Starting phenix.real_space_refine on Sun Dec 10 17:06:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl5_21230/12_2023/6vl5_21230.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl5_21230/12_2023/6vl5_21230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl5_21230/12_2023/6vl5_21230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl5_21230/12_2023/6vl5_21230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl5_21230/12_2023/6vl5_21230.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl5_21230/12_2023/6vl5_21230.pdb" } resolution = 4.5 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 9378 2.51 5 N 2478 2.21 5 O 3084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15039 Number of models: 1 Model: "" Number of chains: 42 Chain: "C" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3536 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 3 Chain: "D" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "A" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3536 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 3 Chain: "B" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "E" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3536 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 3 Chain: "F" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "G" 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: 6 Unresolved non-hydrogen chiralities: 5 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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 6 Unresolved non-hydrogen chiralities: 5 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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: 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: 6 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: 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: "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: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.62, per 1000 atoms: 0.57 Number of scatterers: 15039 At special positions: 0 Unit cell: (126.5, 127.65, 117.3, 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 99 16.00 O 3084 8.00 N 2478 7.00 C 9378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.07 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=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.10 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 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=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.10 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 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=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.10 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 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 G 3 " - " MAN G 4 " " BMA Q 3 " - " MAN Q 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA Q 3 " - " MAN Q 5 " " BMA a 3 " - " MAN a 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " 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 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 d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " 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-ASN " NAG A 608 " - " ASN A 160 " " NAG A 609 " - " ASN A 276 " " NAG A 612 " - " ASN A 386 " " NAG A 613 " - " ASN A 363 " " NAG A 618 " - " ASN A 133 " " NAG A 627 " - " ASN A 289 " " NAG A 630 " - " ASN A 339 " " NAG A 631 " - " ASN A 355 " " NAG A 632 " - " ASN A 392 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 608 " - " ASN C 160 " " NAG C 609 " - " ASN C 276 " " NAG C 612 " - " ASN C 386 " " NAG C 613 " - " ASN C 363 " " NAG C 618 " - " ASN C 133 " " NAG C 627 " - " ASN C 289 " " NAG C 630 " - " ASN C 339 " " NAG C 631 " - " ASN C 355 " " NAG C 632 " - " ASN C 392 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 611 " " NAG E 608 " - " ASN E 160 " " NAG E 609 " - " ASN E 276 " " NAG E 612 " - " ASN E 386 " " NAG E 613 " - " ASN E 363 " " NAG E 618 " - " ASN E 133 " " NAG E 627 " - " ASN E 289 " " NAG E 630 " - " ASN E 339 " " NAG E 631 " - " ASN E 355 " " NAG E 632 " - " ASN E 392 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN C 262 " " NAG H 1 " - " ASN C 448 " " NAG I 1 " - " ASN C 295 " " NAG J 1 " - " ASN C 234 " " NAG K 1 " - " ASN C 197 " " NAG L 1 " - " ASN C 156 " " NAG M 1 " - " ASN C 301 " " NAG N 1 " - " ASN C 88 " " NAG O 1 " - " ASN C 241 " " NAG P 1 " - " ASN C 332 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 295 " " NAG T 1 " - " ASN A 234 " " NAG U 1 " - " ASN A 197 " " NAG V 1 " - " ASN A 156 " " NAG W 1 " - " ASN A 301 " " NAG X 1 " - " ASN A 88 " " NAG Y 1 " - " ASN A 241 " " NAG Z 1 " - " ASN A 332 " " NAG a 1 " - " ASN E 262 " " NAG b 1 " - " ASN E 448 " " NAG c 1 " - " ASN E 295 " " NAG d 1 " - " ASN E 234 " " NAG e 1 " - " ASN E 197 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 301 " " NAG h 1 " - " ASN E 88 " " NAG i 1 " - " ASN E 241 " " NAG j 1 " - " ASN E 332 " Time building additional restraints: 7.21 Conformation dependent library (CDL) restraints added in 2.7 seconds 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 33 sheets defined 29.1% alpha, 52.