Starting phenix.real_space_refine on Wed Jul 30 20:25:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ijv_60644/07_2025/9ijv_60644.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ijv_60644/07_2025/9ijv_60644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ijv_60644/07_2025/9ijv_60644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ijv_60644/07_2025/9ijv_60644.map" model { file = "/net/cci-nas-00/data/ceres_data/9ijv_60644/07_2025/9ijv_60644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ijv_60644/07_2025/9ijv_60644.cif" } resolution = 2.42 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= -0.000 sd= 0.102 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 4 9.91 5 S 88 5.16 5 C 7845 2.51 5 N 2155 2.21 5 O 2648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12740 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2986 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2990 Classifications: {'peptide': 387} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "C" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2990 Classifications: {'peptide': 387} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "D" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2990 Classifications: {'peptide': 387} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.23, per 1000 atoms: 0.65 Number of scatterers: 12740 At special positions: 0 Unit cell: (75.328, 107.856, 111.28, 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 4 19.99 S 88 16.00 O 2648 8.00 N 2155 7.00 C 7845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.02 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.02 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.02 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 175 " - pdb=" SG CYS C 193 " distance=2.02 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.02 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.01 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.04 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.06 Simple disulfide: pdb=" SG CYS D 175 " - pdb=" SG CYS D 193 " distance=2.02 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.02 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.03 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 H 4 " - " MAN H 5 " " MAN L 4 " - " MAN L 5 " " MAN P 4 " - " MAN P 5 " " MAN T 4 " - " MAN T 5 " ALPHA1-3 " BMA H 3 " - " MAN H 4 " " MAN H 6 " - " MAN H 7 " " BMA L 3 " - " MAN L 4 " " MAN L 6 " - " MAN L 7 " " BMA P 3 " - " MAN P 4 " " MAN P 6 " - " MAN P 7 " " BMA T 3 " - " MAN T 4 " " MAN T 6 " - " MAN T 7 " ALPHA1-6 " BMA H 3 " - " MAN H 6 " " BMA L 3 " - " MAN L 6 " " BMA P 3 " - " MAN P 6 " " BMA T 3 " - " MAN T 6 " BETA1-4 " 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 H 2 " - " BMA H 3 " " 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 L 2 " - " BMA L 3 " " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " 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-ASN " NAG A 501 " - " ASN A 86 " " NAG A 502 " - " ASN A 234 " " NAG B 501 " - " ASN B 86 " " NAG B 502 " - " ASN B 234 " " NAG C 501 " - " ASN C 86 " " NAG C 502 " - " ASN C 234 " " NAG D 501 " - " ASN D 86 " " NAG D 502 " - " ASN D 234 " " NAG E 1 " - " ASN A 146 " " NAG F 1 " - " ASN A 367 " " NAG G 1 " - " ASN A 329 " " NAG H 1 " - " ASN A 200 " " NAG I 1 " - " ASN B 146 " " NAG J 1 " - " ASN B 367 " " NAG K 1 " - " ASN B 329 " " NAG L 1 " - " ASN B 200 " " NAG M 1 " - " ASN C 146 " " NAG N 1 " - " ASN C 367 " " NAG O 1 " - " ASN C 329 " " NAG P 1 " - " ASN C 200 " " NAG Q 1 " - " ASN D 146 " " NAG R 1 " - " ASN D 367 " " NAG S 1 " - " ASN D 329 " " NAG T 1 " - " ASN D 200 " Time building additional restraints: 3.96 Conformation dependent library (CDL) restraints added in 1.8 seconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2792 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 24 sheets defined 3.2% alpha, 41.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 104 through 111 removed outlier: 4.471A pdb=" N GLY A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.584A pdb=" N ASN A 146 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 removed outlier: 3.572A pdb=" N ALA B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.522A pdb=" N ASN B 146 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 110 removed outlier: 3.604A pdb=" N ALA C 110 " --> pdb=" O ILE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.538A pdb=" N ALA D 110 " --> pdb=" O ILE D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.661A pdb=" N ASN D 146 " --> pdb=" O VAL D 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 5.373A pdb=" N PHE A 97 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR A 449 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N CYS A 447 " --> pdb=" O PRO A 99 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.704A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 157 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N CYS A 175 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N MET A 160 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLN A 173 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.644A pdb=" N ALA A 201 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL A 216 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA A 203 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER A 214 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N PHE A 205 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 removed outlier: 3.775A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.457A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.499A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ASP A 402 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N GLU A 375 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 