Starting phenix.real_space_refine on Tue Mar 19 17:23:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8x_21111/03_2024/6v8x_21111_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8x_21111/03_2024/6v8x_21111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8x_21111/03_2024/6v8x_21111.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8x_21111/03_2024/6v8x_21111.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8x_21111/03_2024/6v8x_21111_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8x_21111/03_2024/6v8x_21111_neut.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.142 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 15531 2.51 5 N 4170 2.21 5 O 4977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 298": "NH1" <-> "NH2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 298": "NH1" <-> "NH2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 298": "NH1" <-> "NH2" Residue "I PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24825 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3453 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 4 Chain: "B" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "C" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1710 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 206} Chain: "D" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1615 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 195} Chain: "E" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3453 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 4 Chain: "F" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "G" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1710 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 206} Chain: "H" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1615 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 195} Chain: "I" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3453 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 4 Chain: "J" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "K" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1710 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 206} Chain: "L" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1615 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 195} Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.06, per 1000 atoms: 0.53 Number of scatterers: 24825 At special positions: 0 Unit cell: (184.13, 202.543, 125.642, 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 147 16.00 O 4977 8.00 N 4170 7.00 C 15531 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.07 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.01 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.07 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.12 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=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.11 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.09 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.24 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.31 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.00 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=1.91 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 98 " distance=1.98 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS D 216 " distance=2.00 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.19 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.07 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.01 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.07 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.12 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.10 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.09 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.24 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.31 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.00 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=1.91 Simple disulfide: pdb=" SG CYS G 32 " - pdb=" SG CYS G 98 " distance=1.98 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 216 " - pdb=" SG CYS H 216 " distance=2.00 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.19 Simple disulfide: pdb=" SG CYS H 136 " - pdb=" SG CYS H 196 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.07 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.01 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.06 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.12 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.04 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.11 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.09 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.24 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.31 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.00 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=1.91 Simple disulfide: pdb=" SG CYS K 32 " - pdb=" SG CYS K 98 " distance=1.98 Simple disulfide: pdb=" SG CYS K 140 " - pdb=" SG CYS K 