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.893A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.519A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 535 removed outlier: 3.537A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 543 through 544 No H-bonds generated for 'chain 'D' and resid 543 through 544' Processing helix chain 'D' and resid 545 through 549 Processing helix chain 'D' and resid 569 through 596 removed outlier: 3.733A pdb=" N ARG D 579 " --> pdb=" O GLN D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.893A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.895A 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 387 through 391 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.518A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 535 removed outlier: 3.537A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 543 through 544 No H-bonds generated for 'chain 'B' and resid 543 through 544' Processing helix chain 'B' and resid 545 through 549 Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.733A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.893A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.893A 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 387 through 391 Processing helix chain 'E' and resid 425 through 429 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.520A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 removed outlier: 3.536A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 542 Processing helix chain 'F' and resid 543 through 544 No H-bonds generated for 'chain 'F' and resid 543 through 544' Processing helix chain 'F' and resid 545 through 549 Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.733A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 661 Processing sheet with id=AA1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.406A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 removed outlier: 3.840A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.479A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.546A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 273 removed outlier: 4.045A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 5.469A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 316 through 323A removed outlier: 5.491A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.934A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 394 through 396 removed outlier: 6.377A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.405A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AB5, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AB6, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'A' and resid 169 through 177 removed outlier: 3.841A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.480A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.546A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.982A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.878A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 271 through 273 removed outlier: 4.046A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 5.470A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 316 through 323A removed outlier: 5.492A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.933A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 10.878A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.982A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 394 through 396 removed outlier: 6.377A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.404A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AC8, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC9, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.840A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.480A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.546A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.414A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.982A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.879A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 271 through 273 removed outlier: 4.046A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 5.470A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 316 through 323A removed outlier: 5.492A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.933A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 10.879A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.982A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.414A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 394 through 396 removed outlier: 6.378A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1827 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: 6.24 Time building geometry restraints manager: 7.70 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: 3278 1.32 - 1.45: 4445 1.45 - 1.58: 7459 1.58 - 1.71: 4 1.71 - 1.84: 129 Bond restraints: 15315 Sorted by residual: bond pdb=" NE ARG E 308 " pdb=" CZ ARG E 308 " ideal model delta sigma weight residual 1.326 1.365 -0.039 1.10e-02 8.26e+03 1.27e+01 bond pdb=" CZ ARG C 503 " pdb=" NH2 ARG C 503 " ideal model delta sigma weight residual 1.330 1.284 0.046 1.30e-02 5.92e+03 1.25e+01 bond pdb=" NE ARG A 308 " pdb=" CZ ARG A 308 " ideal model delta sigma weight residual 1.326 1.365 -0.039 1.10e-02 8.26e+03 1.24e+01 bond pdb=" CA ASN C 279 " pdb=" CB ASN C 279 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.27e-02 6.20e+03 1.24e+01 bond pdb=" CB HIS C 85 " pdb=" CG HIS C 85 " ideal model delta sigma weight residual 1.497 1.448 0.049 1.40e-02 5.10e+03 1.24e+01 ... (remaining 15310 not shown) Histogram of bond angle deviations from ideal: 99.23 - 106.23: 502 106.23 - 113.23: 8664 113.23 - 120.23: 5694 120.23 - 127.23: 5726 127.23 - 134.23: 207 Bond angle restraints: 20793 Sorted by residual: angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.87 128.10 -8.23 1.04e+00 9.25e-01 6.26e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.87 128.04 -8.17 1.04e+00 9.25e-01 6.17e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.87 128.04 -8.17 1.04e+00 9.25e-01 6.17e+01 angle pdb=" N ILE A 213 " pdb=" CA ILE A 213 " pdb=" C ILE A 213 " ideal model delta sigma weight residual 107.84 99.50 8.34 1.11e+00 8.12e-01 5.64e+01 angle pdb=" N ILE E 213 " pdb=" CA ILE E 213 " pdb=" C ILE E 213 " ideal model delta sigma weight residual 107.84 99.53 8.31 1.11e+00 8.12e-01 5.61e+01 ... (remaining 20788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 9823 17.65 - 35.29: 434 35.29 - 52.94: 93 52.94 - 70.58: 24 70.58 - 88.23: 9 Dihedral angle restraints: 10383 sinusoidal: 5418 harmonic: 4965 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -128.83 42.83 1 1.00e+01 1.00e-02 2.56e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -128.82 42.82 1 1.00e+01 1.00e-02 2.56e+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 -128.80 42.80 1 1.00e+01 1.00e-02 2.56e+01 ... (remaining 10380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1927 0.111 - 0.223: 651 0.223 - 0.334: 65 0.334 - 0.445: 12 0.445 - 0.557: 3 Chirality restraints: 2658 Sorted by residual: chirality pdb=" C1 BMA Q 3 " pdb=" O4 NAG Q 2 " pdb=" C2 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.00e+02 chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.88e+01 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.65e+01 ... (remaining 2655 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 339 " -0.078 2.00e-02 2.50e+03 8.08e-02 8.16e+01 pdb=" CG ASN A 339 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 339 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 339 " 0.126 2.00e-02 2.50e+03 pdb=" C1 NAG A 630 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 339 " -0.078 2.00e-02 2.50e+03 8.07e-02 8.15e+01 pdb=" CG ASN C 339 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN C 339 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C 339 " 0.126 2.00e-02 2.50e+03 pdb=" C1 NAG C 630 " -0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 339 " -0.078 2.00e-02 2.50e+03 8.07e-02 8.14e+01 pdb=" CG ASN E 339 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN E 339 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN E 339 " 0.126 2.00e-02 2.50e+03 pdb=" C1 NAG E 630 " -0.096 2.00e-02 2.50e+03 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3191 2.77 - 3.31: 13968 3.31 - 3.84: 25723 3.84 - 4.37: 30643 4.37 - 4.90: 48262 Nonbonded interactions: 121787 Sorted by model distance: nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR E 37 " pdb=" OG1 THR E 499 " model vdw 2.243 2.440 nonbonded pdb=" NZ LYS C 46 " pdb=" OD2 ASP D 632 " model vdw 2.367 2.520 nonbonded pdb=" NZ LYS A 46 " pdb=" OD2 ASP B 632 " model vdw 2.368 2.520 ... (remaining 121782 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'a' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'a' } pdb_interpretation.ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set refine NCS operators NCS operators will be refined. 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: 0.390 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: 2.500 Check model and map are aligned: 0.240 Set scattering table: 0.130 Process input model: 44.940 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.019 0.090 15315 Z= 1.204 Angle : 1.725 8.336 20793 Z= 1.095 Chirality : 0.104 0.557 2658 Planarity : 0.009 0.043 2499 Dihedral : 10.428 88.227 7068 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.20 % Allowed : 1.57 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 1683 helix: 0.15 (0.24), residues: 426 sheet: 1.08 (0.23), residues: 405 loop : 0.76 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.011 TRP A 479 HIS 0.010 0.002 HIS E 85 PHE 0.031 0.006 PHE E 383 TYR 0.040 0.007 TYR E 319 ARG 0.010 0.001 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1497 time to fit residues: 21.4737 Evaluate