10.421A pdb=" N ARG A 400 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 11.318A pdb=" N PHE A 377 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 13.266A pdb=" N VAL A 398 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 15.896A pdb=" N VAL A 379 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 16.232A pdb=" N VAL A 396 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 102 removed outlier: 5.197A pdb=" N PHE B 97 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N THR B 449 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N CYS B 447 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.782A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 158 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS B 172 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.534A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.772A pdb=" N VAL B 231 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.617A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 311 " --> pdb=" O ASN B 306 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.545A pdb=" N TRP B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B 363 " --> pdb=" O TRP B 352 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU B 372 " --> pdb=" O ASP B 399 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP B 399 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS B 378 " --> pdb=" O ASN B 393 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ASN B 393 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 102 removed outlier: 3.698A pdb=" N GLY C 96 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL C 445 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS C 102 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ARG C 420 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.712A pdb=" N TRP C 115 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N THR C 138 " --> pdb=" O TRP C 115 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N THR C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN C 136 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C 157 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C 158 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS C 172 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 179 through 184 removed outlier: 6.421A pdb=" N TYR C 207 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU C 211 " --> pdb=" O TYR C 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 231 through 233 removed outlier: 3.691A pdb=" N VAL C 231 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU C 258 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ILE C 262 " --> pdb=" O GLU C 258 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 276 through 283 removed outlier: 5.400A pdb=" N GLU C 277 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG C 292 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 353 through 356 removed outlier: 6.794A pdb=" N LEU C 372 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASP C 399 " --> pdb=" O LEU C 372 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TYR C 374 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS C 378 " --> pdb=" O ASN C 393 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASN C 393 " --> pdb=" O LYS C 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 96 through 102 removed outlier: 3.667A pdb=" N GLY D 96 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL D 445 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS D 102 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG D 420 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.735A pdb=" N TRP D 115 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N THR D 138 " --> pdb=" O TRP D 115 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N THR D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN D 136 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR D 157 " --> pdb=" O GLY D 135 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU D 158 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS D 172 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 179 through 184 removed outlier: 4.185A pdb=" N ASP D 197 " --> pdb=" O ASN D 200 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TYR D 207 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 231 through 233 removed outlier: 3.711A pdb=" N VAL D 231 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 276 through 283 removed outlier: 5.358A pdb=" N GLU D 277 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ARG D 292 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 352 through 356 removed outlier: 4.491A pdb=" N TRP D 352 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY D 363 " --> pdb=" O TRP D 352 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU D 372 " --> pdb=" O ASP D 399 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASP D 399 " --> pdb=" O LEU D 372 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR D 374 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS D 378 " --> pdb=" O ASN D 393 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASN D 393 " --> pdb=" O LYS D 378 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1026 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: 3.84 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2125 1.31 - 1.45: 3784 1.45 - 1.58: 6991 1.58 - 1.71: 0 1.71 - 1.84: 104 Bond restraints: 13004 Sorted by residual: bond pdb=" CA SER C 315 " pdb=" CB SER C 315 " ideal model delta sigma weight residual 1.538 1.464 0.074 1.22e-02 6.72e+03 3.72e+01 bond pdb=" C ASN D 200 " pdb=" O ASN D 200 " ideal model delta sigma weight residual 1.236 1.185 0.050 8.80e-03 1.29e+04 3.25e+01 bond pdb=" C VAL D 349 " pdb=" O VAL D 349 " ideal model delta sigma weight residual 1.235 1.181 0.054 1.02e-02 9.61e+03 2.80e+01 bond pdb=" CA SER C 298 " pdb=" CB SER C 298 " ideal model delta sigma weight residual 1.537 1.469 0.068 1.41e-02 5.03e+03 2.30e+01 bond pdb=" C THR C 236 " pdb=" O THR C 236 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.22e-02 6.72e+03 2.09e+01 ... (remaining 12999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 16909 2.96 - 5.92: 616 5.92 - 8.89: 84 8.89 - 11.85: 25 11.85 - 14.81: 10 Bond angle restraints: 17644 Sorted by residual: angle pdb=" N PRO B 386 " pdb=" CA PRO B 386 " pdb=" C PRO B 386 " ideal model delta sigma weight residual 111.41 96.60 14.81 1.50e+00 4.44e-01 9.75e+01 angle pdb=" N SER C 298 " pdb=" CA SER C 298 " pdb=" C SER C 298 " ideal model delta sigma weight residual 114.12 101.35 12.77 1.39e+00 5.18e-01 8.44e+01 angle pdb=" N PRO A 386 " pdb=" CA PRO A 386 " pdb=" C PRO A 386 " ideal model delta sigma weight residual 111.22 98.44 12.78 1.40e+00 5.10e-01 8.34e+01 angle pdb=" N THR A 95 " pdb=" CA THR A 95 " pdb=" C THR A 95 " ideal model delta sigma weight residual 113.97 103.00 10.97 1.28e+00 6.10e-01 7.34e+01 angle pdb=" N PRO C 386 " pdb=" CA PRO C 386 " pdb=" C PRO C 386 " ideal model delta sigma weight residual 111.19 98.47 12.72 1.57e+00 4.06e-01 6.57e+01 ... (remaining 17639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.12: 7855 24.12 - 48.23: 507 48.23 - 72.35: 80 72.35 - 96.46: 39 96.46 - 120.58: 35 Dihedral angle restraints: 8516 sinusoidal: 4132 harmonic: 4384 Sorted by residual: dihedral pdb=" CB CYS B 183 " pdb=" SG CYS B 183 " pdb=" SG CYS B 230 " pdb=" CB CYS B 230 " ideal model delta sinusoidal sigma weight residual -86.00 -170.97 84.97 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS C 183 " pdb=" SG CYS C 183 " pdb=" SG CYS C 230 " pdb=" CB CYS C 230 " ideal model delta sinusoidal sigma weight residual -86.00 -170.48 84.48 1 1.00e+01 1.00e-02 8.68e+01 dihedral pdb=" CB CYS D 183 " pdb=" SG CYS D 183 " pdb=" SG CYS D 230 " pdb=" CB CYS D 230 " ideal model delta sinusoidal sigma weight residual -86.00 -165.96 79.96 1 1.00e+01 1.00e-02 7.93e+01 ... (remaining 8513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 1984 0.164 - 0.327: 84 0.327 - 0.491: 20 0.491 - 0.654: 9 0.654 - 0.818: 3 Chirality restraints: 2100 Sorted by residual: chirality pdb=" C1 MAN T 6 " pdb=" O6 BMA T 3 " pdb=" C2 MAN T 6 " pdb=" O5 MAN T 6 " both_signs ideal model delta sigma weight residual False 2.40 1.58 0.82 2.00e-02 2.50e+03 1.67e+03 chirality pdb=" C1 MAN P 5 " pdb=" O2 MAN P 4 " pdb=" C2 MAN P 5 " pdb=" O5 MAN P 5 " both_signs ideal model delta sigma weight residual False 2.40 1.66 0.74 2.00e-02 2.50e+03 1.39e+03 chirality pdb=" C1 MAN H 5 " pdb=" O2 MAN H 4 " pdb=" C2 MAN H 5 " pdb=" O5 MAN H 5 " both_signs ideal model delta sigma weight residual False 2.40 1.76 0.64 2.00e-02 2.50e+03 1.03e+03 ... (remaining 2097 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " 0.305 2.00e-02 2.50e+03 2.68e-01 8.98e+02 pdb=" C7 NAG R 1 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " 0.081 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " -0.480 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " 0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " 0.312 2.00e-02 2.50e+03 2.64e-01 8.69e+02 pdb=" C7 NAG N 2 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " -0.455 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " -0.282 2.00e-02 2.50e+03 2.39e-01 7.17e+02 pdb=" C7 NAG J 1 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " -0.177 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " 0.412 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " -0.027 2.00e-02 2.50e+03 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 117 2.55 - 3.14: 9698 3.14 - 3.72: 21322 3.72 - 4.31: 33164 4.31 - 4.90: 52504 Nonbonded interactions: 116805 Sorted by model distance: nonbonded pdb=" O ASP A 293 " pdb="CA CA A 503 " model vdw 1.958 2.510 nonbonded pdb=" O ASP D 293 " pdb="CA CA D 503 " model vdw 1.981 2.510 nonbonded pdb=" O HIS A 347 " pdb="CA CA A 503 " model vdw 2.046 2.510 nonbonded pdb=" O GLY D 345 " pdb="CA CA D 503 " model vdw 2.065 2.510 nonbonded pdb=" OG SER C 334 " pdb=" OE2 GLU C 343 " model vdw 2.118 3.040 ... (remaining 116800 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 83 through 430 or (resid 431 and (name N or name CA or nam \ e C or name O or name CB )) or resid 432 through 469 or resid 501 through 503)) selection = (chain 'C' and (resid 83 through 430 or (resid 431 and (name N or name CA or nam \ e C or name O or name CB )) or resid 432 through 469 or resid 501 through 503)) selection = (chain 'D' and (resid 83 through 430 or (resid 431 and (name N or name CA or nam \ e C or name O or name CB )) or resid 432 through 469 or resid 501 through 503)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'H' selection = chain 'L' selection = chain 'P' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 31.630 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 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:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 : 0.008 0.076 13100 Z= 0.484 Angle : 1.399 27.116 17896 Z= 0.748 Chirality : 0.092 0.818 2100 Planarity : 0.022 0.432 2196 Dihedral : 17.908 120.581 5616 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.64 % Favored : 96.23 % Rotamer: Outliers : 0.30 % Allowed : 14.77 % Favored : 84.93 % Cbeta Deviations : 1.07 % Peptide Plane: Cis-proline : 14.29 % 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: -0.55 (0.21), residues: 1540 helix: -0.75 (0.92), residues: 24 sheet: 0.11 (0.22), residues: 596 loop : -0.65 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 178 HIS 0.007 0.001 HIS A 310 PHE 0.013 0.002 PHE A 354 TYR 0.014 0.002 TYR B 