Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 9 22:50:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3v_29710/07_2023/8g3v_29710.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3v_29710/07_2023/8g3v_29710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3v_29710/07_2023/8g3v_29710.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3v_29710/07_2023/8g3v_29710.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3v_29710/07_2023/8g3v_29710.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3v_29710/07_2023/8g3v_29710.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.048 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: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 116 5.16 5 C 12484 2.51 5 N 3416 2.21 5 O 4024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 85": "NH1" <-> "NH2" Residue "G ARG 107": "NH1" <-> "NH2" Residue "G ARG 118": "NH1" <-> "NH2" Residue "G ARG 150": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 156": "NH1" <-> "NH2" Residue "G ARG 210": "NH1" <-> "NH2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "G TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 283": "NH1" <-> "NH2" Residue "G ARG 288": "NH1" <-> "NH2" Residue "G ARG 292": "NH1" <-> "NH2" Residue "G ARG 300": "NH1" <-> "NH2" Residue "G ARG 327": "NH1" <-> "NH2" Residue "G ARG 364": "NH1" <-> "NH2" Residue "G ARG 371": "NH1" <-> "NH2" Residue "G ARG 394": "NH1" <-> "NH2" Residue "G ARG 400": "NH1" <-> "NH2" Residue "G ARG 403": "NH1" <-> "NH2" Residue "G ARG 420": "NH1" <-> "NH2" Residue "G ARG 428": "NH1" <-> "NH2" Residue "G ARG 430": "NH1" <-> "NH2" Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ARG 27": "NH1" <-> "NH2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "H ARG 85": "NH1" <-> "NH2" Residue "H ARG 107": "NH1" <-> "NH2" Residue "H ARG 118": "NH1" <-> "NH2" Residue "H ARG 150": "NH1" <-> "NH2" Residue "H ARG 152": "NH1" <-> "NH2" Residue "H ARG 156": "NH1" <-> "NH2" Residue "H ARG 210": "NH1" <-> "NH2" Residue "H ARG 224": "NH1" <-> "NH2" Residue "H TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 283": "NH1" <-> "NH2" Residue "H ARG 288": "NH1" <-> "NH2" Residue "H ARG 292": "NH1" <-> "NH2" Residue "H ARG 300": "NH1" <-> "NH2" Residue "H ARG 327": "NH1" <-> "NH2" Residue "H ARG 364": "NH1" <-> "NH2" Residue "H ARG 371": "NH1" <-> "NH2" Residue "H ARG 394": "NH1" <-> "NH2" Residue "H ARG 400": "NH1" <-> "NH2" Residue "H ARG 403": "NH1" <-> "NH2" Residue "H ARG 420": "NH1" <-> "NH2" Residue "H ARG 428": "NH1" <-> "NH2" Residue "H ARG 430": "NH1" <-> "NH2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 24": "NH1" <-> "NH2" Residue "M ARG 27": "NH1" <-> "NH2" Residue "M ARG 45": "NH1" <-> "NH2" Residue "M ARG 54": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "I ARG 85": "NH1" <-> "NH2" Residue "I ARG 107": "NH1" <-> "NH2" Residue "I ARG 118": "NH1" <-> "NH2" Residue "I ARG 150": "NH1" <-> "NH2" Residue "I ARG 152": "NH1" <-> "NH2" Residue "I ARG 156": "NH1" <-> "NH2" Residue "I ARG 210": "NH1" <-> "NH2" Residue "I ARG 224": "NH1" <-> "NH2" Residue "I TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 283": "NH1" <-> "NH2" Residue "I ARG 288": "NH1" <-> "NH2" Residue "I ARG 292": "NH1" <-> "NH2" Residue "I ARG 300": "NH1" <-> "NH2" Residue "I ARG 327": "NH1" <-> "NH2" Residue "I ARG 364": "NH1" <-> "NH2" Residue "I ARG 371": "NH1" <-> "NH2" Residue "I ARG 394": "NH1" <-> "NH2" Residue "I ARG 400": "NH1" <-> "NH2" Residue "I ARG 403": "NH1" <-> "NH2" Residue "I ARG 420": "NH1" <-> "NH2" Residue "I ARG 428": "NH1" <-> "NH2" Residue "I ARG 430": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 87": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N ARG 24": "NH1" <-> "NH2" Residue "N ARG 27": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N ARG 54": "NH1" <-> "NH2" Residue "N ARG 61": "NH1" <-> "NH2" Residue "J ARG 85": "NH1" <-> "NH2" Residue "J ARG 107": "NH1" <-> "NH2" Residue "J ARG 118": "NH1" <-> "NH2" Residue "J ARG 150": "NH1" <-> "NH2" Residue "J ARG 152": "NH1" <-> "NH2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "J ARG 210": "NH1" <-> "NH2" Residue "J ARG 224": "NH1" <-> "NH2" Residue "J TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 283": "NH1" <-> "NH2" Residue "J ARG 288": "NH1" <-> "NH2" Residue "J ARG 292": "NH1" <-> "NH2" Residue "J ARG 300": "NH1" <-> "NH2" Residue "J ARG 327": "NH1" <-> "NH2" Residue "J ARG 364": "NH1" <-> "NH2" Residue "J ARG 371": "NH1" <-> "NH2" Residue "J ARG 394": "NH1" <-> "NH2" Residue "J ARG 400": "NH1" <-> "NH2" Residue "J ARG 403": "NH1" <-> "NH2" Residue "J ARG 420": "NH1" <-> "NH2" Residue "J ARG 428": "NH1" <-> "NH2" Residue "J ARG 430": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 