Starting phenix.real_space_refine on Fri Jul 3 06:59:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ijv_60644/07_2026/9ijv_60644.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ijv_60644/07_2026/9ijv_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ijv_60644/07_2026/9ijv_60644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ijv_60644/07_2026/9ijv_60644.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ijv_60644/07_2026/9ijv_60644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ijv_60644/07_2026/9ijv_60644.map" } resolution = 2.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 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, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.06, per 1000 atoms: 0.24 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: 1.23 Conformation dependent library (CDL) restraints added in 515.7 milliseconds 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: 0.37 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: 2.05 Time building geometry restraints manager: 1.59 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 3.250 nonbonded pdb=" O ASP D 293 " pdb="CA CA D 503 " model vdw 1.981 3.250 nonbonded pdb=" O HIS A 347 " pdb="CA CA A 503 " model vdw 2.046 3.250 nonbonded pdb=" O GLY D 345 " pdb="CA CA D 503 " model vdw 2.065 3.250 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 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 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 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: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.660 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 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:7.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 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 : 7.31 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.001 ARG A 150 TYR 0.014 0.002 TYR B 155 PHE 0.013 0.002 PHE A 354 TRP 0.015 0.002 TRP B 178 HIS 0.007 0.001 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00765 / 0.48 (13004) covalent geometry : angle 1.26274 / 0.72 (17644) SS BOND : bond 0.00698 / 0.40 ( 36) SS BOND : angle 1.38737 / 0.95 ( 72) hydrogen bonds : bond 0.20493 / 14.26 ( 367) hydrogen bonds : angle 9.20697 / 6.33 ( 1026) link_ALPHA1-2 : bond 0.00292 / 0.14 ( 4) link_ALPHA1-2 : angle 4.19647 / 2.22 ( 12) link_ALPHA1-3 : bond 0.02292 / 1.08 ( 8) link_ALPHA1-3 : angle 9.18896 / 4.64 ( 24) link_ALPHA1-6 : bond 0.04966 / 2.45 ( 4) link_ALPHA1-6 : angle 8.09308 / 4.36 ( 12) link_BETA1-4 : bond 0.01587 / 0.97 ( 20) link_BETA1-4 : angle 4.89523 / 3.11 ( 60) link_NAG-ASN : bond 0.01804 / 1.09 ( 24) link_NAG-ASN : angle 5.64964 / 4.03 ( 72) *********************** 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 : 0.487 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: 0.8258 (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: 0.6114 time to fit residues: 150.5814 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 : 0.452 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 HIS A 393 ASN B 147 ASN B 306 ASN B 385 ASN C 161 ASN C 465 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.136904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.113226 restraints weight = 12728.928| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.52 r_work: 0.3237 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1663 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= 0.175 Angle : 0.854 20.490 17896 Z= 0.395 Chirality : 0.052 0.372 2100 Planarity : 0.004 0.042 2196 Dihedral : 12.785 110.047 2900 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 1.86 % Allowed : 16.18 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.21), residues: 1540 helix: -0.07 (0.88), residues: 28 sheet: 0.35 (0.21), residues: 604 loop : -0.55 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 150 TYR 0.015 0.002 TYR B 121 PHE 0.016 0.002 