155 ARG 0.008 0.001 ARG A 150 Details of bonding type rmsd link_NAG-ASN : bond 0.01804 ( 24) link_NAG-ASN : angle 5.64964 ( 72) link_ALPHA1-6 : bond 0.04966 ( 4) link_ALPHA1-6 : angle 8.09308 ( 12) link_BETA1-4 : bond 0.01587 ( 20) link_BETA1-4 : angle 4.89523 ( 60) link_ALPHA1-2 : bond 0.00292 ( 4) link_ALPHA1-2 : angle 4.19647 ( 12) link_ALPHA1-3 : bond 0.02292 ( 8) link_ALPHA1-3 : angle 9.18896 ( 24) hydrogen bonds : bond 0.20493 ( 367) hydrogen bonds : angle 9.20697 ( 1026) SS BOND : bond 0.00698 ( 36) SS BOND : angle 1.38737 ( 72) covalent geometry : bond 0.00765 (13004) covalent geometry : angle 1.26274 (17644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 225 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7406 (m-30) cc_final: 0.7120 (m-30) REVERT: A 381 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7591 (mm-30) REVERT: A 415 LYS cc_start: 0.7899 (tttp) cc_final: 0.7377 (mtmt) REVERT: B 399 ASP cc_start: 0.7994 (t70) cc_final: 0.7722 (t70) REVERT: B 416 SER cc_start: 0.8026 (p) cc_final: 0.7551 (m) REVERT: B 465 ASN cc_start: 0.8257 (t0) cc_final: 0.8025 (m110) REVERT: C 150 ARG cc_start: 0.7241 (ttt180) cc_final: 0.6868 (mtm180) REVERT: C 313 VAL cc_start: 0.8605 (t) cc_final: 0.8365 (m) REVERT: C 415 LYS cc_start: 0.8392 (tttt) cc_final: 0.8105 (ttmp) REVERT: D 308 LYS cc_start: 0.8054 (mtmt) cc_final: 0.7708 (mtpt) REVERT: D 368 GLU cc_start: 0.8046 (mp0) cc_final: 0.7829 (mp0) REVERT: D 431 LYS cc_start: 0.7212 (tppt) cc_final: 0.6790 (tptp) REVERT: D 465 ASN cc_start: 0.8021 (m-40) cc_final: 0.7764 (p0) outliers start: 4 outliers final: 2 residues processed: 227 average time/residue: 1.3677 time to fit residues: 337.4398 Evaluate side-chains 142 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 465 ASN Chi-restraints excluded: chain D residue 307 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 HIS A 393 ASN B 306 ASN B 385 ASN C 161 ASN C 465 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.128935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.103695 restraints weight = 12866.628| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.69 r_work: 0.3078 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13100 Z= 0.240 Angle : 0.903 19.867 17896 Z= 0.423 Chirality : 0.054 0.356 2100 Planarity : 0.005 0.041 2196 Dihedral : 13.017 109.667 2900 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 2.38 % Allowed : 15.22 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.39 (0.21), residues: 1540 helix: -0.91 (0.86), residues: 24 sheet: 0.30 (0.21), residues: 604 loop : -0.61 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 115 HIS 0.006 0.001 HIS D 144 PHE 0.016 0.002 PHE B 354 TYR 0.016 0.003 TYR B 121 ARG 0.007 0.001 ARG A 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00625 ( 24) link_NAG-ASN : angle 4.74613 ( 72) link_ALPHA1-6 : bond 0.00793 ( 4) link_ALPHA1-6 : angle 2.49933 ( 12) link_BETA1-4 : bond 0.01112 ( 20) link_BETA1-4 : angle 3.81550 ( 60) link_ALPHA1-2 : bond 0.01219 ( 4) link_ALPHA1-2 : angle 2.30631 ( 12) link_ALPHA1-3 : bond 0.00639 ( 8) link_ALPHA1-3 : angle 5.48202 ( 24) hydrogen bonds : bond 0.05321 ( 367) hydrogen bonds : angle 7.48075 ( 1026) SS BOND : bond 0.00484 ( 36) SS BOND : angle 1.43610 ( 72) covalent geometry : bond 0.00515 (13004) covalent geometry : angle 0.79303 (17644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8858 (mt0) REVERT: A 210 ARG cc_start: 0.8474 (ptp90) cc_final: 0.8268 (ptp-110) REVERT: A 343 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7695 (mt-10) REVERT: A 381 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7465 (mm-30) REVERT: A 415 LYS cc_start: 0.8398 (tttp) cc_final: 0.7610 (mtmt) REVERT: B 273 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: B 416 SER cc_start: 0.7752 (p) cc_final: 0.7453 (m) REVERT: B 465 ASN cc_start: 0.8340 (t0) cc_final: 0.8055 (m110) REVERT: C 127 ASP cc_start: 0.7805 (m-30) cc_final: 0.7599 (m-30) REVERT: C 150 ARG cc_start: 0.7268 (ttt180) cc_final: 0.6766 (mtm180) REVERT: C 210 ARG cc_start: 0.8792 (ptp90) cc_final: 0.8591 (ptp-110) REVERT: C 261 LYS cc_start: 0.8313 (ttmm) cc_final: 0.7998 (tptp) REVERT: C 399 ASP cc_start: 0.8128 (t70) cc_final: 0.7779 (m-30) REVERT: C 415 LYS cc_start: 0.8545 (tttt) cc_final: 0.8185 (tttp) REVERT: D 368 GLU cc_start: 0.8169 (mp0) cc_final: 0.7901 (mp0) REVERT: D 387 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8224 (ttmm) REVERT: D 465 ASN cc_start: 0.8397 (m-40) cc_final: 0.7847 (p0) outliers start: 32 outliers final: 11 residues processed: 171 average time/residue: 1.3569 time to fit residues: 251.6221 Evaluate side-chains 138 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 387 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 39 optimal weight: 0.8980 chunk 112 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 111 optimal weight: 0.5980 chunk 149 optimal weight: 0.0570 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 HIS B 147 ASN ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 HIS B 358 ASN C 465 ASN D 147 ASN D 273 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.136653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.113003 restraints weight = 13032.457| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.55 r_work: 0.3239 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13100 Z= 0.133 Angle : 0.746 12.078 17896 Z= 0.348 Chirality : 0.049 0.358 2100 Planarity : 0.003 0.042 2196 Dihedral : 11.555 98.575 2898 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.73 % Favored : 97.21 % Rotamer: Outliers : 1.41 % Allowed : 17.07 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.43 (0.21), residues: 1540 helix: 0.13 (0.91), residues: 28 sheet: 0.19 (0.22), residues: 572 loop : -0.57 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 