn7_9166/02_2023/6mn7_9166.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mn7_9166/02_2023/6mn7_9166.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mn7_9166/02_2023/6mn7_9166.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mn7_9166/02_2023/6mn7_9166.pdb" } resolution = 4.8 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= 0.001 sd= 0.011 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 Process input model Symmetric amino acids flipped Residue "G TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 21447 Number of models: 1 Model: "" Number of chains: 66 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: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1830 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 222} Chain: "H" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1830 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 222} Chain: "I" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1830 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 222} Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 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: 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: 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: "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: 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: "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: 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: "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: 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: 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: "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: 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: "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: 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: "g" 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: "h" 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: "i" 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: "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: 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: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: 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: "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: 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: "w" 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: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 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: 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: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "3" 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: "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: 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: "6" 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: "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: "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: 11.69, per 1000 atoms: 0.55 Number of scatterers: 21447 At special positions: 0 Unit cell: (156.2, 156.2, 140.8, 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 135 16.00 O 4536 8.00 N 3411 7.00 C 13365 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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 96 " distance=2.05 Simple disulfide: pdb=" SG CYS G 150 " - pdb=" SG CYS G 215 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 215 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.05 Simple disulfide: pdb=" SG CYS I 150 " - pdb=" SG CYS I 215 " 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 "HETATM20254 O5 NAG k 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19481 O5 NAG T 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM20999 O5 NAG 0 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM20254 O5 NAG k 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19481 O5 NAG T 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM20999 O5 NAG 0 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19337 O5 NAG R 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM20855 O5 NAG y 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM20110 O5 NAG i 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM20677 O5 NAG u 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19159 O5 NAG N 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19932 O5 NAG e 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19187 O5 NAG O 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19960 O5 NAG f 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM20705 O5 NAG v 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 0 4 " - " MAN 0 5 " " MAN 0 5 " - " MAN 0 6 " " MAN 0 8 " - " MAN 0 9 " " MAN P 4 " - " MAN P 5 " " MAN T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " " MAN T 8 " - " MAN T 9 " " MAN g 4 " - " MAN g 5 " " MAN k 4 " - " MAN k 5 " " MAN k 5 " - " MAN k 6 " " MAN k 8 " - " MAN k 9 " " MAN w 4 " - " MAN w 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " MAN 0 7 " - " MAN 0 10 " " BMA P 3 " - " MAN P 4 " " MAN P 6 " - " MAN P 7 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 7 " " MAN S 4 " - " MAN S 5 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 10 " " BMA g 3 " - " MAN g 4 " " MAN g 6 " - " MAN g 7 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 7 " " MAN j 4 " - " MAN j 5 " " BMA k 3 " - " MAN k 4 " " MAN k 7 " - " MAN k 10 " " BMA w 3 " - " MAN w 4 " " MAN w 6 " - " MAN w 7 " " BMA y 3 " - " MAN y 