PHE B 410 TRP 0.013 0.002 TRP A 178 HIS 0.004 0.001 HIS D 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (13004) covalent geometry : angle 0.74116 / 0.37 (17644) SS BOND : bond 0.00638 / 0.48 ( 36) SS BOND : angle 1.15499 / 0.82 ( 72) hydrogen bonds : bond 0.04761 / 3.26 ( 367) hydrogen bonds : angle 7.38397 / 5.07 ( 1026) link_ALPHA1-2 : bond 0.01189 / 0.60 ( 4) link_ALPHA1-2 : angle 2.22882 / 1.14 ( 12) link_ALPHA1-3 : bond 0.00739 / 0.35 ( 8) link_ALPHA1-3 : angle 5.36180 / 2.94 ( 24) link_ALPHA1-6 : bond 0.00981 / 0.49 ( 4) link_ALPHA1-6 : angle 2.18364 / 1.18 ( 12) link_BETA1-4 : bond 0.01108 / 0.69 ( 20) link_BETA1-4 : angle 3.77082 / 2.45 ( 60) link_NAG-ASN : bond 0.00636 / 0.33 ( 24) link_NAG-ASN : angle 4.69695 / 2.87 ( 72) *********************** 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 180 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7597 (mt-10) REVERT: A 381 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7540 (mp0) REVERT: A 415 LYS cc_start: 0.8357 (tttp) cc_final: 0.7617 (mtmt) REVERT: B 416 SER cc_start: 0.7628 (p) cc_final: 0.7379 (m) REVERT: B 465 ASN cc_start: 0.8255 (t0) cc_final: 0.8034 (m110) REVERT: C 127 ASP cc_start: 0.7750 (m-30) cc_final: 0.7543 (m-30) REVERT: C 150 ARG cc_start: 0.7237 (ttt180) cc_final: 0.6842 (mtm180) REVERT: C 210 ARG cc_start: 0.8695 (ptp90) cc_final: 0.8468 (ptp-110) REVERT: C 261 LYS cc_start: 0.8258 (ttmm) cc_final: 0.7969 (tptp) REVERT: C 399 ASP cc_start: 0.7999 (t70) cc_final: 0.7662 (m-30) REVERT: C 415 LYS cc_start: 0.8543 (tttt) cc_final: 0.8199 (tttp) REVERT: D 465 ASN cc_start: 0.8262 (m-40) cc_final: 0.7808 (p0) outliers start: 25 outliers final: 9 residues processed: 170 average time/residue: 0.5635 time to fit residues: 104.3121 Evaluate side-chains 133 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 LEU 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 148 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain D residue 314 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 0.0770 chunk 62 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 HIS B 147 ASN B 264 HIS C 465 ASN D 147 ASN D 347 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.137224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.113412 restraints weight = 12998.580| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.55 r_work: 0.3243 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13100 Z= 0.147 Angle : 0.750 12.310 17896 Z= 0.350 Chirality : 0.049 0.366 2100 Planarity : 0.003 0.042 2196 Dihedral : 11.537 100.127 2896 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.75 % Rotamer: Outliers : 2.38 % Allowed : 16.78 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.21), residues: 1540 helix: -0.50 (0.94), residues: 24 sheet: 0.16 (0.22), residues: 552 loop : -0.52 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 150 TYR 0.013 0.002 TYR D 121 PHE 0.013 0.002 PHE B 354 TRP 0.013 0.001 TRP C 178 HIS 0.003 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (13004) covalent geometry : angle 0.66690 / 0.33 (17644) SS BOND : bond 0.00312 / 0.21 ( 36) SS BOND : angle 0.85546 / 0.61 ( 72) hydrogen bonds : bond 0.04270 / 2.92 ( 367) hydrogen bonds : angle 7.04191 / 4.81 ( 1026) link_ALPHA1-2 : bond 0.01452 / 0.74 ( 4) link_ALPHA1-2 : angle 2.01355 / 1.06 ( 12) link_ALPHA1-3 : bond 0.00468 / 0.24 ( 8) link_ALPHA1-3 : angle 4.99060 / 2.76 ( 24) link_ALPHA1-6 : bond 0.00689 / 0.34 ( 4) link_ALPHA1-6 : angle 1.67129 / 0.89 ( 12) link_BETA1-4 : bond 0.01154 / 0.71 ( 20) link_BETA1-4 : angle 3.49642 / 2.24 ( 60) link_NAG-ASN : bond 0.00455 / 0.25 ( 24) link_NAG-ASN : angle 3.25011 / 2.11 ( 72) *********************** 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 168 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8024 (m-30) cc_final: 0.7778 (m-30) REVERT: A 343 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7841 (mt-10) REVERT: A 381 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7502 (mp0) REVERT: A 415 LYS cc_start: 0.8316 (tttp) cc_final: 0.7659 (mtmt) REVERT: B 465 ASN cc_start: 0.8253 (t0) cc_final: 0.8051 (m110) REVERT: C 150 ARG cc_start: 0.7258 (ttt180) cc_final: 0.6845 (mtm180) REVERT: C 261 LYS cc_start: 0.8286 (ttmm) cc_final: 0.8067 (tptp) REVERT: C 399 ASP cc_start: 0.8063 (t70) cc_final: 0.7753 (m-30) REVERT: C 415 LYS cc_start: 0.8614 (tttt) cc_final: 0.8317 (ttpp) REVERT: D 387 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8090 (mmtm) REVERT: D 465 ASN cc_start: 0.8329 (m-40) cc_final: 0.7766 (p0) outliers start: 32 outliers final: 10 residues processed: 156 average time/residue: 0.5963 time to fit residues: 101.3821 Evaluate side-chains 130 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 LEU 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 83 GLU Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 387 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 146 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 HIS B 91 GLN D 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.127319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.101870 restraints weight = 12792.137| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.67 r_work: 0.3054 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13100 Z= 0.287 Angle : 0.865 13.122 17896 Z= 0.413 Chirality : 0.054 0.382 2100 Planarity : 0.005 0.042 2196 Dihedral : 12.111 104.253 2896 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.30 % Rotamer: Outliers : 2.90 % Allowed : 16.56 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.20), residues: 1540 helix: -0.65 (0.89), residues: 24 sheet: 0.17 (0.21), residues: 580 loop : -0.63 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 156 TYR 0.016 0.003 TYR D 121 PHE 0.016 0.003 PHE C 97 TRP 0.018 0.002 TRP C 178 HIS 0.004 0.001 HIS D 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.29 (13004) covalent geometry : angle 0.77429 / 0.39 (17644) SS BOND : bond 0.00515 / 0.32 ( 36) SS BOND : angle 1.44628 / 1.02 ( 72) hydrogen bonds : bond 0.05151 / 3.55 ( 367) hydrogen bonds : angle 7.32773 / 5.00 ( 1026) link_ALPHA1-2 : bond 0.01512 / 0.77 ( 4) link_ALPHA1-2 : angle 2.20039 / 1.16 ( 12) link_ALPHA1-3 : bond 0.00456 / 0.24 ( 8) link_ALPHA1-3 : angle 5.10044 / 2.82 ( 24) link_ALPHA1-6 : bond 0.00440 / 0.21 ( 4) link_ALPHA1-6 : angle 2.17965 / 1.17 ( 12) link_BETA1-4 : bond 0.01049 / 0.66 ( 20) link_BETA1-4 : angle 3.64914 / 2.33 ( 60) link_NAG-ASN : bond 0.00658 / 0.38 ( 24) link_NAG-ASN : angle 3.95314 / 2.65 ( 72) *********************** 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 166 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8123 (m-30) cc_final: 0.7826 (m-30) REVERT: A 304 ASP cc_start: 0.8165 (m-30) cc_final: 0.7964 (m-30) REVERT: A 381 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7389 (mp0) REVERT: A 415 LYS cc_start: 0.8536 (tttp) cc_final: 0.7633 (mtmt) REVERT: B 128 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8287 (pttm) REVERT: B 416 SER cc_start: 0.7628 (p) cc_final: 0.7390 (m) REVERT: C 150 ARG cc_start: 0.7346 (ttt180) cc_final: 0.6734 (mtm180) REVERT: C 261 LYS cc_start: 0.8504 (ttmm) cc_final: 0.8185 (tptp) REVERT: C 399 ASP cc_start: 0.8142 (t70) cc_final: 0.7864 (m-30) REVERT: C 415 LYS cc_start: 0.8658 (tttt) cc_final: 0.8283 (tttp) REVERT: C 432 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6653 (mp0) REVERT: D 309 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7443 (m-30) REVERT: D 465 ASN cc_start: 0.8384 (m-40) cc_final: 0.7782 (p0) outliers start: 39 outliers final: 20 residues processed: 153 average time/residue: 0.5819 time to fit residues: 97.5426 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 : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 LEU 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 435 GLU Chi-restraints