178 HIS 0.004 0.001 HIS B 184 PHE 0.012 0.002 PHE B 354 TYR 0.014 0.002 TYR D 121 ARG 0.006 0.000 ARG A 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 24) link_NAG-ASN : angle 3.22447 ( 72) link_ALPHA1-6 : bond 0.00724 ( 4) link_ALPHA1-6 : angle 1.54955 ( 12) link_BETA1-4 : bond 0.01141 ( 20) link_BETA1-4 : angle 3.43886 ( 60) link_ALPHA1-2 : bond 0.01423 ( 4) link_ALPHA1-2 : angle 2.00932 ( 12) link_ALPHA1-3 : bond 0.00508 ( 8) link_ALPHA1-3 : angle 4.94323 ( 24) hydrogen bonds : bond 0.04119 ( 367) hydrogen bonds : angle 7.04938 ( 1026) SS BOND : bond 0.00279 ( 36) SS BOND : angle 0.91295 ( 72) covalent geometry : bond 0.00272 (13004) covalent geometry : angle 0.66407 (17644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8584 (ptp90) cc_final: 0.8376 (ptp-110) REVERT: A 304 ASP cc_start: 0.8035 (m-30) cc_final: 0.7823 (m-30) REVERT: A 343 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7863 (mt-10) REVERT: A 381 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7517 (mp0) REVERT: A 415 LYS cc_start: 0.8321 (tttp) cc_final: 0.7661 (mtmt) REVERT: B 273 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7758 (mt0) REVERT: B 356 ASP cc_start: 0.8129 (t0) cc_final: 0.7928 (t0) REVERT: C 150 ARG cc_start: 0.7265 (ttt180) cc_final: 0.6840 (mtm180) REVERT: C 261 LYS cc_start: 0.8328 (ttmm) cc_final: 0.8049 (tptp) REVERT: C 399 ASP cc_start: 0.8093 (t70) cc_final: 0.7832 (m-30) REVERT: C 415 LYS cc_start: 0.8615 (tttt) cc_final: 0.8340 (ttpp) REVERT: C 432 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6627 (mp0) REVERT: D 387 LYS cc_start: 0.8340 (ttmm) cc_final: 0.8123 (mmtm) REVERT: D 435 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7756 (mp0) REVERT: D 465 ASN cc_start: 0.8366 (m-40) cc_final: 0.7811 (p0) outliers start: 19 outliers final: 7 residues processed: 153 average time/residue: 1.3079 time to fit residues: 218.1788 Evaluate side-chains 127 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 432 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 99 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 142 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 HIS B 91 GLN B 465 ASN D 391 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.127457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.102093 restraints weight = 12878.034| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.69 r_work: 0.3061 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13100 Z= 0.251 Angle : 0.837 13.767 17896 Z= 0.398 Chirality : 0.053 0.378 2100 Planarity : 0.004 0.042 2196 Dihedral : 11.936 103.028 2896 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.51 % Favored : 96.43 % Rotamer: Outliers : 2.52 % Allowed : 16.04 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.53 (0.20), residues: 1540 helix: -0.69 (0.88), residues: 24 sheet: 0.16 (0.21), residues: 608 loop : -0.67 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 178 HIS 0.004 0.001 HIS C 144 PHE 0.015 0.002 PHE C 97 TYR 0.016 0.002 TYR D 121 ARG 0.006 0.001 ARG A 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00515 ( 24) link_NAG-ASN : angle 3.84259 ( 72) link_ALPHA1-6 : bond 0.00481 ( 4) link_ALPHA1-6 : angle 1.97593 ( 12) link_BETA1-4 : bond 0.01040 ( 20) link_BETA1-4 : angle 3.59761 ( 60) link_ALPHA1-2 : bond 0.01509 ( 4) link_ALPHA1-2 : angle 2.14931 ( 12) link_ALPHA1-3 : bond 0.00429 ( 8) link_ALPHA1-3 : angle 4.99652 ( 24) hydrogen bonds : bond 0.04893 ( 367) hydrogen bonds : angle 7.26226 ( 1026) SS BOND : bond 0.00471 ( 36) SS BOND : angle 1.32082 ( 72) covalent geometry : bond 0.00548 (13004) covalent geometry : angle 0.74770 (17644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8800 (ptp90) cc_final: 0.8522 (ptp-110) REVERT: A 251 ASP cc_start: 0.8076 (m-30) cc_final: 0.7737 (m-30) REVERT: A 304 ASP cc_start: 0.8100 (m-30) cc_final: 0.7889 (m-30) REVERT: A 381 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7374 (mp0) REVERT: A 415 LYS cc_start: 0.8519 (tttp) cc_final: 0.7629 (mtmt) REVERT: B 128 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8297 (pttm) REVERT: B 356 ASP cc_start: 0.8216 (t0) cc_final: 0.8013 (t0) REVERT: B 416 SER cc_start: 0.7598 (p) cc_final: 0.7360 (m) REVERT: C 150 ARG cc_start: 0.7348 (ttt180) cc_final: 0.6731 (mtm180) REVERT: C 261 LYS cc_start: 0.8510 (ttmm) cc_final: 0.8197 (tptp) REVERT: C 399 ASP cc_start: 0.8156 (t70) cc_final: 0.7887 (m-30) REVERT: C 415 LYS cc_start: 0.8627 (tttt) cc_final: 0.8271 (tttp) REVERT: C 432 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: D 387 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8244 (mmtm) REVERT: D 435 GLU cc_start: 0.8092 (mp0) cc_final: 0.7762 (mp0) REVERT: D 465 ASN cc_start: 0.8414 (m-40) cc_final: 0.7802 (p0) outliers start: 34 outliers final: 16 residues processed: 149 average time/residue: 1.2675 time to fit residues: 207.2311 Evaluate side-chains 134 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 387 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 114 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 111 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 125 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 HIS B 391 GLN B 465 ASN D 273 GLN D 347 HIS D 391 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.127863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.102551 restraints weight = 12944.020| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.69 r_work: 0.3067 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13100 Z= 0.224 Angle : 0.803 11.758 17896 Z= 0.383 Chirality : 0.051 0.359 2100 Planarity : 0.004 0.043 2196 Dihedral : 11.780 101.649 2896 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.62 % Rotamer: Outliers : 2.52 % Allowed : 16.56 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.58 (0.20), residues: 1540 helix: -0.70 (0.88), residues: 24 sheet: 0.13 (0.21), residues: 608 loop : -0.71 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 178 HIS 0.003 0.001 HIS D 144 PHE 0.014 0.002 PHE A 354 TYR 0.016 0.002 TYR B 121 ARG 0.005 0.001 ARG A 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 24) link_NAG-ASN : angle 3.45489 ( 72) link_ALPHA1-6 : bond 0.00426 ( 4) link_ALPHA1-6 : angle 1.76099 ( 12) link_BETA1-4 : bond 0.01017 ( 20) link_BETA1-4 : angle 3.45368 ( 60) link_ALPHA1-2 : bond 0.01453 ( 4) link_ALPHA1-2 : angle 2.12908 ( 12) link_ALPHA1-3 : bond 0.00459 ( 8) link_ALPHA1-3 : angle 4.90381 ( 24) hydrogen bonds : bond 0.04601 ( 367) hydrogen bonds : angle 7.11774 ( 1026) SS BOND : bond 0.00416 ( 36) SS BOND : angle 1.24208 ( 72) covalent geometry : bond 0.00484 (13004) covalent geometry : angle 0.72182 (17644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8825 (ptp90) cc_final: 0.8548 (ptp-170) REVERT: A 251 ASP cc_start: 0.8079 (m-30) cc_final: 0.7734 (m-30) REVERT: A 304 ASP cc_start: 0.8106 (m-30) cc_final: 0.7882 (m-30) REVERT: A 381 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7356 (mp0) REVERT: A 415 LYS cc_start: 0.8557 (tttp) cc_final: 0.7499 (mtmt) REVERT: B 273 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7799 (mt0) REVERT: B 416 SER cc_start: 0.7641 (p) cc_final: 0.7396 (m) REVERT: C 150 ARG cc_start: 0.7350 (ttt180) cc_final: 0.6758 (mtm180) REVERT: C 261 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8174 (tptp) REVERT: C 399 ASP cc_start: 0.8210 (t70) cc_final: 0.7994 (m-30) REVERT: C 415 LYS cc_start: 0.8673 (tttt) cc_final: 0.8321 (tttp) REVERT: C 432 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6564 (mp0) REVERT: D 400 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7564 (ttm-80) REVERT: D 435 GLU cc_start: 0.8084 (mp0) cc_final: 0.7721 (mp0) REVERT: D 465 ASN cc_start: 0.8413 (m-40) cc_final: 0.7806 (p0) outliers start: 34 outliers final: 19 residues processed: 149 average time/residue: 1.3694 time to fit residues: 224.7294 Evaluate side-chains 142 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 400 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 133 optimal weight: 0.0030 overall best weight: 1.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN A 336 HIS ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN D 347 HIS D 391 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.107277 restraints weight = 13073.467| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.61 r_work: 0.3147 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13100 Z= 0.173 Angle : 0.763 11.818 17896 Z= 0.361 Chirality : 0.050 0.343 2100 Planarity : 0.004 0.044 2196 Dihedral : 11.392 98.037 2896 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.44 % Favored : 96.49 % Rotamer: Outliers : 2.23 % Allowed : 17.52 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.55 (0.20), residues: 1540 helix: -0.25 (0.85), residues: 28 sheet: 0.14 (0.21), residues: 608 loop : -0.69 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 178 HIS 0.003 0.001 HIS D 184 PHE 0.013 0.002 PHE A 354 TYR 0.014 0.002 TYR B 121 ARG 0.006 0.000 ARG A 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 24) link_NAG-ASN : angle 3.45547 ( 72) link_ALPHA1-6 : bond 0.00473 ( 4) link_ALPHA1-6 : angle 1.46765 ( 12) link_BETA1-4 : bond 0.01050 ( 20) link_BETA1-4 : angle 3.31663 ( 60) link_ALPHA1-2 : bond 0.01409 ( 4) link_ALPHA1-2 : angle 2.12729 ( 12) link_ALPHA1-3 : bond 0.00442 ( 8) link_ALPHA1-3 : angle 4.74088 ( 24) hydrogen bonds : bond 0.04146 ( 367) hydrogen bonds : angle 6.94335 ( 1026) SS BOND : bond 0.00340 ( 36) SS BOND : angle 1.02894 ( 72) covalent geometry : bond 0.00367 (13004) covalent geometry : angle 0.68239 (17644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 4.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7968 (m-30) cc_final: 0.7650 (m-30) REVERT: A 304 ASP cc_start: 0.8111 (m-30) cc_final: 0.7892 (m-30) REVERT: A 381 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7487 (mp0) REVERT: A 415 LYS cc_start: 0.8535 (tttp) cc_final: 0.7543 (mtmt) REVERT: A 465 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7906 (m-40) REVERT: B 128 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8327 (pttm) REVERT: B 273 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7787 (mt0) REVERT: C 150 ARG cc_start: 0.7333 (ttt180) cc_final: 0.6824 (mtm180) REVERT: C 261 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8220 (tptp) REVERT: C 415 LYS cc_start: 0.8702 (tttt) cc_final: 0.8380 (tttp) REVERT: C 432 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6510 (mp0) REVERT: D 465 ASN cc_start: 0.8415 (m-40) cc_final: 0.7867 (p0) outliers start: 30 outliers final: 16 residues processed: 149 average time/residue: 1.6205 time to fit residues: 263.4733 Evaluate side-chains 141 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 34 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 140 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 113 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 HIS ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 HIS D 391 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.133725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.109161 restraints weight = 12730.060| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.60 r_work: 0.3174 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13100 Z= 0.145 Angle : 0.780 22.330 17896 Z= 0.364 Chirality : 0.062 1.565 2100 Planarity : 0.004 0.045 2196 Dihedral : 11.189 95.776 2896 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.36 % Rotamer: Outliers : 1.86 % Allowed : 18.49 % Favored : 79.66 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 14.29 % 