side-chains 54 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.441 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5824 Evaluate side-chains 70 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.1483 time to fit residues: 11.1827 Evaluate side-chains 30 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.126 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1647 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0044 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 : 0.001 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: 0.0012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 70 optimal weight: 0.0370 chunk 43 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 50 optimal weight: 0.0050 chunk 80 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 152 optimal weight: 0.0060 overall best weight: 1.1890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.146 15315 Z= 0.499 Angle : 1.113 16.347 20793 Z= 0.588 Chirality : 0.062 0.329 2658 Planarity : 0.008 0.063 2499 Dihedral : 7.720 59.354 3834 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 23.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.14 % Favored : 97.68 % Rotamer: Outliers : 0.78 % Allowed : 5.09 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.19), residues: 1683 helix: -0.13 (0.23), residues: 390 sheet: 0.64 (0.23), residues: 435 loop : -0.47 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.006 TRP F 610 HIS 0.014 0.004 HIS E 66 PHE 0.025 0.003 PHE E 383 TYR 0.023 0.004 TYR A 40 ARG 0.027 0.001 ARG F 588 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.444 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 79 average time/residue: 0.1753 time to fit residues: 16.9434 Evaluate side-chains 52 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.474 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6609 Evaluate side-chains 49 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.1462 time to fit residues: 7.6545 Evaluate side-chains 28 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.131 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1678 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: 0.0044 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 : 0.002 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 : 0.002 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 0.6980 chunk 47 optimal weight: 0.0970 chunk 126 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 136 optimal weight: 0.0060 chunk 151 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 122 optimal weight: 0.4980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 540 GLN Total number of N/Q/H flips: 1 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: 0.8037 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.259 15315 Z= 0.869 Angle : 1.403 21.590 20793 Z= 0.755 Chirality : 0.068 0.638 2658 Planarity : 0.013 0.268 2499 Dihedral : 7.900 58.717 3834 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 32.63 Ramachandran Plot: Outliers : 0.71 % Allowed : 2.50 % Favored : 96.79 % Rotamer: Outliers : 0.59 % Allowed : 4.11 % Favored : 95.30 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.19), residues: 1683 helix: -0.77 (0.22), residues: 393 sheet: 0.35 (0.24), residues: 408 loop : -0.66 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.009 TRP B 628 HIS 0.016 0.003 HIS A 66 PHE 0.016 0.003 PHE D 522 TYR 0.048 0.004 TYR A 40 ARG 0.052 0.004 ARG D 579 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.475 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 67 average time/residue: 0.1409 time to fit residues: 12.1486 Evaluate side-chains 47 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0359 time to fit residues: 0.5989 Evaluate side-chains 39 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1182 time to fit residues: 5.0973 Evaluate side-chains 25 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.110 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1421 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: 0.0040 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: 0.0016 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0019 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: 0.0012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 162 optimal weight: 30.0000 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 652 GLN ** 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.259 15315 Z= 0.872 Angle : 1.402 21.590 20793 Z= 0.755 Chirality : 0.072 0.761 2658 Planarity : 0.013 0.268 2499 Dihedral : 7.900 58.717 3834 Min Nonbonded Distance : 0.955 Molprobity Statistics. All-atom Clashscore : 43.94 Ramachandran Plot: Outliers : 0.71 % Allowed : 2.50 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.19), residues: 1683 helix: -0.77 (0.22), residues: 393 sheet: 0.35 (0.24), residues: 408 loop : -0.66 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.009 TRP F 628 HIS 0.016 0.003 HIS A 66 PHE 0.016 0.003 PHE F 522 TYR 0.048 0.004 