excluded: chain B residue 92 CYS 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 369 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 343 GLU 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 309 ASP Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 78 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 HIS B 147 ASN B 391 GLN B 465 ASN D 273 GLN D 347 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.128302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.102845 restraints weight = 12837.375| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.68 r_work: 0.3071 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13100 Z= 0.225 Angle : 0.808 11.851 17896 Z= 0.385 Chirality : 0.052 0.360 2100 Planarity : 0.004 0.044 2196 Dihedral : 11.792 101.621 2896 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.20), residues: 1540 helix: -0.46 (0.94), residues: 24 sheet: 0.13 (0.21), residues: 584 loop : -0.71 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 150 TYR 0.016 0.002 TYR B 121 PHE 0.014 0.002 PHE A 354 TRP 0.018 0.002 TRP C 178 HIS 0.004 0.001 HIS C 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.22 (13004) covalent geometry : angle 0.72430 / 0.37 (17644) SS BOND : bond 0.00417 / 0.27 ( 36) SS BOND : angle 1.23395 / 0.88 ( 72) hydrogen bonds : bond 0.04647 / 3.21 ( 367) hydrogen bonds : angle 7.13779 / 4.87 ( 1026) link_ALPHA1-2 : bond 0.01467 / 0.75 ( 4) link_ALPHA1-2 : angle 2.16192 / 1.15 ( 12) link_ALPHA1-3 : bond 0.00452 / 0.25 ( 8) link_ALPHA1-3 : angle 4.91781 / 2.75 ( 24) link_ALPHA1-6 : bond 0.00413 / 0.20 ( 4) link_ALPHA1-6 : angle 1.75186 / 0.95 ( 12) link_BETA1-4 : bond 0.01029 / 0.64 ( 20) link_BETA1-4 : angle 3.46783 / 2.21 ( 60) link_NAG-ASN : bond 0.00423 / 0.24 ( 24) link_NAG-ASN : angle 3.55603 / 2.43 ( 72) *********************** 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 160 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8108 (m-30) cc_final: 0.7727 (m-30) REVERT: A 304 ASP cc_start: 0.8098 (m-30) cc_final: 0.7875 (m-30) REVERT: A 381 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7382 (mp0) REVERT: A 415 LYS cc_start: 0.8552 (tttp) cc_final: 0.7494 (mtmt) REVERT: B 128 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8301 (pttm) REVERT: B 416 SER cc_start: 0.7508 (p) cc_final: 0.7287 (m) REVERT: C 150 ARG cc_start: 0.7363 (ttt180) cc_final: 0.6759 (mtm180) REVERT: C 261 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8224 (tptp) REVERT: C 399 ASP cc_start: 0.8181 (t70) cc_final: 0.7962 (m-30) REVERT: C 415 LYS cc_start: 0.8659 (tttt) cc_final: 0.8299 (tttp) REVERT: C 432 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6555 (mp0) REVERT: D 308 LYS cc_start: 0.7808 (mtmt) cc_final: 0.7555 (mttm) REVERT: D 309 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7375 (m-30) REVERT: D 465 ASN cc_start: 0.8371 (m-40) cc_final: 0.7762 (p0) outliers start: 30 outliers final: 18 residues processed: 150 average time/residue: 0.5263 time to fit residues: 86.4824 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 : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 LEU 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 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 83 GLU Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 68 optimal weight: 0.2980 chunk 136 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 94 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 122 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 HIS ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN D 273 GLN 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 = 0.3602 r_free = 0.3602 target = 0.134974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.110523 restraints weight = 12727.187| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.59 r_work: 0.3192 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13100 Z= 0.135 Angle : 