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: -0.51 (0.21), residues: 1540 helix: 0.09 (0.91), residues: 28 sheet: 0.15 (0.21), residues: 608 loop : -0.67 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 87 HIS 0.003 0.001 HIS B 184 PHE 0.012 0.002 PHE A 354 TYR 0.014 0.002 TYR D 121 ARG 0.014 0.000 ARG A 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 24) link_NAG-ASN : angle 3.55925 ( 72) link_ALPHA1-6 : bond 0.00522 ( 4) link_ALPHA1-6 : angle 1.31644 ( 12) link_BETA1-4 : bond 0.01070 ( 20) link_BETA1-4 : angle 3.20704 ( 60) link_ALPHA1-2 : bond 0.01451 ( 4) link_ALPHA1-2 : angle 2.18182 ( 12) link_ALPHA1-3 : bond 0.00473 ( 8) link_ALPHA1-3 : angle 4.64431 ( 24) hydrogen bonds : bond 0.03816 ( 367) hydrogen bonds : angle 6.81540 ( 1026) SS BOND : bond 0.00277 ( 36) SS BOND : angle 0.88216 ( 72) covalent geometry : bond 0.00302 (13004) covalent geometry : angle 0.70286 (17644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7912 (m-30) cc_final: 0.7602 (m-30) REVERT: A 304 ASP cc_start: 0.8100 (m-30) cc_final: 0.7881 (m-30) REVERT: A 381 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7479 (mp0) REVERT: A 415 LYS cc_start: 0.8531 (tttp) cc_final: 0.7539 (mtmt) REVERT: B 128 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8311 (pttm) REVERT: B 273 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7775 (mt0) REVERT: C 150 ARG cc_start: 0.7306 (ttt180) cc_final: 0.6781 (mtm180) REVERT: C 261 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8102 (tptp) REVERT: C 415 LYS cc_start: 0.8741 (tttt) cc_final: 0.8472 (tttp) REVERT: C 432 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6483 (mp0) REVERT: D 465 ASN cc_start: 0.8413 (m-40) cc_final: 0.7854 (p0) outliers start: 25 outliers final: 18 residues processed: 145 average time/residue: 1.7884 time to fit residues: 283.1549 Evaluate side-chains 141 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 9 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 102 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 HIS ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN D 347 HIS D 391 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.132855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.107987 restraints weight = 12883.819| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.62 r_work: 0.3155 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13100 Z= 0.173 Angle : 0.769 11.025 17896 Z= 0.363 Chirality : 0.053 0.848 2100 Planarity : 0.004 0.046 2196 Dihedral : 11.172 93.456 2896 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.36 % Rotamer: Outliers : 2.45 % Allowed : 18.11 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.53 (0.20), residues: 1540 helix: -0.10 (0.86), residues: 28 sheet: 0.13 (0.21), residues: 608 loop : -0.68 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 87 HIS 0.003 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.014 0.002 TYR D 121 ARG 0.009 0.000 ARG A 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 24) link_NAG-ASN : angle 3.61649 ( 72) link_ALPHA1-6 : bond 0.00442 ( 4) link_ALPHA1-6 : angle 1.46935 ( 12) link_BETA1-4 : bond 0.01045 ( 20) link_BETA1-4 : angle 3.26351 ( 60) link_ALPHA1-2 : bond 0.01497 ( 4) link_ALPHA1-2 : angle 2.26158 ( 12) link_ALPHA1-3 : bond 0.00433 ( 8) link_ALPHA1-3 : angle 4.66872 ( 24) hydrogen bonds : bond 0.04040 ( 367) hydrogen bonds : angle 6.84787 ( 1026) SS BOND : bond 0.00323 ( 36) SS BOND : angle 1.00220 ( 72) covalent geometry : bond 0.00367 (13004) covalent geometry : angle 0.68647 (17644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7958 (m-30) cc_final: 0.7636 (m-30) REVERT: A 304 ASP cc_start: 0.8092 (m-30) cc_final: 0.7873 (m-30) REVERT: A 381 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7484 (mp0) REVERT: A 415 LYS cc_start: 0.8546 (tttp) cc_final: 0.7530 (mtmt) REVERT: A 465 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7864 (m-40) REVERT: B 128 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8366 (pttm) REVERT: B 416 SER cc_start: 0.7458 (p) cc_final: 0.7255 (m) REVERT: C 150 ARG cc_start: 0.7315 (ttt180) cc_final: 0.6788 (mtm180) REVERT: C 261 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8220 (tptp) REVERT: C 415 LYS cc_start: 0.8760 (tttt) cc_final: 0.8476 (tttp) REVERT: C 432 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6491 (mp0) REVERT: D 465 ASN cc_start: 0.8416 (m-40) cc_final: 0.7869 (p0) outliers start: 33 outliers final: 22 residues processed: 145 average time/residue: 1.2277 time to fit residues: 195.0017 Evaluate side-chains 143 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 121 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 96 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 ASN ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN D 347 HIS D 391 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.134568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.109987 restraints weight = 12850.553| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.62 r_work: 0.3184 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13100 Z= 0.140 Angle : 0.734 10.555 17896 Z= 0.346 Chirality : 0.051 0.721 2100 Planarity : 0.003 0.046 2196 Dihedral : 10.930 90.683 2896 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.77 % Favored : 96.17 % Rotamer: Outliers : 2.00 % Allowed : 18.78 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.61 (0.20), residues: 1540 helix: 0.13 (0.90), residues: 28 sheet: 0.05 (0.22), residues: 576 loop : -0.69 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 87 HIS 0.003 0.001 HIS B 184 PHE 0.013 0.002 PHE A 354 TYR 0.013 0.002 TYR D 121 ARG 0.009 0.000 ARG A 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 24) link_NAG-ASN : angle 3.23072 ( 72) link_ALPHA1-6 : bond 0.00484 ( 