87": "NH1" <-> "NH2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "O ARG 18": "NH1" <-> "NH2" Residue "O ARG 24": "NH1" <-> "NH2" Residue "O ARG 27": "NH1" <-> "NH2" Residue "O ARG 45": "NH1" <-> "NH2" Residue "O ARG 54": "NH1" <-> "NH2" Residue "O ARG 61": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 20045 Number of models: 1 Model: "" Number of chains: 28 Chain: "G" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 375} Chain: "A" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "L" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 375} Chain: "B" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "M" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "I" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 375} Chain: "C" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "N" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "J" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 375} Chain: "D" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "O" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.26, per 1000 atoms: 0.46 Number of scatterers: 20045 At special positions: 0 Unit cell: (131.97, 131.97, 102.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 116 16.00 O 4024 8.00 N 3416 7.00 C 12484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 417 " distance=2.06 Simple disulfide: pdb=" SG CYS G 124 " - pdb=" SG CYS G 129 " distance=2.07 Simple disulfide: pdb=" SG CYS G 175 " - pdb=" SG CYS G 193 " distance=2.03 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 230 " distance=2.08 Simple disulfide: pdb=" SG CYS G 232 " - pdb=" SG CYS G 237 " distance=2.11 Simple disulfide: pdb=" SG CYS G 278 " - pdb=" SG CYS G 291 " distance=2.11 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 289 " distance=2.10 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.10 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 447 " distance=2.15 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.06 Simple disulfide: pdb=" SG CYS H 92 " - pdb=" SG CYS H 417 " distance=2.06 Simple disulfide: pdb=" SG CYS H 124 " - pdb=" SG CYS H 129 " distance=2.07 Simple disulfide: pdb=" SG CYS H 175 " - pdb=" SG CYS H 193 " distance=2.03 Simple disulfide: pdb=" SG CYS H 183 " - pdb=" SG CYS H 230 " distance=2.07 Simple disulfide: pdb=" SG CYS H 232 " - pdb=" SG CYS H 237 " distance=2.11 Simple disulfide: pdb=" SG CYS H 278 " - pdb=" SG CYS H 291 " distance=2.11 Simple disulfide: pdb=" SG CYS H 280 " - pdb=" SG CYS H 289 " distance=2.10 Simple disulfide: pdb=" SG CYS H 318 " - pdb=" SG CYS H 337 " distance=2.10 Simple disulfide: pdb=" SG CYS H 421 " - pdb=" SG CYS H 447 " distance=2.15 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.05 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.07 Simple disulfide: pdb=" SG CYS I 92 " - pdb=" SG CYS I 417 " distance=2.06 Simple disulfide: pdb=" SG CYS I 124 " - pdb=" SG CYS I 129 " distance=2.07 Simple disulfide: pdb=" SG CYS I 175 " - pdb=" SG CYS I 193 " distance=2.03 Simple disulfide: pdb=" SG CYS I 183 " - pdb=" SG CYS I 230 " distance=2.08 Simple disulfide: pdb=" SG CYS I 232 " - pdb=" SG CYS I 237 " distance=2.11 Simple disulfide: pdb=" SG CYS I 278 " - pdb=" SG CYS I 291 " distance=2.11 Simple disulfide: pdb=" SG CYS I 280 " - pdb=" SG CYS I 289 " distance=2.10 Simple disulfide: pdb=" SG CYS I 318 " - pdb=" SG CYS I 337 " distance=2.10 Simple disulfide: pdb=" SG CYS I 421 " - pdb=" SG CYS I 447 " distance=2.15 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.05 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.07 Simple disulfide: pdb=" SG CYS J 92 " - pdb=" SG CYS J 417 " distance=2.06 Simple disulfide: pdb=" SG CYS J 124 " - pdb=" SG CYS J 129 " distance=2.07 Simple disulfide: pdb=" SG CYS J 175 " - pdb=" SG CYS J 193 " distance=2.03 Simple disulfide: pdb=" SG CYS J 183 " - pdb=" SG CYS J 230 " distance=2.08 Simple disulfide: pdb=" SG CYS J 232 " - pdb=" SG CYS J 237 " distance=2.11 Simple disulfide: pdb=" SG CYS J 278 " - pdb=" SG CYS J 291 " distance=2.11 Simple disulfide: pdb=" SG CYS J 280 " - pdb=" SG CYS J 289 " distance=2.10 Simple disulfide: pdb=" SG CYS J 318 " - pdb=" SG CYS J 337 " distance=2.10 Simple disulfide: pdb=" SG CYS J 421 " - pdb=" SG CYS J 447 " distance=2.15 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.05 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.06 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 ALPHA1-2 " MAN F 4 " - " MAN F 5 " " MAN Q 4 " - " MAN Q 5 " " MAN T 4 " - " MAN T 5 " " MAN W 4 " - " MAN W 5 " ALPHA1-3 " BMA F 3 " - " MAN F 4 " " MAN F 6 " - " MAN F 7 " " BMA Q 3 " - " MAN Q 4 " " MAN Q 6 " - " MAN Q 7 " " BMA T 3 " - " MAN T 4 " " MAN T 6 " - " MAN T 7 " " BMA W 3 " - " MAN W 4 " " MAN W 6 " - " MAN W 7 " ALPHA1-6 " BMA F 3 " - " MAN F 6 " " MAN F 6 " - " MAN F 8 " " BMA Q 3 " - " MAN Q 6 " " MAN Q 6 " - " MAN Q 8 " " BMA T 3 " - " MAN T 6 " " MAN T 6 " - " MAN T 8 " " BMA W 3 " - " MAN W 6 " " MAN W 6 " - " MAN W 8 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG K 1 " - " NAG K 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 T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG E 1 " - " ASN G 86 " " NAG F 1 " - " ASN G 200 " " NAG G1101 " - " ASN G 146 " " NAG G1102 " - " ASN G 367 " " NAG H1101 " - " ASN H 146 " " NAG H1102 " - " ASN H 367 " " NAG I1101 " - " ASN I 146 " " NAG I1102 " - " ASN I 367 " " NAG J1101 " - " ASN J 146 " " NAG J1102 " - " ASN J 367 " " NAG K 1 " - " ASN G 234 " " NAG P 1 " - " ASN H 86 " " NAG Q 1 " - " ASN H 200 " " NAG R 1 " - " ASN H 234 " " NAG S 1 " - " ASN I 86 " " NAG T 1 " - " ASN I 200 " " NAG U 1 " - " ASN I 234 " " NAG V 1 " - " ASN J 86 " " NAG W 1 " - " ASN J 200 " " NAG X 1 " - " ASN J 234 " Time building additional restraints: 8.69 Conformation dependent library (CDL) restraints added in 2.7 seconds 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 48 sheets defined 5.1% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'G' and resid 104 through 110 Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.690A pdb=" N ASN G 146 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 32 removed outlier: 3.560A pdb=" N LYS A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.658A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 110 Processing helix chain 'H' and resid 142 through 146 removed outlier: 3.691A pdb=" N ASN H 146 " --> pdb=" O VAL H 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.558A pdb=" N LYS B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.659A pdb=" N PHE M 83 " --> pdb=" O SER M 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 110 Processing helix chain 'I' and resid 142 through 146 removed outlier: 3.689A pdb=" N ASN I 146 " --> pdb=" O VAL I 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.561A pdb=" N LYS C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.658A pdb=" N PHE N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 110 Processing helix chain 'J' and resid 142 through 146 removed outlier: 3.679A pdb=" N ASN J 146 " --> pdb=" O VAL J 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.561A pdb=" N LYS D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.658A pdb=" N PHE O 83 " --> pdb=" O SER O 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 96 through 102 removed outlier: 3.802A pdb=" N GLY G 96 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL G 445 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS G 102 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE G 443 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG G 420 " --> pdb=" O GLY G 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 115 through 124 removed outlier: 4.796A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS G 172 " --> pdb=" O MET G 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 179 through 184 removed outlier: 4.116A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP G 213 " --> pdb=" O PHE G 205 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR G 207 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU G 211 " --> pdb=" O TYR G 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 231 through 233 removed outlier: 6.527A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE G 262 " --> pdb=" O GLU G 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 276 through 283 removed outlier: 5.381A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 353 through 356 removed outlier: 7.082A pdb=" N ASP G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.439A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.497A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.487A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.241A pdb=" N VAL G 396 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.249A pdb=" N LEU A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY A 50 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A 40 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.391A pdb=" N PHE A 117 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.849A pdb=" N GLN L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER L 67 " --> pdb=" O GLN L 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.474A pdb=" N LEU L 33 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 96 through 102 removed outlier: 3.804A pdb=" N GLY H 96 " --> pdb=" O THR H 449 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL H 445 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS H 102 " --> pdb=" O ILE H 443 