0.779 20.753 17896 Z= 0.361 Chirality : 0.063 1.675 2100 Planarity : 0.004 0.044 2196 Dihedral : 11.268 97.840 2896 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.62 % Rotamer: Outliers : 1.48 % Allowed : 18.86 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.20), residues: 1540 helix: 0.19 (0.94), residues: 28 sheet: 0.03 (0.22), residues: 556 loop : -0.68 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 85 TYR 0.014 0.002 TYR D 121 PHE 0.013 0.002 PHE D 410 TRP 0.014 0.001 TRP B 115 HIS 0.004 0.001 HIS B 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (13004) covalent geometry : angle 0.70049 / 0.34 (17644) SS BOND : bond 0.00261 / 0.18 ( 36) SS BOND : angle 0.81825 / 0.60 ( 72) hydrogen bonds : bond 0.03706 / 2.57 ( 367) hydrogen bonds : angle 6.82055 / 4.64 ( 1026) link_ALPHA1-2 : bond 0.01413 / 0.73 ( 4) link_ALPHA1-2 : angle 2.12392 / 1.13 ( 12) link_ALPHA1-3 : bond 0.00506 / 0.28 ( 8) link_ALPHA1-3 : angle 4.65469 / 2.63 ( 24) link_ALPHA1-6 : bond 0.00608 / 0.30 ( 4) link_ALPHA1-6 : angle 1.21310 / 0.66 ( 12) link_BETA1-4 : bond 0.01086 / 0.67 ( 20) link_BETA1-4 : angle 3.19753 / 2.06 ( 60) link_NAG-ASN : bond 0.00243 / 0.16 ( 24) link_NAG-ASN : angle 3.61355 / 2.41 ( 72) *********************** 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 148 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7948 (m-30) cc_final: 0.7638 (m-30) REVERT: A 304 ASP cc_start: 0.8112 (m-30) cc_final: 0.7884 (m-30) REVERT: A 381 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7464 (mp0) REVERT: A 415 LYS cc_start: 0.8492 (tttp) cc_final: 0.7533 (mtmt) REVERT: B 128 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8227 (pttm) REVERT: C 150 ARG cc_start: 0.7260 (ttt180) cc_final: 0.6780 (mtm180) REVERT: C 261 LYS cc_start: 0.8448 (ttmm) cc_final: 0.8119 (tptp) REVERT: C 415 LYS cc_start: 0.8697 (tttt) cc_final: 0.8370 (tttp) REVERT: C 432 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6507 (mp0) REVERT: D 309 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7243 (m-30) REVERT: D 465 ASN cc_start: 0.8373 (m-40) cc_final: 0.7831 (p0) outliers start: 20 outliers final: 11 residues processed: 143 average time/residue: 0.5393 time to fit residues: 84.2025 Evaluate side-chains 136 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 LEU 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 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 183 CYS Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 314 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 47 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 139 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 GLN A 336 HIS B 147 ASN B 358 ASN ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN D 273 GLN D 347 HIS D 391 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.100748 restraints weight = 12880.040| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.68 r_work: 0.3039 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 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 : 0.007 0.074 13100 Z= 0.339 Angle : 0.910 12.742 17896 Z= 0.436 Chirality : 0.061 1.111 2100 Planarity : 0.005 0.046 2196 Dihedral : 11.997 97.755 2896 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.70 % Favored : 96.23 % Rotamer: Outliers : 2.60 % Allowed : 17.52 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.20), residues: 1540 helix: -0.60 (0.90), residues: 24 sheet: 0.06 (0.21), residues: 584 loop : -0.79 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 150 TYR 0.016 0.003 TYR B 121 PHE 0.019 0.003 PHE A 410 TRP 0.021 0.003 TRP A 87 HIS 0.005 0.001 HIS D 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00749 / 0.34 (13004) covalent geometry : angle 0.81948 / 0.42 (17644) SS BOND : bond 0.00560 / 0.35 ( 36) SS BOND : angle 1.57667 / 1.11 ( 72) hydrogen bonds : bond 0.05213 / 3.61 ( 367) hydrogen bonds : angle 7.26775 / 4.94 ( 