196 " distance=2.04 Simple disulfide: pdb=" SG CYS K 216 " - pdb=" SG CYS L 216 " distance=2.00 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.19 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 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 Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA Y 3 " - " MAN Y 4 " " BMA k 3 " - " MAN k 4 " BETA1-4 " 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 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 W 1 " - " NAG W 2 " " 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 a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " 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 h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG 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 o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 613 " - " ASN A 448 " " NAG A 617 " - " ASN A 355 " " NAG A 627 " - " ASN A 133 " " NAG A 632 " - " ASN A 339 " " NAG B 701 " - " ASN B 611 " " NAG E 613 " - " ASN E 448 " " NAG E 617 " - " ASN E 355 " " NAG E 627 " - " ASN E 133 " " NAG E 632 " - " ASN E 339 " " NAG F 701 " - " ASN F 611 " " NAG I 613 " - " ASN I 448 " " NAG I 617 " - " ASN I 355 " " NAG I 627 " - " ASN I 133 " " NAG I 632 " - " ASN I 339 " " NAG J 701 " - " ASN J 611 " " NAG M 1 " - " ASN A 363 " " NAG N 1 " - " ASN A 392 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 276 " " NAG R 1 " - " ASN A 295 " " NAG S 1 " - " ASN A 160 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 197 " " NAG V 1 " - " ASN A 88 " " NAG W 1 " - " ASN A 332 " " NAG X 1 " - " ASN A 301 " " NAG Y 1 " - " ASN E 363 " " NAG Z 1 " - " ASN E 392 " " NAG a 1 " - " ASN E 386 " " NAG b 1 " - " ASN E 262 " " NAG c 1 " - " ASN E 276 " " NAG d 1 " - " ASN E 295 " " NAG e 1 " - " ASN E 160 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 197 " " NAG h 1 " - " ASN E 88 " " NAG i 1 " - " ASN E 332 " " NAG j 1 " - " ASN E 301 " " NAG k 1 " - " ASN I 363 " " NAG l 1 " - " ASN I 392 " " NAG m 1 " - " ASN I 386 " " NAG n 1 " - " ASN I 262 " " NAG o 1 " - " ASN I 276 " " NAG p 1 " - " ASN I 295 " " NAG q 1 " - " ASN I 160 " " NAG r 1 " - " ASN I 156 " " NAG s 1 " - " ASN I 197 " " NAG t 1 " - " ASN I 88 " " NAG u 1 " - " ASN I 332 " " NAG v 1 " - " ASN I 301 " Time building additional restraints: 9.81 Conformation dependent library (CDL) restraints added in 3.8 seconds 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 66 sheets defined 16.2% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.553A pdb=" N LEU A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP A 113 " --> pdb=" O ILE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 4.050A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 354 removed outlier: 3.534A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 478 removed outlier: 3.945A pdb=" N ASP A 477 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 478 " --> pdb=" O MET A 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 474 through 478' Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.872A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 596 removed outlier: 3.807A pdb=" N GLY B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.675A pdb=" N SER B 615 " --> pdb=" O SER B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 4.036A pdb=" N TRP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 removed outlier: 4.091A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 646 removed outlier: 3.657A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 664 removed outlier: 5.107A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 4.030A pdb=" N CYS C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.722A pdb=" N GLN C 64 " --> pdb=" O ARG C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.651A pdb=" N THR C 87 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 204 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 187 through 192 removed outlier: 4.140A pdb=" N LYS D 192 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 115 removed outlier: 3.554A pdb=" N LEU E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 4.050A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 354 removed outlier: 3.534A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 474 through 478 removed outlier: 3.945A pdb=" N ASP E 477 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN E 478 " --> pdb=" O MET E 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 474 through 478' Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.872A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 596 removed outlier: 3.807A pdb=" N GLY F 572 " --> pdb=" O LEU F 568 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 removed outlier: 3.674A pdb=" N SER F 615 " --> pdb=" O SER F 612 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 removed outlier: 4.036A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 4.091A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 646 removed outlier: 