TYR A 40 ARG 0.052 0.004 ARG B 579 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1216 time to fit residues: 9.0528 Evaluate side-chains 41 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.435 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6018 Evaluate side-chains 41 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1362 time to fit residues: 6.1389 Evaluate side-chains 26 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.112 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1460 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: 0.0041 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: 0.0016 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: 0.0022 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 67 optimal weight: 0.0030 chunk 138 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 0 optimal weight: 0.7980 chunk 82 optimal weight: 0.0470 chunk 145 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.4888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 540 GLN D 607 ASN 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: 0.8055 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 15315 Z= 0.366 Angle : 0.986 10.176 20793 Z= 0.536 Chirality : 0.058 0.281 2658 Planarity : 0.008 0.129 2499 Dihedral : 7.678 56.219 3834 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.39 % Allowed : 2.54 % Favored : 97.06 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.19), residues: 1683 helix: -1.13 (0.24), residues: 378 sheet: 0.01 (0.22), residues: 441 loop : -0.79 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.006 TRP B 628 HIS 0.009 0.003 HIS A 85 PHE 0.022 0.002 PHE D 522 TYR 0.027 0.003 TYR E 173 ARG 0.015 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.449 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 58 average time/residue: 0.1236 time to fit residues: 9.5307 Evaluate side-chains 42 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.466 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6055 Evaluate side-chains 46 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1731 time to fit residues: 8.5634 Evaluate side-chains 26 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.127 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1639 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: 0.0044 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: 0.0019 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: 0.0023 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 0.0000 chunk 40 optimal weight: 0.0050 chunk 162 optimal weight: 4.9990 chunk 134 optimal weight: 0.0030 chunk 75 optimal weight: 8.9990 chunk 13 optimal weight: 0.0970 chunk 53 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** 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... 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: 0.8058 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.177 15315 Z= 0.549 Angle : 1.110 24.777 20793 Z= 0.592 Chirality : 0.061 0.691 2658 Planarity : 0.006 0.053 2499 Dihedral : 7.746 55.611 3834 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 24.77 Ramachandran Plot: Outliers : 0.71 % Allowed : 4.10 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.19), residues: 1683 helix: -1.20 (0.23), residues: 378 sheet: -0.05 (0.22), residues: 441 loop : -0.78 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.007 TRP B 628 HIS 0.057 0.005 HIS C 66 PHE 0.017 0.002 PHE D 522 TYR 0.031 0.004 TYR A 39 ARG 0.012 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.457 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1228 time to fit residues: 8.3487 Evaluate side-chains 36 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.540 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5853 Evaluate side-chains 40 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0967 time to fit residues: 4.4064 Evaluate side-chains 23 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.111 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1446 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: 0.0038 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: 0.0014 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: 0.0020 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 136 optimal weight: 0.4980 chunk 90 optimal weight: 0.2980 chunk 161 optimal weight: 0.9990 chunk 101 optimal weight: 40.0000 chunk 98 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** 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... 