4 " " BMA z 3 " - " MAN z 7 " " MAN z 4 " - " MAN z 5 " ALPHA1-6 " BMA 0 3 " - " MAN 0 7 " " MAN 0 7 " - " MAN 0 8 " " BMA P 3 " - " MAN P 6 " " BMA R 3 " - " MAN R 5 " " BMA S 3 " - " MAN S 4 " " MAN S 4 " - " MAN S 6 " " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 8 " " BMA g 3 " - " MAN g 6 " " BMA i 3 " - " MAN i 5 " " BMA j 3 " - " MAN j 4 " " MAN j 4 " - " MAN j 6 " " BMA k 3 " - " MAN k 7 " " MAN k 7 " - " MAN k 8 " " BMA w 3 " - " MAN w 6 " " BMA y 3 " - " MAN y 5 " " BMA z 3 " - " MAN z 4 " " MAN z 4 " - " MAN z 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG 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 a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG 0 1 " - " ASN D 332 " " NAG 1 1 " - " ASN D 355 " " NAG 2 1 " - " ASN D 363 " " NAG 3 1 " - " ASN D 386 " " NAG 4 1 " - " ASN D 392 " " NAG 5 1 " - " ASN D 448 " " NAG 6 1 " - " ASN E 611 " " NAG 7 1 " - " ASN F 611 " " NAG A 648 " - " ASN A 339 " " NAG B 703 " - " ASN B 618 " " NAG B 704 " - " ASN B 637 " " NAG C 648 " - " ASN C 339 " " NAG D 648 " - " ASN D 339 " " NAG E 703 " - " ASN E 618 " " NAG E 704 " - " ASN E 637 " " NAG F 703 " - " ASN F 618 " " NAG F 704 " - " ASN F 637 " " NAG J 1 " - " ASN A 88 " " NAG K 1 " - " ASN A 133 " " NAG L 1 " - " ASN A 156 " " NAG M 1 " - " ASN A 160 " " NAG N 1 " - " ASN A 197 " " NAG O 1 " - " ASN A 234 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 276 " " NAG R 1 " - " ASN A 295 " " NAG S 1 " - " ASN A 301 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 355 " " NAG V 1 " - " ASN A 363 " " NAG W 1 " - " ASN A 386 " " NAG X 1 " - " ASN A 392 " " NAG Y 1 " - " ASN A 448 " " NAG Z 1 " - " ASN B 611 " " NAG a 1 " - " ASN C 88 " " NAG b 1 " - " ASN C 133 " " NAG c 1 " - " ASN C 156 " " NAG d 1 " - " ASN C 160 " " NAG e 1 " - " ASN C 197 " " NAG f 1 " - " ASN C 234 " " NAG g 1 " - " ASN C 262 " " NAG h 1 " - " ASN C 276 " " NAG i 1 " - " ASN C 295 " " NAG j 1 " - " ASN C 301 " " NAG k 1 " - " ASN C 332 " " NAG l 1 " - " ASN C 355 " " NAG m 1 " - " ASN C 363 " " NAG n 1 " - " ASN C 386 " " NAG o 1 " - " ASN C 392 " " NAG p 1 " - " ASN C 448 " " NAG q 1 " - " ASN D 88 " " NAG r 1 " - " ASN D 133 " " NAG s 1 " - " ASN D 156 " " NAG t 1 " - " ASN D 160 " " NAG u 1 " - " ASN D 197 " " NAG v 1 " - " ASN D 234 " " NAG w 1 " - " ASN D 262 " " NAG x 1 " - " ASN D 276 " " NAG y 1 " - " ASN D 295 " " NAG z 1 " - " ASN D 301 " Time building additional restraints: 12.63 Conformation dependent library (CDL) restraints added in 2.8 seconds 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 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 48 sheets defined 20.5% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 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: 3.678A 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: 4.271A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.905A 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: 4.060A 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: 4.216A 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: 4.083A 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: 3.979A 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: 3.678A 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: 3.679A 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: 4.060A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) removed outlier: 4.620A 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: 4.140A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) removed outlier: 4.085A 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: 4.058A 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: 3.728A 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 28 through 32 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 206 through 210 removed outlier: 3.557A pdb=" N PHE G 210 " --> pdb=" O SER G 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 206 through 210 removed outlier: 3.555A pdb=" N PHE H 210 " --> pdb=" O SER H 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 206 through 210 removed outlier: 3.556A pdb=" N PHE I 210 " --> pdb=" O SER I 207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA2, 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=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 131 Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 161 Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.481A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.818A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.701A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.551A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.295A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.551A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.701A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 306 through 307 Processing sheet with id=AB2, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AB3, 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=AB4, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB5, first strand: chain 'C' and resid 92 through 94 Processing sheet with id=AB6, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 161 Processing sheet with id=AB8, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.480A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.819A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.702A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.551A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.296A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.551A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.702A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 