3.657A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 664 removed outlier: 5.108A pdb=" N GLN F 652 " --> pdb=" O GLU F 648 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLN F 653 " --> pdb=" O SER F 649 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP F 659 " --> pdb=" O LYS F 655 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU F 660 " --> pdb=" O ASN F 656 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 4.030A pdb=" N CYS G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.722A pdb=" N GLN G 64 " --> pdb=" O ARG G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.651A pdb=" N THR G 87 " --> pdb=" O VAL G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 204 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'H' and resid 187 through 192 removed outlier: 4.139A pdb=" N LYS H 192 " --> pdb=" O GLU H 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 115 removed outlier: 3.553A pdb=" N LEU I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP I 113 " --> pdb=" O ILE I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 removed outlier: 4.050A pdb=" N CYS I 126 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 354 removed outlier: 3.534A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 474 through 478 removed outlier: 3.945A pdb=" N ASP I 477 " --> pdb=" O ASP I 474 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN I 478 " --> pdb=" O MET I 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 474 through 478' Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.872A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 566 through 596 removed outlier: 3.807A pdb=" N GLY J 572 " --> pdb=" O LEU J 568 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN J 575 " --> pdb=" O TRP J 571 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA J 578 " --> pdb=" O LYS J 574 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU J 581 " --> pdb=" O GLN J 577 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL J 583 " --> pdb=" O ARG J 579 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP J 589 " --> pdb=" O ARG J 585 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU J 592 " --> pdb=" O ARG J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 611 through 615 removed outlier: 3.674A pdb=" N SER J 615 " --> pdb=" O SER J 612 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 624 removed outlier: 4.036A pdb=" N TRP J 623 " --> pdb=" O LEU J 619 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 635 removed outlier: 4.091A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE J 635 " --> pdb=" O TRP J 631 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 646 removed outlier: 3.657A pdb=" N ILE J 642 " --> pdb=" O TYR J 638 " (cutoff:3.500A) Processing helix chain 'J' and resid 646 through 664 removed outlier: 5.108A pdb=" N GLN J 652 " --> pdb=" O GLU J 648 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLN J 653 " --> pdb=" O SER J 649 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP J 659 " --> pdb=" O LYS J 655 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU J 660 " --> pdb=" O ASN J 656 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.030A pdb=" N CYS K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.722A pdb=" N GLN K 64 " --> pdb=" O ARG K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.652A pdb=" N THR K 87 " --> pdb=" O VAL K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 204 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 187 through 192 removed outlier: 4.140A pdb=" N LYS L 192 " --> pdb=" O GLU L 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.535A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.704A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 227 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.817A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 172 Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 172 removed outlier: 4.671A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.406A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.810A 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: 6.243A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.203A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.236A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.935A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.933A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 297 current: chain 'A' and resid 358 through 361 removed outlier: 3.541A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.933A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.935A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.236A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.203A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 444 through 456 current: chain 'A' and resid 413 through 415 Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AB2, first strand: chain 'A' and resid 383 through 385 Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AB4, first