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE H 443 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG H 420 " --> pdb=" O GLY H 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 115 through 124 removed outlier: 4.797A pdb=" N TRP H 115 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR H 138 " --> pdb=" O TRP H 115 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N THR H 117 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN H 136 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU H 119 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU H 134 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR H 157 " --> pdb=" O GLY H 135 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU H 158 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS H 172 " --> pdb=" O MET H 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 179 through 184 removed outlier: 4.121A pdb=" N ASP H 197 " --> pdb=" O ASN H 200 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP H 213 " --> pdb=" O PHE H 205 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TYR H 207 " --> pdb=" O LEU H 211 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU H 211 " --> pdb=" O TYR H 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 231 through 233 removed outlier: 6.524A pdb=" N GLU H 258 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE H 262 " --> pdb=" O GLU H 258 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 276 through 283 removed outlier: 5.381A pdb=" N GLU H 277 " --> pdb=" O ARG H 292 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG H 292 " --> pdb=" O GLU H 277 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 353 through 356 removed outlier: 7.085A pdb=" N ASP H 402 " --> pdb=" O GLY H 373 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N GLU H 375 " --> pdb=" O ARG H 400 " (cutoff:3.500A) removed outlier: 10.428A pdb=" N ARG H 400 " --> pdb=" O GLU H 375 " (cutoff:3.500A) removed outlier: 11.418A pdb=" N PHE H 377 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 13.500A pdb=" N VAL H 398 " --> pdb=" O PHE H 377 " (cutoff:3.500A) removed outlier: 15.525A pdb=" N VAL H 379 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 16.245A pdb=" N VAL H 396 " --> pdb=" O VAL H 379 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AC2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.252A pdb=" N LEU B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA B 40 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.391A pdb=" N PHE B 117 " --> pdb=" O THR B 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AC5, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.849A pdb=" N GLN M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER M 67 " --> pdb=" O GLN M 70 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.475A pdb=" N LEU M 33 " --> pdb=" O PHE M 49 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 96 through 102 removed outlier: 3.801A pdb=" N GLY I 96 " --> pdb=" O THR I 449 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL I 445 " --> pdb=" O PHE I 100 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS I 102 " --> pdb=" O ILE I 443 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE I 443 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG I 420 " --> pdb=" O GLY I 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 115 through 124 removed outlier: 4.795A pdb=" N TRP I 115 " --> pdb=" O THR I 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR I 138 " --> pdb=" O TRP I 115 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR I 117 " --> pdb=" O GLN I 136 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN I 136 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU I 119 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU I 134 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR I 157 " --> pdb=" O GLY I 135 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU I 158 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS I 172 " --> pdb=" O MET I 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 179 through 184 removed outlier: 4.114A pdb=" N ASP I 197 " --> pdb=" O ASN I 200 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP I 213 " --> pdb=" O PHE I 205 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR I 207 " --> pdb=" O LEU I 211 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU I 211 " --> pdb=" O TYR I 207 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 231 through 233 removed outlier: 6.524A pdb=" N GLU I 258 " --> pdb=" O ILE I 262 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE I 262 " --> pdb=" O GLU I 258 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 276 through 283 removed outlier: 5.384A pdb=" N GLU I 277 " --> pdb=" O