1026) link_ALPHA1-2 : bond 0.01633 / 0.83 ( 4) link_ALPHA1-2 : angle 2.43099 / 1.30 ( 12) link_ALPHA1-3 : bond 0.00480 / 0.25 ( 8) link_ALPHA1-3 : angle 5.10187 / 2.84 ( 24) link_ALPHA1-6 : bond 0.00394 / 0.19 ( 4) link_ALPHA1-6 : angle 2.25392 / 1.20 ( 12) link_BETA1-4 : bond 0.00999 / 0.63 ( 20) link_BETA1-4 : angle 3.64815 / 2.32 ( 60) link_NAG-ASN : bond 0.00655 / 0.37 ( 24) link_NAG-ASN : angle 4.14062 / 2.89 ( 72) *********************** 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 155 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8190 (m-30) cc_final: 0.7866 (m-30) REVERT: A 381 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7427 (mm-30) REVERT: A 415 LYS cc_start: 0.8595 (tttp) cc_final: 0.7509 (mtmt) REVERT: B 128 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8370 (pttm) REVERT: B 416 SER cc_start: 0.7734 (p) cc_final: 0.7484 (m) REVERT: C 150 ARG cc_start: 0.7418 (ttt180) cc_final: 0.6787 (mtm180) REVERT: C 261 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8206 (tptp) REVERT: C 415 LYS cc_start: 0.8696 (tttt) cc_final: 0.8315 (tttp) REVERT: C 432 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: D 308 LYS cc_start: 0.7812 (mtmt) cc_final: 0.7498 (mtpt) REVERT: D 309 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7424 (m-30) REVERT: D 465 ASN cc_start: 0.8394 (m-40) cc_final: 0.7836 (p0) outliers start: 35 outliers final: 21 residues processed: 142 average time/residue: 0.5596 time to fit residues: 87.4310 Evaluate side-chains 141 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 LEU 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 A residue 443 ILE Chi-restraints excluded: chain B residue 92 CYS 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 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 307 ILE Chi-restraints excluded: chain D residue 309 ASP 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 57 optimal weight: 0.0030 chunk 117 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 128 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3584 r_free = 0.3584 target = 0.133611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.109036 restraints weight = 12790.228| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.60 r_work: 0.3170 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13100 Z= 0.146 Angle : 0.746 10.992 17896 Z= 0.352 Chirality : 0.052 0.775 2100 Planarity : 0.003 0.045 2196 Dihedral : 11.245 93.729 2896 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.62 % Rotamer: Outliers : 1.86 % Allowed : 18.56 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.20), residues: 1540 helix: -0.05 (0.89), residues: 28 sheet: 0.02 (0.22), residues: 556 loop : -0.72 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 150 TYR 0.014 0.002 TYR D 121 PHE 0.015 0.002 PHE A 410 TRP 0.023 0.002 TRP A 87 HIS 0.003 0.001 HIS B 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (13004) covalent geometry : angle 0.67197 / 0.34 (17644) SS BOND : bond 0.00288 / 0.19 ( 36) SS BOND : angle 0.92204 / 0.68 ( 72) hydrogen bonds : bond 0.03908 / 2.71 ( 367) hydrogen bonds : angle 6.82837 / 4.63 ( 1026) link_ALPHA1-2 : bond 0.01437 / 0.74 ( 4) link_ALPHA1-2 : angle 2.19542 / 1.18 ( 12) link_ALPHA1-3 : bond 0.00483 / 0.27 ( 8) link_ALPHA1-3 : angle 4.67971 / 2.65 ( 24) link_ALPHA1-6 : bond 0.00464 / 0.23 ( 4) link_ALPHA1-6 : angle 1.33227 / 0.72 ( 12) link_BETA1-4 : bond 0.01054 / 0.65 ( 20) link_BETA1-4 : angle 3.17399 / 2.04 ( 60) link_NAG-ASN : bond 0.00273 / 0.16 ( 24) link_NAG-ASN : angle 3.16688 / 2.21 ( 72) *********************** 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 149 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7995 (m-30) cc_final: 0.7664 (m-30) REVERT: A 381 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7454 (mp0) REVERT: A 415 LYS cc_start: 0.8548 (tttp) cc_final: 0.7556 (mtmt) REVERT: B 128 