306 through 307 Processing sheet with id=AC3, first strand: chain 'D' and resid 494 through 499 Processing sheet with id=AC4, 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=AC5, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC6, first strand: chain 'D' and resid 92 through 94 Processing sheet with id=AC7, first strand: chain 'D' and resid 129 through 131 Processing sheet with id=AC8, first strand: chain 'D' and resid 154 through 161 Processing sheet with id=AC9, first strand: chain 'D' and resid 201 through 203 removed outlier: 6.482A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 259 through 261 removed outlier: 3.819A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.702A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.551A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 271 through 273 removed outlier: 7.295A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.551A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.702A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N PHE D 468 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=AD4, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD5, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.481A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 11 Processing sheet with id=AD7, first strand: chain 'G' and resid 132 through 134 Processing sheet with id=AD8, first strand: chain 'G' and resid 137 through 140 removed outlier: 6.367A pdb=" N PHE G 160 " --> pdb=" O TYR G 176 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR G 176 " --> pdb=" O PHE G 160 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TRP G 162 " --> pdb=" O LEU G 174 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 137 through 140 Processing sheet with id=AE1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.482A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AE4, first strand: chain 'H' and resid 132 through 134 Processing sheet with id=AE5, first strand: chain 'H' and resid 137 through 140 removed outlier: 6.366A pdb=" N PHE H 160 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR H 176 " --> pdb=" O PHE H 160 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TRP H 162 " --> pdb=" O LEU H 174 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 137 through 140 Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.481A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 10 through 11 Processing sheet with id=AF1, first strand: chain 'I' and resid 132 through 134 Processing sheet with id=AF2, first strand: chain 'I' and resid 137 through 140 removed outlier: 6.366A pdb=" N PHE I 160 " --> pdb=" O TYR I 176 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR I 176 " --> pdb=" O PHE I 160 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TRP I 162 " --> pdb=" O LEU I 174 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 137 through 140 750 hydrogen bonds defined for protein. 1872 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: 9.16 Time building geometry restraints manager: 13.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3466 1.32 - 1.45: 6813 1.45 - 1.57: 11367 1.57 - 1.70: 29 1.70 - 1.83: 201 Bond restraints: 21876 Sorted by residual: bond pdb=" CA GLU G 128 " pdb=" C GLU G 128 " ideal model delta sigma weight residual 1.523 1.832 -0.309 1.34e-02 5.57e+03 5.31e+02 bond pdb=" CA GLU H 128 " pdb=" C GLU H 128 " ideal model delta sigma weight residual 1.523 1.831 -0.308 1.34e-02 5.57e+03 5.27e+02 bond pdb=" CA GLU I 128 " pdb=" C GLU I 128 " ideal model delta sigma weight residual 1.523 1.830 -0.307 1.34e-02 5.57e+03 5.24e+02 bond pdb=" CA SER G 127 " pdb=" C SER G 127 " ideal model delta sigma weight residual 1.522 1.792 -0.270 1.20e-02 6.94e+03 5.07e+02 bond pdb=" CA SER I 127 " pdb=" C SER I 127 " ideal model delta sigma weight residual 1.522 1.792 -0.270 1.20e-02 6.94e+03 5.05e+02 ... (remaining 21871 not shown) Histogram of bond angle deviations from ideal: 92.69 - 104.01: 467 104.01 - 115.33: 14709 115.33 - 126.65: 14124 126.65 - 137.97: 388 137.97 - 149.29: 30 Bond angle restraints: 29718 Sorted by residual: angle pdb=" C2 NAG F 704 " pdb=" C1 NAG F 704 " pdb=" O5 NAG F 704 " ideal model delta sigma weight residual 109.64 99.56 10.08 5.38e-01 3.45e+00 3.51e+02 angle pdb=" C2 NAG E 704 " pdb=" C1 NAG E 704 " pdb=" O5 NAG E 704 " ideal model delta sigma weight residual 109.64 99.57 10.07 5.38e-01 3.45e+00 3.50e+02 angle pdb=" C2 NAG n 1 " pdb=" C1 NAG n 1 " pdb=" O5 NAG n 1 " ideal model delta sigma weight residual 109.64 99.58 10.06 5.38e-01 3.45e+00 3.49e+02 angle pdb=" C2 NAG s 1 " pdb=" C1 NAG s 1 " pdb=" O5 NAG s 1 " ideal model delta sigma weight residual 109.64 99.59 10.05 5.38e-01 3.45e+00 3.49e+02 angle pdb=" C2 NAG 3 1 " pdb=" C1 NAG 3 1 " pdb=" O5 NAG 3 1 " ideal model delta sigma weight residual 109.64 99.60 10.04 5.38e-01 3.45e+00 3.48e+02 ... (remaining 29713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 12327 16.93 - 33.86: 606 33.86 - 50.78: 96 50.78 - 67.71: 57 67.71 - 84.64: 12 Dihedral angle restraints: 13098 sinusoidal: 6141 harmonic: 6957 Sorted by residual: 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 -162.28 76.28 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 -162.26 76.26 1 1.00e+01 1.00e-02 7.32e+01 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 -162.26 76.26 1 1.00e+01 1.00e-02 7.32e+01 ... (remaining 13095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.228: 3678 0.228 - 0.455: 177 0.455 - 0.682: 12 0.682 - 0.910: 8 0.910 - 1.137: 7 Chirality restraints: 3882 Sorted by residual: chirality pdb=" C1 MAN P 7 " pdb=" O3 MAN P 6 " pdb=" C2 MAN P 7 " pdb=" O5 MAN P 7 " both_signs ideal model delta sigma weight residual False 2.40 1.61 0.79 2.00e-02 2.50e+03 1.54e+03 chirality pdb=" C1 MAN w 7 " pdb=" O3 MAN w 6 " pdb=" C2 MAN w 7 " pdb=" O5 MAN w 7 " both_signs ideal model delta sigma weight residual False 2.40 1.62 0.78 2.00e-02 2.50e+03 1.51e+03 chirality pdb=" C1 MAN g 7 " pdb=" O3 MAN g 6 " pdb=" C2 MAN g 7 " pdb=" O5 MAN g 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 3879 not shown) Planarity restraints: 3558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 301 " -0.069 2.00e-02 2.50e+03 3.47e-01 1.50e+03 pdb=" CG ASN C 301 " -0.111 2.00e-02 2.50e+03 pdb=" OD1 ASN C 301 " 0.236 2.00e-02 2.50e+03 pdb=" ND2 ASN C 301 " -0.541 2.00e-02 2.50e+03 pdb=" C1 NAG j 1 " 0.485 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 301 " -0.062 2.00e-02 2.50e+03 3.44e-01 1.48e+03 pdb=" CG ASN A 301 " -0.113 2.00e-02 2.50e+03 pdb=" OD1 ASN A 301 " 0.226 2.00e-02 2.50e+03 pdb=" ND2 ASN A 301 " -0.537 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " 0.486 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG z 1 " -0.281 2.00e-02 2.50e+03 2.35e-01 6.92e+02 pdb=" C7 NAG z 1 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG z 1 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG z 1 " 0.398 2.00e-02 2.50e+03 pdb=" O7 NAG z 1 " -0.007 2.00e-02 2.50e+03 ... (remaining 3555 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.10: 35 2.10 - 2.80: 5976 2.80 - 3.50: 27906 3.50 - 4.20: 51330 4.20 - 4.90: 82497 Nonbonded interactions: 167744 Sorted by model distance: nonbonded pdb=" NH1 ARG A 327 " pdb=" O ASN G 103 " model vdw 1.395 2.520 nonbonded pdb=" NH1 ARG D 327 " pdb=" O ASN H 103 " model vdw 1.416 2.520 nonbonded pdb=" CD1 ILE A 323 " pdb=" OG1 THR G 28 " model vdw 1.450 3.460 nonbonded pdb=" CD1 ILE D 323 " pdb=" OG1 THR H 28 " model vdw 1.454 3.460 nonbonded pdb=" CD1 ILE C 323 " pdb=" OG1 THR I 28 " model vdw 1.468 3.460 ... (remaining 167739 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 'T' selection = chain 'k' } ncs_group { reference = chain '1' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'l' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain '2' selection = chain '3' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'Q' selection = chain 'V' selection = chain 'W' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'h' selection = chain 'm' selection = chain 'n' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'x' } 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 'P' selection = chain 'S' selection = chain 'g' selection = chain 'j' selection = chain 'w' selection = chain 'z' } ncs_group { reference = chain 'R' selection = chain 'i' selection = chain 'y' } Set up NCS constraints Number of NCS constrained groups: 8 pdb_interpretation.ncs_group { reference = chain '0' selection = chain 'T' selection = chain 'k' } pdb_interpretation.ncs_group { reference = chain '1' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'l' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 'u' selection = chain 'v' } pdb_interpretation.ncs_group { reference = chain '2' selection = chain '3' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'Q' selection = chain 'V' selection = chain 'W' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'h' selection = chain 'm' selection = chain 'n' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'x' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } pdb_interpretation.ncs_group { reference = chain 'P' selection = chain 'S' selection = chain 'g' selection = chain 'j' selection = chain 'w' selection = chain 'z' } pdb_interpretation.ncs_group { reference = chain 'R' selection = chain 'i' selection = chain 'y' } Set refine NCS operators NCS operators will be refined. Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 13365 2.51 5 N 3411 2.21 5 O 4536 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: 0.280 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: 2.800 Check model and map are aligned: 0.280 Process input model: 61.930 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1942 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.016 0.309 21876 Z= 1.069 Angle : 2.165 38.486 29718 Z= 1.627 Chirality : 0.120 1.137 3882 Planarity : 0.019 0.235 3498 Dihedral : 10.633 84.640 8505 Min Nonbonded Distance : 1.395 Molprobity Statistics. All-atom Clashscore : 35.74 Ramachandran Plot: Outliers : 2.03 % Allowed : 8.57 % Favored : 89.41 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.54 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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: -2.34 (0.16), residues: 2370 helix: -2.39 (0.20), residues: 417 sheet: -0.71 (0.18), residues: 774 loop : -1.76 (0.16), residues: 1179 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0060 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0023 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0024 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0016 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0026 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 55 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 