ARG I 292 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG I 292 " --> pdb=" O GLU I 277 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 353 through 356 removed outlier: 7.093A pdb=" N ASP I 402 " --> pdb=" O GLY I 373 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N GLU I 375 " --> pdb=" O ARG I 400 " (cutoff:3.500A) removed outlier: 10.448A pdb=" N ARG I 400 " --> pdb=" O GLU I 375 " (cutoff:3.500A) removed outlier: 11.415A pdb=" N PHE I 377 " --> pdb=" O VAL I 398 " (cutoff:3.500A) removed outlier: 13.491A pdb=" N VAL I 398 " --> pdb=" O PHE I 377 " (cutoff:3.500A) removed outlier: 15.522A pdb=" N VAL I 379 " --> pdb=" O VAL I 396 " (cutoff:3.500A) removed outlier: 16.245A pdb=" N VAL I 396 " --> pdb=" O VAL I 379 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AD5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.261A pdb=" N LEU C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA C 40 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.394A pdb=" N PHE C 117 " --> pdb=" O THR C 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AD8, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.849A pdb=" N GLN N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER N 67 " --> pdb=" O GLN N 70 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.476A pdb=" N LEU N 33 " --> pdb=" O PHE N 49 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 96 through 102 removed outlier: 3.801A pdb=" N GLY J 96 " --> pdb=" O THR J 449 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL J 445 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LYS J 102 " --> pdb=" O ILE J 443 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE J 443 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ARG J 420 " --> pdb=" O GLY J 448 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 115 through 124 removed outlier: 4.798A pdb=" N TRP J 115 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR J 138 " --> pdb=" O TRP J 115 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR J 117 " --> pdb=" O GLN J 136 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN J 136 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLU J 119 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU J 134 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR J 157 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU J 158 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS J 172 " --> pdb=" O MET J 160 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 179 through 184 removed outlier: 4.119A pdb=" N ASP J 197 " --> pdb=" O ASN J 200 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP J 213 " --> pdb=" O PHE J 205 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TYR J 207 " --> pdb=" O LEU J 211 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU J 211 " --> pdb=" O TYR J 207 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 231 through 233 removed outlier: 6.525A pdb=" N GLU J 258 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE J 262 " --> pdb=" O GLU J 258 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 276 through 283 removed outlier: 5.383A pdb=" N GLU J 277 " --> pdb=" O ARG J 292 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG J 292 " --> pdb=" O GLU J 277 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 353 through 356 removed outlier: 7.092A pdb=" N ASP J 402 " --> pdb=" O GLY J 373 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N GLU J 375 " --> pdb=" O ARG J 400 " (cutoff:3.500A) removed outlier: 10.449A pdb=" N ARG J 400 " --> pdb=" O GLU J 375 " (cutoff:3.500A) removed outlier: 11.414A pdb=" N PHE J 377 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 13.493A pdb=" N VAL J 398 " --> pdb=" O PHE J 377 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N VAL J 379 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 16.245A pdb=" N VAL J 396 " --> pdb=" O VAL J 379 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AE8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.259A pdb=" N LEU D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA D 40 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.394A pdb=" N PHE D 117 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 104 through 105 Processing sheet with id=AF2, first strand: chain 'O' and resid 4 through 7 removed outlier: 3.850A pdb=" N GLN O 70 " --> pdb=" O SER O 67 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER O 67 " --> pdb=" O GLN O 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.477A pdb=" N LEU O 33 " --> pdb=" O PHE O 49 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) 684 hydrogen bonds defined for protein. 