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8282 (ptpp) REVERT: C 150 ARG cc_start: 0.7318 (ttt180) cc_final: 0.6799 (mtm180) REVERT: C 261 LYS cc_start: 0.8421 (ttmm) cc_final: 0.8074 (tptp) REVERT: C 328 LYS cc_start: 0.8018 (mtpp) cc_final: 0.7809 (mtmt) REVERT: C 415 LYS cc_start: 0.8755 (tttt) cc_final: 0.8471 (tttp) REVERT: C 432 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6437 (mp0) REVERT: D 309 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7213 (m-30) REVERT: D 375 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8188 (pt0) REVERT: D 465 ASN cc_start: 0.8382 (m-40) cc_final: 0.7852 (p0) outliers start: 25 outliers final: 15 residues processed: 144 average time/residue: 0.5861 time to fit residues: 92.1080 Evaluate side-chains 138 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 LEU 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 221 ASP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 83 GLU 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 309 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 147 ASN ** 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 = 0.3534 r_free = 0.3534 target = 0.129281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.104450 restraints weight = 12856.100| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.59 r_work: 0.3104 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 13100 Z= 0.290 Angle : 0.867 12.173 17896 Z= 0.416 Chirality : 0.056 0.732 2100 Planarity : 0.005 0.045 2196 Dihedral : 11.784 93.319 2896 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.09 % Favored : 95.84 % Rotamer: Outliers : 2.38 % Allowed : 18.04 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.20), residues: 1540 helix: -0.58 (0.90), residues: 24 sheet: 0.06 (0.21), residues: 584 loop : -0.75 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 150 TYR 0.016 0.003 TYR B 121 PHE 0.020 0.003 PHE A 410 TRP 0.018 0.002 TRP C 178 HIS 0.004 0.001 HIS D 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.29 (13004) covalent geometry : angle 0.78120 / 0.40 (17644) SS BOND : bond 0.00501 / 0.31 ( 36) SS BOND : angle 1.52319 / 1.05 ( 72) hydrogen bonds : bond 0.04931 / 3.41 ( 367) hydrogen bonds : angle 7.18990 / 4.88 ( 1026) link_ALPHA1-2 : bond 0.01638 / 0.84 ( 4) link_ALPHA1-2 : angle 2.45686 / 1.32 ( 12) link_ALPHA1-3 : bond 0.00428 / 0.23 ( 8) link_ALPHA1-3 : angle 4.95762 / 2.78 ( 24) link_ALPHA1-6 : bond 0.00388 / 0.19 ( 4) link_ALPHA1-6 : angle 1.93565 / 1.03 ( 12) link_BETA1-4 : bond 0.01006 / 0.63 ( 20) link_BETA1-4 : angle 3.56989 / 2.27 ( 60) link_NAG-ASN : bond 0.00564 / 0.33 ( 24) link_NAG-ASN : angle 3.78563 / 2.72 ( 72) *********************** 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 150 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8165 (m-30) cc_final: 0.7867 (m-30) REVERT: A 381 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7510 (mm-30) REVERT: A 415 LYS cc_start: 0.8556 (tttp) cc_final: 0.7543 (mtmt) REVERT: B 128 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8397 (pttm) REVERT: B 416 SER cc_start: 0.7574 (p) cc_final: 0.7361 (m) REVERT: C 150 ARG cc_start: 0.7438 (ttt180) cc_final: 0.6836 (mtm180) REVERT: C 261 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8268 (tptp) REVERT: C 415 LYS cc_start: 0.8767 (tttt) cc_final: 0.8395 (tttp) REVERT: C 432 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: D 308 LYS cc_start: 0.7853 (mtmt) cc_final: 0.7569 (mtpt) REVERT: D 309 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7288 (m-30) REVERT: D 375 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8327 (pt0) REVERT: D 465 ASN cc_start: 0.8392 (m-40) cc_final: 0.7951 (p0) outliers start: 32 outliers final: 18 residues processed: 140 average time/residue: 0.5673 time to fit residues: 86.9156 Evaluate side-chains 137 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 LEU 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 