strand: chain 'C' and resid 19 through 23 Processing sheet with id=AB5, first strand: chain 'C' and resid 57 through 59 removed outlier: 3.996A pdb=" N ASN C 58 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU C 46 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TRP C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 121 through 123 Processing sheet with id=AB7, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB8, first strand: chain 'C' and resid 153 through 154 removed outlier: 3.801A pdb=" N VAL C 198 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL C 207 " --> pdb=" O VAL C 198 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AC1, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.696A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.694A pdb=" N TYR D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER D 65 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER D 63 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 117 through 118 removed outlier: 5.389A pdb=" N ASN D 139 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU D 177 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 150 through 152 Processing sheet with id=AC5, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.535A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.705A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS E 227 " --> pdb=" O SER E 243 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AC8, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.817A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 169 through 172 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 172 removed outlier: 4.671A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.405A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.242A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.202A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.235A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.933A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 297 current: chain 'E' and resid 358 through 361 removed outlier: 3.541A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 271 through 273 removed outlier: 10.933A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.235A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.202A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 444 through 456 current: chain 'E' and resid 413 through 415 Processing sheet with id=AD5, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AD6, first strand: chain 'E' and resid 383 through 385 Processing sheet with id=AD7, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AD8, first strand: chain 'G' and resid 19 through 23 Processing sheet with id=AD9, first strand: chain 'G' and resid 57 through 59 removed outlier: 3.995A pdb=" N ASN G 58 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU G 46 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 121 through 123 Processing sheet with id=AE2, first strand: chain 'G' and resid 136 through 137 Processing sheet with id=AE3, first strand: chain 'G' and resid 153 through 154 removed outlier: 3.800A pdb=" N VAL G 198 " --> pdb=" O VAL G 207 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL G 207 " --> pdb=" O VAL G 198 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.696A pdb=" N TRP H 35 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 19 through 24 removed outlier: 3.694A pdb=" N TYR H 71 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER H 65 " --> pdb=" O ASN H 72 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER H 63 " --> pdb=" O THR H 74 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 117 through 118 removed outlier: 5.390A pdb=" N ASN H 139 " --> pdb=" O LEU H 177 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU H 177 " --> pdb=" O ASN H 139 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 150 through 152 Processing sheet with id=AE9, first strand: chain 'I' and resid 494 through 499 removed outlier: 5.535A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.705A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS I 227 " --> pdb=" O SER I 243 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 55 through 56 Processing sheet with id=AF3, first strand: chain 'I' and resid 91 through 92 removed outlier: 3.817A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 169 through 172 Processing sheet with id=AF5, first strand: chain 'I' and resid 169 through 172 removed outlier: 4.671A pdb=" N LYS I 189 " --> pdb=" O CYS I 131 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 200 through 203 removed outlier: 6.405A pdb=" N ALA I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TYR I 435 " --> pdb=" O ALA I 200 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.243A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 12.203A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 12.236A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.933A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 