1728 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: 6.93 Time building geometry restraints manager: 9.15 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: 3703 1.32 - 1.45: 5439 1.45 - 1.57: 11206 1.57 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 20492 Sorted by residual: bond pdb=" N VAL O 58 " pdb=" CA VAL O 58 " ideal model delta sigma weight residual 1.460 1.493 -0.034 7.50e-03 1.78e+04 2.00e+01 bond pdb=" CA SER J 457 " pdb=" CB SER J 457 " ideal model delta sigma weight residual 1.534 1.460 0.074 1.72e-02 3.38e+03 1.85e+01 bond pdb=" CA SER H 457 " pdb=" CB SER H 457 " ideal model delta sigma weight residual 1.534 1.463 0.070 1.72e-02 3.38e+03 1.67e+01 bond pdb=" N VAL G 165 " pdb=" CA VAL G 165 " ideal model delta sigma weight residual 1.460 1.490 -0.029 7.30e-03 1.88e+04 1.61e+01 bond pdb=" N VAL I 165 " pdb=" CA VAL I 165 " ideal model delta sigma weight residual 1.460 1.490 -0.029 7.30e-03 1.88e+04 1.61e+01 ... (remaining 20487 not shown) Histogram of bond angle deviations from ideal: 97.77 - 105.27: 396 105.27 - 112.76: 9945 112.76 - 120.25: 9451 120.25 - 127.75: 7792 127.75 - 135.24: 240 Bond angle restraints: 27824 Sorted by residual: angle pdb=" C ARG I 430 " pdb=" N LYS I 431 " pdb=" CA LYS I 431 " ideal model delta sigma weight residual 121.54 133.45 -11.91 1.91e+00 2.74e-01 3.89e+01 angle pdb=" C ARG G 430 " pdb=" N LYS G 431 " pdb=" CA LYS G 431 " ideal model delta sigma weight residual 121.54 133.42 -11.88 1.91e+00 2.74e-01 3.87e+01 angle pdb=" C ARG J 430 " pdb=" N LYS J 431 " pdb=" CA LYS J 431 " ideal model delta sigma weight residual 121.54 133.41 -11.87 1.91e+00 2.74e-01 3.86e+01 angle pdb=" C ARG H 430 " pdb=" N LYS H 431 " pdb=" CA LYS H 431 " ideal model delta sigma weight residual 121.54 133.40 -11.86 1.91e+00 2.74e-01 3.86e+01 angle pdb=" N ILE J 397 " pdb=" CA ILE J 397 " pdb=" C ILE J 397 " ideal model delta sigma weight residual 111.67 106.00 5.67 9.50e-01 1.11e+00 3.56e+01 ... (remaining 27819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 10731 17.39 - 34.78: 744 34.78 - 52.17: 135 52.17 - 69.56: 63 69.56 - 86.95: 19 Dihedral angle restraints: 11692 sinusoidal: 4580 harmonic: 7112 Sorted by residual: dihedral pdb=" CA ARG G 430 " pdb=" C ARG G 430 " pdb=" N LYS G 431 " pdb=" CA LYS G 431 " ideal model delta harmonic sigma weight residual -180.00 -143.33 -36.67 0 5.00e+00 4.00e-02 5.38e+01 dihedral pdb=" CA ARG H 430 " pdb=" C ARG H 430 " pdb=" N LYS H 431 " pdb=" CA LYS H 431 " ideal model delta harmonic sigma weight residual -180.00 -143.45 -36.55 0 5.00e+00 4.00e-02 5.34e+01 dihedral pdb=" CA ARG J 430 " pdb=" C ARG J 430 " pdb=" N LYS J 431 " pdb=" CA LYS J 431 " ideal model delta harmonic sigma weight residual -180.00 -143.50 -36.50 0 5.00e+00 4.00e-02 5.33e+01 ... (remaining 11689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1388 0.056 - 0.113: 1105 0.113 - 0.169: 483 0.169 - 0.225: 185 0.225 - 0.282: 35 Chirality restraints: 3196 Sorted by residual: chirality pdb=" C1 MAN Q 4 " pdb=" O3 BMA Q 3 " pdb=" C2 MAN Q 4 " pdb=" O5 MAN Q 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.93e+01 chirality pdb=" C1 MAN W 4 " pdb=" O3 BMA W 3 " pdb=" C2 MAN W 4 " pdb=" O5 MAN W 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.67e+01 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.11e+01 ... (remaining 3193 not shown) Planarity restraints: 3520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 1 " -0.088 2.00e-02 2.50e+03 7.60e-02 7.21e+01 pdb=" C7 NAG Q 1 " 0.061 2.00e-02 2.50e+03 pdb=" C8 NAG Q 1 " -0.078 2.00e-02 2.50e+03 pdb=" N2 NAG Q 1 " 0.107 2.00e-02 2.50e+03 pdb=" O7 NAG Q 1 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.087 2.00e-02 2.50e+03 7.54e-02 7.11e+01 pdb=" C7 NAG F 1 " -0.059 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.077 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.107 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 1 " 0.087 2.00e-02 2.50e+03 7.48e-02 7.00e+01 pdb=" C7 NAG W 1 " -0.058 2.00e-02 2.50e+03 pdb=" C8 NAG W 1 " 0.076 2.00e-02 2.50e+03 pdb=" N2 NAG W 1 " -0.107 2.00e-02 2.50e+03 pdb=" O7 NAG W 1 " 0.001 2.00e-02 2.50e+03 ... (remaining 3517 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2596 2.79 - 3.31: 19147 3.31 - 3.84: 35950 3.84 - 4.37: 46110 4.37 - 4.90: 73522 Nonbonded interactions: 177325 Sorted by model distance: nonbonded pdb=" O ASP G 293 " pdb="CA CA G1103 " model vdw 2.257 2.510 nonbonded pdb=" O ASP I 293 " pdb="CA CA I1103 " model vdw 2.257 2.510 nonbonded pdb=" O ASP H 293 " pdb="CA CA H1103 " model vdw 2.257 2.510 nonbonded pdb=" O ASP J 293 " pdb="CA CA J1103 " model vdw 2.265 2.510 nonbonded pdb=" O GLY J 345 " pdb="CA CA J1103 " model vdw 2.323 2.510 ... (remaining 177320 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 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'F' selection = chain 'Q' selection = chain 'T' selection = chain 'W' } ncs_group { reference = (chain 'G' and (resid 82 through 469 or resid 1101 through 1103)) selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.920 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 50.000 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 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 : 0.014 0.079 20492 Z= 0.916 Angle : 1.611 11.913 27824 Z= 1.043 Chirality : 0.092 0.282 3196 Planarity : 0.010 0.076 3500 Dihedral : 13.678 86.949 7032 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.88 % Favored : 95.