4) link_ALPHA1-6 : angle 1.33693 ( 12) link_BETA1-4 : bond 0.01043 ( 20) link_BETA1-4 : angle 3.09868 ( 60) link_ALPHA1-2 : bond 0.01456 ( 4) link_ALPHA1-2 : angle 2.26900 ( 12) link_ALPHA1-3 : bond 0.00459 ( 8) link_ALPHA1-3 : angle 4.56630 ( 24) hydrogen bonds : bond 0.03720 ( 367) hydrogen bonds : angle 6.70296 ( 1026) SS BOND : bond 0.00275 ( 36) SS BOND : angle 1.06813 ( 72) covalent geometry : bond 0.00293 (13004) covalent geometry : angle 0.65854 (17644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7920 (m-30) cc_final: 0.7619 (m-30) REVERT: A 304 ASP cc_start: 0.8077 (m-30) cc_final: 0.7863 (m-30) REVERT: A 381 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7484 (mp0) REVERT: A 390 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8418 (mp) REVERT: A 415 LYS cc_start: 0.8506 (tttp) cc_final: 0.7517 (mtmt) REVERT: B 128 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8326 (pttm) REVERT: C 150 ARG cc_start: 0.7279 (ttt180) cc_final: 0.6776 (mtm180) REVERT: C 261 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8069 (tptp) REVERT: C 415 LYS cc_start: 0.8764 (tttt) cc_final: 0.8481 (tttp) REVERT: C 432 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6485 (mp0) REVERT: D 375 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8189 (pt0) REVERT: D 465 ASN cc_start: 0.8422 (m-40) cc_final: 0.7873 (p0) outliers start: 27 outliers final: 18 residues processed: 142 average time/residue: 1.2582 time to fit residues: 195.4736 Evaluate side-chains 139 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 375 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 60 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN C 347 HIS D 141 ASN D 347 HIS D 391 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.137528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.114710 restraints weight = 13626.488| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.51 r_work: 0.3258 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13100 Z= 0.169 Angle : 0.756 10.773 17896 Z= 0.359 Chirality : 0.052 0.582 2100 Planarity : 0.004 0.046 2196 Dihedral : 10.985 88.608 2896 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.00 % Allowed : 18.71 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.52 (0.20), residues: 1540 helix: -0.10 (0.85), residues: 28 sheet: 0.15 (0.21), residues: 608 loop : -0.68 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 87 HIS 0.003 0.001 HIS C 347 PHE 0.013 0.002 PHE A 354 TYR 0.014 0.002 TYR D 121 ARG 0.009 0.000 ARG A 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 24) link_NAG-ASN : angle 3.38348 ( 72) link_ALPHA1-6 : bond 0.00438 ( 4) link_ALPHA1-6 : angle 1.46782 ( 12) link_BETA1-4 : bond 0.01018 ( 20) link_BETA1-4 : angle 3.20519 ( 60) link_ALPHA1-2 : bond 0.01520 ( 4) link_ALPHA1-2 : angle 2.35924 ( 12) link_ALPHA1-3 : bond 0.00405 ( 8) link_ALPHA1-3 : angle 4.62113 ( 24) hydrogen bonds : bond 0.03993 ( 367) hydrogen bonds : angle 6.78732 ( 1026) SS BOND : bond 0.00330 ( 36) SS BOND : angle 1.13500 ( 72) covalent geometry : bond 0.00360 (13004) covalent geometry : angle 0.67723 (17644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7853 (m-30) cc_final: 0.7583 (m-30) REVERT: A 381 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7652 (mp0) REVERT: A 390 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8436 (mp) REVERT: A 415 LYS cc_start: 0.8486 (tttp) cc_final: 0.7541 (mtmt) REVERT: C 150 ARG cc_start: 0.7371 (ttt180) cc_final: 0.6857 (mtm180) REVERT: C 261 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8176 (tptp) REVERT: C 415 LYS cc_start: 0.8717 (tttt) cc_final: 0.8473 (tttp) REVERT: C 432 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: D 375 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8122 (pt0) REVERT: D 435 GLU cc_start: 0.7894 (mp0) cc_final: 0.7645 (mp0) REVERT: D 465 ASN cc_start: 0.8331 (m-40) cc_final: 0.7928 (p0) outliers start: 27 outliers final: 20 residues processed: 144 average time/residue: 1.3104 time to fit residues: 206.3991 Evaluate side-chains 137 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 375 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 12 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN C 347 HIS D 141 ASN D 347 HIS D 391 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.135682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.112826 restraints weight = 13497.891| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.50 r_work: 0.3232 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 13100 Z= 0.227 Angle : 0.824 12.949 17896 Z= 0.395 Chirality : 0.056 0.827 2100 Planarity : 0.004 0.045 2196 Dihedral : 11.248 87.772 2896 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.23 % Allowed : 18.71 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.59 (0.20), residues: 1540 helix: -0.64 (0.87), residues: 24 sheet: 0.12 (0.21), residues: 608 loop : -0.72 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 87 HIS 0.004 0.001 HIS C 347 PHE 0.013 0.002 PHE C 97 TYR 0.015 0.002 TYR B 121 ARG 0.009 0.001 ARG A 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 24) link_NAG-ASN : angle 3.50442 ( 72) link_ALPHA1-6 : bond 0.00386 ( 4) link_ALPHA1-6 : angle 1.69410 ( 12) link_BETA1-4 : bond 0.00988 ( 20) link_BETA1-4 : angle 3.34285 ( 60) link_ALPHA1-2 : bond 0.01584 ( 4) link_ALPHA1-2 : angle 2.43338 ( 12) link_ALPHA1-3 : bond 0.00403 ( 8) link_ALPHA1-3 : angle 4.76562 ( 24) hydrogen bonds : bond 0.04494 ( 367) hydrogen bonds : angle 6.97408 ( 1026) SS BOND : bond 0.00445 ( 36) SS BOND : angle 1.94205 ( 72) covalent geometry : bond 0.00494 (13004) covalent geometry : angle 0.74088 (17644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8927.48 seconds wall clock time: 160 minutes 56.37 seconds (9656.37 seconds total)