284 through 297 current: chain 'I' and resid 358 through 361 removed outlier: 3.541A pdb=" N SER I 393 " --> pdb=" O PHE I 361 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 271 through 273 removed outlier: 10.933A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.236A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 12.203A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 444 through 456 current: chain 'I' and resid 413 through 415 Processing sheet with id=AF9, first strand: chain 'I' and resid 304 through 308 Processing sheet with id=AG1, first strand: chain 'I' and resid 383 through 385 Processing sheet with id=AG2, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AG3, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AG4, first strand: chain 'K' and resid 57 through 59 removed outlier: 3.997A pdb=" N ASN K 58 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU K 46 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 121 through 123 Processing sheet with id=AG6, first strand: chain 'K' and resid 136 through 137 Processing sheet with id=AG7, first strand: chain 'K' and resid 153 through 154 removed outlier: 3.800A pdb=" N VAL K 198 " --> pdb=" O VAL K 207 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL K 207 " --> pdb=" O VAL K 198 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 169 through 170 Processing sheet with id=AG9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.696A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.694A pdb=" N TYR L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER L 65 " --> pdb=" O ASN L 72 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 117 through 118 removed outlier: 5.389A pdb=" N ASN L 139 " --> pdb=" O LEU L 177 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU L 177 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 150 through 152 594 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.52 Time building geometry restraints manager: 10.65 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: 5411 1.32 - 1.46: 8151 1.46 - 1.59: 11581 1.59 - 1.72: 3 1.72 - 1.86: 192 Bond restraints: 25338 Sorted by residual: bond pdb=" N PRO I 299 " pdb=" CD PRO I 299 " ideal model delta sigma weight residual 1.473 1.577 -0.104 1.40e-02 5.10e+03 5.53e+01 bond pdb=" N PRO A 299 " pdb=" CD PRO A 299 " ideal model delta sigma weight residual 1.473 1.576 -0.103 1.40e-02 5.10e+03 5.44e+01 bond pdb=" N PRO E 299 " pdb=" CD PRO E 299 " ideal model delta sigma weight residual 1.473 1.576 -0.103 1.40e-02 5.10e+03 5.43e+01 bond pdb=" CB TRP G 50 " pdb=" CG TRP G 50 " ideal model delta sigma weight residual 1.498 1.300 0.198 3.10e-02 1.04e+03 4.09e+01 bond pdb=" CB TRP K 50 " pdb=" CG TRP K 50 " ideal model delta sigma weight residual 1.498 1.300 0.198 3.10e-02 1.04e+03 4.09e+01 ... (remaining 25333 not shown) Histogram of bond angle deviations from ideal: 94.27 - 102.27: 99 102.27 - 110.27: 7591 110.27 - 118.26: 12663 118.26 - 126.26: 13535 126.26 - 134.26: 528 Bond angle restraints: 34416 Sorted by residual: angle pdb=" C SER D 65 " pdb=" N ARG D 66 " pdb=" CA ARG D 66 " ideal model delta sigma weight residual 121.70 134.19 -12.49 1.80e+00 3.09e-01 4.81e+01 angle pdb=" C SER L 65 " pdb=" N ARG L 66 " pdb=" CA ARG L 66 " ideal model delta sigma weight residual 121.70 134.16 -12.46 1.80e+00 3.09e-01 4.79e+01 angle pdb=" C SER H 65 " pdb=" N ARG H 66 " pdb=" CA ARG H 66 " ideal model delta sigma weight residual 121.70 134.12 -12.42 1.80e+00 3.09e-01 4.76e+01 angle pdb=" C TRP C 50 " pdb=" CA TRP C 50 " pdb=" CB TRP C 50 " ideal model delta sigma weight residual 112.63 98.15 14.48 2.16e+00 2.14e-01 4.50e+01 angle pdb=" C TRP K 50 " pdb=" CA TRP K 50 " pdb=" CB TRP K 50 " ideal model delta sigma weight residual 112.63 98.16 14.47 2.16e+00 2.14e-01 4.49e+01 ... (remaining 34411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.64: 15802 22.64 - 45.28: 522 45.28 - 67.92: 140 67.92 - 90.56: 96 90.56 - 113.21: 57 Dihedral angle restraints: 16617 sinusoidal: 7986 harmonic: 8631 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 175.94 -82.94 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 92 " pdb=" CB CYS G 92 " ideal model delta sinusoidal sigma weight residual 93.00 175.92 -82.92 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 92 " pdb=" CB CYS K 92 " ideal model delta sinusoidal sigma weight residual 93.00 175.92 -82.92 1 1.00e+01 1.00e-02 8.42e+01 ... (remaining 16614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 3635 0.117 - 0.234: 466 0.234 - 0.351: 39 0.351 - 0.468: 12 0.468 - 0.585: 9 Chirality restraints: 4161 Sorted by residual: chirality pdb=" CB ILE E 309 " pdb=" CA ILE E 309 " pdb=" CG1 ILE E 309 " pdb=" CG2 ILE E 309 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.57e+00 chirality pdb=" CB ILE A 309 " pdb=" CA ILE A 309 " pdb=" CG1 ILE A 309 " pdb=" CG2 ILE A 309 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.58 2.00e-01 2.50e+01 8.39e+00 chirality pdb=" CB ILE I 309 " pdb=" CA