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.74 (0.16), residues: 2476 helix: 0.14 (0.94), residues: 24 sheet: 0.03 (0.16), residues: 1012 loop : -0.88 (0.15), residues: 1440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 2.404 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 1.4906 time to fit residues: 553.6711 Evaluate side-chains 270 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 2.162 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 188 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 347 HIS A 62 GLN A 65 GLN L 6 GLN H 347 HIS B 62 GLN B 65 GLN M 6 GLN I 347 HIS C 62 GLN C 65 GLN N 6 GLN J 347 HIS O 6 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 20492 Z= 0.188 Angle : 0.630 5.878 27824 Z= 0.344 Chirality : 0.046 0.150 3196 Planarity : 0.003 0.033 3500 Dihedral : 6.286 21.116 2720 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.58 % Favored : 97.09 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: 0.01 (0.16), residues: 2476 helix: 0.33 (0.94), residues: 24 sheet: 0.28 (0.15), residues: 1064 loop : -0.14 (0.16), residues: 1388 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 276 time to evaluate : 2.393 Fit side-chains outliers start: 28 outliers final: 4 residues processed: 282 average time/residue: 1.2529 time to fit residues: 403.2183 Evaluate side-chains 254 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 250 time to evaluate : 2.420 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 3.0348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 235 optimal weight: 0.0020 chunk 194 optimal weight: 6.9990 chunk 216 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 65 GLN L 6 GLN H 141 ASN B 62 GLN B 65 GLN M 6 GLN I 141 ASN C 62 GLN C 65 GLN N 6 GLN J 141 ASN O 6 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 20492 Z= 0.319 Angle : 0.618 7.402 27824 Z= 0.334 Chirality : 0.047 0.158 3196 Planarity : 0.004 0.041 3500 Dihedral : 5.864 22.336 2720 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.07 % Favored : 96.61 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: 0.13 (0.16), residues: 2476 helix: 0.64 (0.98), residues: 24 sheet: 0.42 (0.15), residues: 1072 loop : -0.11 (0.17), residues: 1380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 256 time to evaluate : 2.244 Fit side-chains outliers start: 51 outliers final: 31 residues processed: 279 average time/residue: 1.2505 time to fit residues: 397.7157 Evaluate side-chains 282 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 251 time to evaluate : 2.213 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 15 residues processed: 16 average time/residue: 0.4454 time to fit residues: 12.7347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 146 optimal weight: 0.0970 chunk 219 optimal weight: 0.5980 chunk 231 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 70 GLN B 62 GLN B 65 GLN M 6 GLN M 70 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 20492 Z= 0.181 Angle : 0.553 9.684 27824 Z= 0.296 Chirality : 0.044 0.147 3196 Planarity : 0.003 0.042 3500 Dihedral : 5.381 21.717 2720 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.26 % Favored : 97.42 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: 0.18 (0.16), residues: 2476 helix: -0.12 (0.93), residues: 28 sheet: 0.54 (0.16), residues: 948 loop : -0.09 (0.16), residues: 1500 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 268 time to evaluate : 2.327 Fit side-chains outliers start: 36 outliers final: 24 residues processed: 287 average time/residue: 1.4009 time to fit residues: 455.7923 Evaluate side-chains 281 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 257 time to evaluate : 2.242 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 15 residues processed: 9 average time/residue: 0.6675 time to fit residues: 10.3772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 197 optimal weight: 0.6980 chunk 160 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 65 GLN L 6 GLN L 70 GLN B 62 GLN B 65 GLN M 6 GLN M 70 GLN C 62 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 20492 Z= 0.364 Angle : 0.615 9.368 27824 Z= 0.329 Chirality : 0.047 0.165 3196 Planarity : 0.004 0.046 3500 Dihedral : 5.654 22.787 2720 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.19 % Favored : 96.49 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: 0.06 (0.16), residues: 2476 helix: 0.56 (0.95), residues: 24 sheet: 0.30 (0.15), residues: 1076 loop : -0.08 (0.17), residues: 1376 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 247 time to evaluate : 2.169 Fit side-chains outliers start: 38 outliers final: 31 residues processed: 265 average time/residue: 1.4088 time to fit residues: 420.5553 Evaluate side-chains 271 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 240 time to evaluate : 2.287 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 15 residues processed: 16 average time/residue: 0.4760 time to fit residues: 13.3656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 232 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 70 GLN B 65 GLN M 6 GLN M 70 GLN C 62 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 20492 Z= 0.284 Angle : 0.584 10.157 27824 Z= 0.313 Chirality : 0.045 0.153 3196 Planarity : 0.004 0.046 3500 Dihedral : 5.496 22.404 2720 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.50 % Favored : 97.17 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: 0.11 (0.16), residues: 2476 helix: -0.35 (0.93), residues: 28 sheet: 0.39 (0.15), residues: 1056 loop : -0.08 (0.17), residues: 1392 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 245 time to evaluate : 2.262 Fit side-chains outliers start: 37 outliers final: 23 residues processed: 269 average time/residue: 1.2911 time to fit residues: 394.0913 Evaluate side-chains 263 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 240 time to evaluate : 2.052 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 15 residues processed: 8 average time/residue: 0.6849 time to fit residues: 9.4408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 195 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 231 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 70 GLN B 65 GLN M 6 GLN M 70 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 20492 Z= 0.219 Angle : 0.565 10.604 27824 Z= 0.300 Chirality : 0.044 0.147 3196 Planarity : 0.003 0.045 3500 Dihedral : 5.327 21.956 2720 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.67 % Favored : 97.09 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: 0.15 (0.16), residues: 2476 helix: -1.65 (0.65), residues: 52 sheet: 0.58 (0.16), residues: 940 loop : -0.08 (0.16), residues: 1484 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 248 time to evaluate : 2.354 Fit side-chains outliers start: 23 outliers final: 19 residues processed: 267 average time/residue: 1.3688 time to fit residues: 413.7226 Evaluate side-chains 256 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 237 time to evaluate : 2.204 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 4 average time/residue: 1.1996 time to fit residues: 8.3371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.4044 > 50: distance: 38 - 130: 6.504 distance: 41 - 127: 5.737 distance: 53 - 113: 4.885 distance: 56 - 110: 6.012 distance: 87 - 88: 5.097 distance: 88 - 89: 10.939 distance: 88 - 95: 4.379 distance: 90 - 91: 3.961 distance: 93 - 94: 6.559 distance: 95 - 96: 3.055 distance: 96 - 99: 4.655 distance: 97 - 98: 6.156 distance: 99 - 100: 3.817 distance: 99 - 101: 4.858 distance: 100 - 102: 5.661 distance: 104 - 105: 3.633 distance: 104 - 107: 3.658 distance: 105 - 106: 7.259 distance: 105 - 110: 3.612 distance: 107 - 109: 6.590 distance: 110 - 111: 6.317 distance: 111 - 112: 8.959 distance: 112 - 113: 6.766 distance: 112 - 120: 8.974 distance: 114 - 115: 3.703 distance: 115 - 116: 6.415 distance: 115 - 117: 4.835 distance: 118 - 119: 7.081 distance: 120 - 121: 6.334 distance: 121 - 122: 5.981 distance: 122 - 123: 4.089 distance: 124 - 125: 4.416 distance: 128 - 129: 4.068 distance: 128 - 131: 6.645 distance: 129 - 130: 3.625 distance: 129 - 133: 6.493 distance: 131 - 132: 6.972 distance: 134 - 135: 11.144 distance: 134 - 137: 3.986 distance: 135 - 136: 20.990 distance: 135 - 142: 33.634 distance: 137 - 138: 6.311 distance: 138 - 139: 5.641 distance: 140 - 141: 3.078 distance: 142 - 143: 11.446 distance: 143 - 144: 8.144 distance: 143 - 146: 7.962 distance: 144 - 145: 7.637 distance: 144 - 150: 10.992 distance: 146 - 147: 16.483 distance: 147 - 148: 14.417 distance: 147 - 149: 13.483 distance: 150 - 151: 3.938 distance: 151 - 152: 4.689 distance: 151 - 154: 4.379 distance: 152 - 153: 4.876 distance: 152 - 156: 9.846 distance: 154 - 155: 6.319 distance: 156 - 157: 30.891 distance: 157 - 158: 10.525 distance: 158 - 159: 8.929 distance: 158 - 160: 12.349