55 average time/residue: 0.2085 time to fit residues: 13.5956 Evaluate side-chains 23 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.378 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5283 Evaluate side-chains 34 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.111 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1582 time to fit residues: 5.9123 Evaluate side-chains 18 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.148 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2111 Evaluate side-chains 42 residues out of total 193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.2375 time to fit residues: 10.7415 Evaluate side-chains 25 residues out of total 193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.422 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0371 time to fit residues: 0.3543 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0052 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0042 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0020 ------------------------------------------------------------------------------- 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: 6.9990 chunk 179 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 121 optimal weight: 0.0270 chunk 95 optimal weight: 7.9990 chunk 185 optimal weight: 0.0170 chunk 71 optimal weight: 0.0980 chunk 112 optimal weight: 8.9990 chunk 138 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 overall best weight: 1.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 HIS ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 217 GLN ** G 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2073 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.028 0.905 21876 Z= 1.790 Angle : 2.106 34.044 29718 Z= 1.029 Chirality : 0.200 4.286 3882 Planarity : 0.010 0.103 3498 Dihedral : 12.754 135.961 4074 Min Nonbonded Distance : 1.401 Molprobity Statistics. All-atom Clashscore : 41.86 Ramachandran Plot: Outliers : 1.01 % Allowed : 8.99 % Favored : 90.00 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.54 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.18 (0.16), residues: 2370 helix: -1.73 (0.22), residues: 432 sheet: -0.77 (0.17), residues: 855 loop : -1.80 (0.18), residues: 1083 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0067 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0025 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0023 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0030 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 38 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 37 average time/residue: 0.1753 time to fit residues: 8.2250 Evaluate side-chains 24 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.422 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4439 time to fit residues: 1.0617 Evaluate side-chains 21 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.127 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1804 time to fit residues: 4.1760 Evaluate side-chains 15 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.114 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1828 Evaluate side-chains 34 residues out of total 193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 34 average time/residue: 0.1585 time to fit residues: 6.2524 Evaluate side-chains 24 residues out of total 193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.204 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0191 time to fit residues: 0.3081 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0051 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0018 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0042 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 770, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.0221 > 50: distance: 0 - 1: 35.286 distance: 0 - 3: 41.684 distance: 1 - 2: 11.083 distance: 1 - 7: 32.191 distance: 3 - 4: 56.371 distance: 4 - 5: 33.602 distance: 4 - 6: 39.724 distance: 7 - 8: 21.752 distance: 7 - 13: 49.730 distance: 8 - 9: 40.339 distance: 8 - 11: 38.219 distance: 9 - 10: 57.262 distance: 9 - 14: 29.856 distance: 11 - 12: 59.460 distance: 14 - 15: 29.269 distance: 15 - 16: 20.138 distance: 15 - 18: 25.327 distance: 16 - 17: 19.949 distance: 16 - 23: 28.142 distance: 18 - 19: 36.261 distance: 19 - 20: 42.198 distance: 20 - 21: 26.270 distance: 20 - 22: 4.122 distance: 23 - 24: 34.456 distance: 24 - 25: 8.737 distance: 24 - 27: 24.780 distance: 25 - 32: 69.651 distance: 27 - 28: 36.567 distance: 28 - 29: 39.954 distance: 29 - 30: 17.361 distance: 29 - 31: 57.356 distance: 32 - 33: 66.123 distance: 33 - 34: 36.135 distance: 33 - 36: 47.873 distance: 34 - 35: 56.427 distance: 36 - 37: 35.550 distance: 36 - 38: 43.062 distance: 37 - 39: 49.875 distance: 41 - 42: 19.184 distance: 42 - 43: 26.479 distance: 42 - 50: 22.798 distance: 45 - 46: 44.098 distance: 45 - 47: 37.059 distance: 46 - 48: 19.990 distance: 48 - 49: 40.374 distance: 50 - 51: 39.888 distance: 51 - 52: 15.314 distance: 51 - 54: 17.237 distance: 52 - 53: 7.086 distance: 52 - 58: 28.048 distance: 54 - 55: 5.168 distance: 55 - 56: 21.041 distance: 55 - 57: 39.768 distance: 58 - 59: 41.735 distance: 59 - 60: 53.702 distance: 59 - 62: 56.057 distance: 60 - 67: 32.072 distance: 62 - 63: 59.266 distance: 63 - 64: 45.018 distance: 64 - 65: 31.570 distance: 64 - 66: 56.827 distance: 67 - 68: 28.386 distance: 68 - 69: 42.123 distance: 68 - 71: 27.700 distance: 69 - 70: 42.919