ILE I 309 " pdb=" CG1 ILE I 309 " pdb=" CG2 ILE I 309 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.58 2.00e-01 2.50e+01 8.38e+00 ... (remaining 4158 not shown) Planarity restraints: 4311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 1 " -0.152 2.00e-02 2.50e+03 1.29e-01 2.07e+02 pdb=" C7 NAG X 1 " 0.029 2.00e-02 2.50e+03 pdb=" C8 NAG X 1 " 0.036 2.00e-02 2.50e+03 pdb=" N2 NAG X 1 " 0.208 2.00e-02 2.50e+03 pdb=" O7 NAG X 1 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 1 " -0.152 2.00e-02 2.50e+03 1.29e-01 2.07e+02 pdb=" C7 NAG j 1 " 0.030 2.00e-02 2.50e+03 pdb=" C8 NAG j 1 " 0.036 2.00e-02 2.50e+03 pdb=" N2 NAG j 1 " 0.207 2.00e-02 2.50e+03 pdb=" O7 NAG j 1 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG v 1 " 0.152 2.00e-02 2.50e+03 1.29e-01 2.07e+02 pdb=" C7 NAG v 1 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG v 1 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG v 1 " -0.208 2.00e-02 2.50e+03 pdb=" O7 NAG v 1 " 0.120 2.00e-02 2.50e+03 ... (remaining 4308 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2726 2.72 - 3.27: 21824 3.27 - 3.81: 37757 3.81 - 4.36: 45871 4.36 - 4.90: 78416 Nonbonded interactions: 186594 Sorted by model distance: nonbonded pdb=" OE1 GLN G 6 " pdb=" OG1 THR G 107 " model vdw 2.180 2.440 nonbonded pdb=" OE1 GLN K 6 " pdb=" OG1 THR K 107 " model vdw 2.180 2.440 nonbonded pdb=" OE1 GLN C 6 " pdb=" OG1 THR C 107 " model vdw 2.180 2.440 nonbonded pdb=" OG1 THR A 303 " pdb=" N ASP A 322 " model vdw 2.257 2.520 nonbonded pdb=" OG1 THR E 303 " pdb=" N ASP E 322 " model vdw 2.257 2.520 ... (remaining 186589 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 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Y' selection = chain 'k' } ncs_group { reference = chain 'N' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'f' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.640 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 62.830 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.570 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 0.017 0.198 25338 Z= 1.117 Angle : 1.481 14.483 34416 Z= 0.782 Chirality : 0.084 0.585 4161 Planarity : 0.009 0.129 4260 Dihedral : 15.174 113.205 10902 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.49 % Favored : 90.59 % Rotamer: Outliers : 0.23 % Allowed : 1.83 % Favored : 97.95 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.90 (0.13), residues: 2943 helix: -4.12 (0.13), residues: 429 sheet: -2.05 (0.16), residues: 843 loop : -2.48 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.006 TRP G 50 HIS 0.011 0.003 HIS E 352 PHE 0.065 0.006 PHE D 98 TYR 0.033 0.005 TYR H 87 ARG 0.035 0.002 ARG I 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 652 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7422 (m-10) cc_final: 0.7099 (m-10) REVERT: A 217 TYR cc_start: 0.7708 (m-80) cc_final: 0.6674 (m-80) REVERT: A 474 ASP cc_start: 0.7215 (t0) cc_final: 0.7006 (t0) REVERT: B 536 THR cc_start: 0.7429 (p) cc_final: 0.7108 (t) REVERT: B 566 LEU cc_start: 0.9086 (pp) cc_final: 0.8187 (tm) REVERT: D 175 TYR cc_start: 0.8105 (m-80) cc_final: 0.7496 (m-10) REVERT: E 474 ASP cc_start: 0.7246 (t0) cc_final: 0.6972 (t0) REVERT: H 77 ASN cc_start: 0.8131 (t0) cc_final: 0.7870 (t0) REVERT: H 175 TYR cc_start: 0.8092 (m-80) cc_final: 0.7563 (m-10) REVERT: I 53 PHE cc_start: 0.7258 (m-10) cc_final: 0.6926 (m-10) REVERT: I 107 ASP cc_start: 0.7813 (m-30) cc_final: 0.7590 (m-30) REVERT: I 217 TYR cc_start: 0.7233 (m-80) cc_final: 0.6981 (m-80) REVERT: I 318 TYR cc_start: 0.7934 (m-80) cc_final: 0.7662 (m-10) REVERT: J 536 THR cc_start: 0.7502 (p) cc_final: 0.7067 (t) REVERT: K 100 ASP cc_start: 0.6601 (t0) cc_final: 0.5650 (p0) REVERT: L 175 TYR cc_start: 0.8071 (m-80) cc_final: 0.7468 (m-10) outliers start: 6 outliers final: 1 residues processed: 655 average time/residue: 1.4587 time to fit residues: 1083.7642 Evaluate side-chains 344 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 343 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 573 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 0.9990 chunk 220 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 75 optimal weight: 30.0000 chunk 148 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 228 optimal weight: 0.7980 chunk 88 optimal weight: 9.9990 chunk 138 optimal weight: 0.8980 chunk 169 optimal weight: 30.0000 chunk 264 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 130 GLN ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN B 616 ASN B 651 ASN C 102 HIS ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN E 432 GLN ** F 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN F 651 ASN G 197 ASN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 GLN ** J 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 607 ASN J 651 ASN K 102 HIS K 197 ASN L 126 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25338 Z= 0.247 Angle : 0.827 9.542 34416 Z= 0.409 Chirality : 0.050 0.287 4161 Planarity : 0.006 0.045 4260 Dihedral : 13.421 81.897 5384 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.83 % Favored : 92.76 % Rotamer: Outliers : 3.96 % Allowed : 13.24 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.07 (0.14), residues: 2943 helix: -2.62 (0.21), residues: 414 sheet: -1.71 (0.17), residues: 840 loop : -2.06 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 45 HIS 0.005 0.001 HIS E 374 PHE 0.020 0.002 PHE C 146 TYR 0.021 0.002 TYR E 318 ARG 0.007 0.001 ARG A 476 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 439 time to evaluate : 2.