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: 0.8070 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.160 15315 Z= 0.488 Angle : 1.096 28.667 20793 Z= 0.573 Chirality : 0.058 0.390 2658 Planarity : 0.006 0.053 2499 Dihedral : 7.691 54.963 3834 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 22.74 Ramachandran Plot: Outliers : 0.89 % Allowed : 4.28 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.19), residues: 1683 helix: -1.41 (0.23), residues: 378 sheet: -0.04 (0.22), residues: 441 loop : -0.82 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.126 0.007 TRP A 96 HIS 0.030 0.003 HIS E 66 PHE 0.016 0.002 PHE B 522 TYR 0.034 0.004 TYR E 217 ARG 0.009 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.427 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1276 time to fit residues: 8.0814 Evaluate side-chains 35 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.463 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5643 Evaluate side-chains 37 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0947 time to fit residues: 4.0338 Evaluate side-chains 23 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.121 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1425 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: 0.0046 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 : 0.002 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 : 0.002 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 80 optimal weight: 0.0570 chunk 15 optimal weight: 0.0270 chunk 127 optimal weight: 0.0270 chunk 147 optimal weight: 0.8980 overall best weight: 1.2016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 HIS E 114 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 653 GLN ** 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.290 15315 Z= 0.679 Angle : 1.207 35.110 20793 Z= 0.624 Chirality : 0.065 0.606 2658 Planarity : 0.006 0.055 2499 Dihedral : 7.685 54.533 3834 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 26.15 Ramachandran Plot: Outliers : 0.89 % Allowed : 4.28 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.19), residues: 1683 helix: -1.48 (0.23), residues: 378 sheet: -0.06 (0.23), residues: 441 loop : -0.87 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.112 0.009 TRP D 610 HIS 0.020 0.003 HIS E 66 PHE 0.014 0.002 PHE B 522 TYR 0.027 0.003 TYR C 217 ARG 0.012 0.001 ARG F 588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.483 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1281 time to fit residues: 8.5866 Evaluate side-chains 43 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.415 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5785 Evaluate side-chains 33 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0956 time to fit residues: 3.6357 Evaluate side-chains 22 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.123 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1677 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: 0.0015 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: 0.0022 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 771, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 57.3703 > 50: distance: 0 - 1: 22.793 distance: 1 - 2: 19.722 distance: 1 - 4: 15.819 distance: 2 - 3: 8.950 distance: 2 - 9: 15.921 distance: 4 - 5: 11.683 distance: 5 - 6: 4.149 distance: 6 - 7: 3.914 distance: 9 - 10: 15.341 distance: 10 - 11: 16.861 distance: 10 - 13: 18.338 distance: 11 - 12: 9.568 distance: 11 - 20: 45.418 distance: 13 - 14: 8.972 distance: 14 - 15: 3.498 distance: 14 - 16: 11.226 distance: 15 - 17: 5.232 distance: 16 - 18: 8.688 distance: 17 - 19: 7.283 distance: 18 - 19: 6.734 distance: 20 - 21: 18.726 distance: 21 - 22: 10.082 distance: 21 - 24: 7.170 distance: 22 - 23: 9.403 distance: 22 - 28: 5.138 distance: 24 - 25: 22.043 distance: 25 - 26: 18.048 distance: 25 - 27: 18.821 distance: 28 - 29: 19.561 distance: 29 - 30: 8.249 distance: 29 - 32: 13.217 distance: 30 - 31: 6.074 distance: 30 - 36: 3.016 distance: 32 - 33: 5.134 distance: 33 - 34: 22.723 distance: 34 - 35: 26.217 distance: 36 - 37: 4.706 distance: 37 - 38: 8.374 distance: 37 - 40: 5.040 distance: 38 - 39: 12.316 distance: 38 - 50: 3.607 distance: 40 - 41: 6.308 distance: 41 - 42: 14.105 distance: 41 - 43: 16.000 distance: 42 - 44: 9.926 distance: 43 - 45: 17.099 distance: 43 - 46: 4.146 distance: 44 - 45: 8.887 distance: 45 - 47: 6.464 distance: 46 - 48: 8.578 distance: 47 - 49: 14.206 distance: 48 - 49: 12.830 distance: 50 - 51: 6.083 distance: 51 - 52: 11.208 distance: 51 - 54: 10.969 distance: 52 - 53: 26.186 distance: 52 - 59: 20.062 distance: 54 - 55: 28.923 distance: 55 - 56: 28.101 distance: 56 - 57: 10.855 distance: 57 - 58: 5.507 distance: 59 - 60: 7.723 distance: 60 - 61: 22.625 distance: 60 - 63: 6.745 distance: 61 - 62: 15.510 distance: 61 - 67: 37.066 distance: 63 - 64: 12.357 distance: 64 - 65: 10.049 distance: 64 - 66: 6.689 distance: 67 - 68: 10.878 distance: 68 - 69: 36.491 distance: 68 - 71: 22.894 distance: 69 - 70: 23.397 distance: 69 - 75: 13.599 distance: 71 - 72: 9.051 distance: 72 - 73: 18.017 distance: 72 - 74: 16.971 distance: 75 - 76: 7.088 distance: 76 - 77: 7.669 distance: 76 - 79: 4.580 distance: 77 - 78: 22.026 distance: 77 - 83: 5.340 distance: 79 - 80: 10.380 distance: 80 - 81: 17.304 distance: 81 - 82: 9.968 distance: 83 - 84: 3.467 distance: 84 - 85: 5.749 distance: 84 - 87: 7.132 distance: 85 - 86: 4.370 distance: 87 - 88: 5.519 distance: 87 - 89: 10.065