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7468 (m-10) cc_final: 0.7225 (m-10) REVERT: A 72 HIS cc_start: 0.5036 (OUTLIER) cc_final: 0.4369 (m-70) REVERT: A 99 ASN cc_start: 0.7765 (t0) cc_final: 0.6862 (t0) REVERT: A 217 TYR cc_start: 0.7570 (m-80) cc_final: 0.6968 (m-80) REVERT: B 573 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8923 (tp) REVERT: C 96 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7213 (mtmt) REVERT: E 95 MET cc_start: 0.8659 (ptm) cc_final: 0.8392 (ptm) REVERT: E 232 LYS cc_start: 0.7603 (mmtt) cc_final: 0.7379 (tmtt) REVERT: E 308 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7984 (mtm-85) REVERT: F 571 TRP cc_start: 0.8340 (m100) cc_final: 0.8096 (m100) REVERT: F 624 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7556 (m-30) REVERT: G 105 ARG cc_start: 0.6833 (ptm-80) cc_final: 0.6578 (ptt90) REVERT: H 11 LEU cc_start: 0.7722 (mm) cc_final: 0.7395 (mt) REVERT: H 77 ASN cc_start: 0.8240 (t0) cc_final: 0.7897 (t0) REVERT: I 46 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.6888 (mmmt) REVERT: I 53 PHE cc_start: 0.7594 (m-10) cc_final: 0.7382 (m-10) REVERT: I 99 ASN cc_start: 0.8026 (t0) cc_final: 0.6754 (t0) REVERT: I 114 GLN cc_start: 0.7472 (mt0) cc_final: 0.6924 (mt0) REVERT: I 217 TYR cc_start: 0.7516 (m-80) cc_final: 0.7309 (m-80) REVERT: I 315 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7968 (mp10) REVERT: I 434 MET cc_start: 0.7539 (ptp) cc_final: 0.7271 (ptp) REVERT: I 499 THR cc_start: 0.7452 (p) cc_final: 0.7189 (t) REVERT: J 575 GLN cc_start: 0.7685 (mp10) cc_final: 0.7480 (mp10) REVERT: K 50 TRP cc_start: 0.8089 (OUTLIER) cc_final: 0.6987 (m-10) REVERT: L 21 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7242 (tp) REVERT: L 103 LYS cc_start: 0.8070 (tptp) cc_final: 0.7580 (tptt) outliers start: 104 outliers final: 29 residues processed: 502 average time/residue: 1.3972 time to fit residues: 800.1248 Evaluate side-chains 371 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 334 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 653 GLN Chi-restraints excluded: chain G residue 50 TRP Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 328 GLN Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 615 SER Chi-restraints excluded: chain J residue 624 ASP Chi-restraints excluded: chain J residue 630 GLN Chi-restraints excluded: chain K residue 50 TRP Chi-restraints excluded: chain K residue 82 ARG Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 79 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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: 51.9305 > 50: distance: 12 - 126: 28.281 distance: 53 - 131: 13.124 distance: 72 - 76: 7.046 distance: 77 - 80: 5.894 distance: 78 - 79: 3.389 distance: 78 - 85: 3.659 distance: 80 - 81: 5.852 distance: 81 - 82: 5.059 distance: 82 - 83: 3.579 distance: 83 - 84: 9.421 distance: 85 - 86: 8.097 distance: 86 - 87: 3.531 distance: 86 - 89: 9.435 distance: 87 - 88: 8.222 distance: 87 - 96: 6.912 distance: 89 - 90: 10.818 distance: 90 - 91: 4.302 distance: 90 - 92: 4.754 distance: 91 - 93: 5.745 distance: 92 - 94: 6.063 distance: 94 - 95: 6.452 distance: 96 - 97: 4.403 distance: 97 - 98: 5.046 distance: 98 - 99: 5.069 distance: 98 - 104: 7.513 distance: 100 - 101: 5.069 distance: 101 - 102: 5.482 distance: 104 - 105: 13.368 distance: 105 - 106: 10.653 distance: 106 - 108: 10.963 distance: 108 - 109: 3.705 distance: 109 - 110: 4.934 distance: 109 - 112: 10.835 distance: 110 - 111: 16.245 distance: 110 - 115: 29.423 distance: 112 - 113: 4.167 distance: 112 - 114: 8.060 distance: 115 - 116: 9.044 distance: 116 - 117: 6.956 distance: 117 - 118: 6.834 distance: 117 - 119: 8.199 distance: 119 - 120: 10.380 distance: 119 - 125: 14.494 distance: 120 - 121: 15.436 distance: 120 - 123: 10.253 distance: 121 - 122: 31.120 distance: 121 - 126: 30.131 distance: 123 - 124: 16.195 distance: 124 - 125: 14.054 distance: 126 - 127: 21.924 distance: 127 - 128: 7.050 distance: 127 - 130: 8.205 distance: 128 - 129: 3.803 distance: 128 - 132: 8.004 distance: 130 - 131: 9.338 distance: 132 - 133: 8.141 distance: 132 - 138: 14.784 distance: 133 - 134: 19.210 distance: 133 - 136: 21.948 distance: 134 - 135: 7.870 distance: 134 - 139: 7.598 distance: 136 - 137: 12.793 distance: 137 - 138: 28.714 distance: 139 - 140: 4.668 distance: 140 - 143: 10.587 distance: 141 - 142: 9.387 distance: 141 - 145: 5.103 distance: 143 - 144: 17.493