435 GLU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 128 LYS 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 C residue 83 GLU 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 307 ILE Chi-restraints excluded: chain D residue 309 ASP 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 37 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 147 ASN ** 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 = 0.3578 r_free = 0.3578 target = 0.132977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.108370 restraints weight = 12844.770| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.59 r_work: 0.3161 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13100 Z= 0.157 Angle : 0.755 11.039 17896 Z= 0.360 Chirality : 0.051 0.562 2100 Planarity : 0.004 0.045 2196 Dihedral : 11.234 90.053 2896 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.63 % Allowed : 19.08 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.20), residues: 1540 helix: -0.14 (0.87), residues: 28 sheet: 0.13 (0.21), residues: 584 loop : -0.71 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 150 TYR 0.013 0.002 TYR B 121 PHE 0.015 0.002 PHE A 410 TRP 0.017 0.002 TRP A 87 HIS 0.003 0.001 HIS B 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (13004) covalent geometry : angle 0.68236 / 0.34 (17644) SS BOND : bond 0.00320 / 0.21 ( 36) SS BOND : angle 1.16983 / 0.79 ( 72) hydrogen bonds : bond 0.04022 / 2.79 ( 367) hydrogen bonds : angle 6.84153 / 4.64 ( 1026) link_ALPHA1-2 : bond 0.01477 / 0.76 ( 4) link_ALPHA1-2 : angle 2.27837 / 1.22 ( 12) link_ALPHA1-3 : bond 0.00460 / 0.26 ( 8) link_ALPHA1-3 : angle 4.68480 / 2.66 ( 24) link_ALPHA1-6 : bond 0.00436 / 0.22 ( 4) link_ALPHA1-6 : angle 1.38226 / 0.74 ( 12) link_BETA1-4 : bond 0.01032 / 0.64 ( 20) link_BETA1-4 : angle 3.17976 / 2.05 ( 60) link_NAG-ASN : bond 0.00308 / 0.17 ( 24) link_NAG-ASN : angle 3.06543 / 2.22 ( 72) ********************** 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 142 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8038 (m-30) cc_final: 0.7695 (m-30) REVERT: A 381 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7448 (mp0) REVERT: A 415 LYS cc_start: 0.8529 (tttp) cc_final: 0.7535 (mtmt) REVERT: B 128 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8328 (pttm) REVERT: C 150 ARG cc_start: 0.7341 (ttt180) cc_final: 0.6803 (mtm180) REVERT: C 261 LYS cc_start: 0.8460 (ttmm) cc_final: 0.8195 (tptp) REVERT: C 328 LYS cc_start: 0.8047 (mtpp) cc_final: 0.7832 (mtmt) REVERT: C 415 LYS cc_start: 0.8751 (tttt) cc_final: 0.8470 (tttp) REVERT: C 432 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6463 (mp0) REVERT: D 309 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7218 (m-30) REVERT: D 375 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8186 (pt0) REVERT: D 465 ASN cc_start: 0.8368 (m-40) cc_final: 0.7856 (p0) outliers start: 22 outliers final: 13 residues processed: 136 average time/residue: 0.6020 time to fit residues: 89.3241 Evaluate side-chains 132 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 LEU 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 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 C residue 83 GLU 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 309 ASP 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 104 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 70 optimal weight: 0.0970 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 GLN B 147 ASN ** 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 = 0.3646 r_free = 0.3646 target = 0.137903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.115248 restraints weight = 13468.210| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.50 r_work: 0.3264 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13100 Z= 0.157 Angle : 0.741 10.689 17896 Z= 0.353 Chirality : 0.050 0.429 2100 Planarity : 0.004 0.046 2196 Dihedral : 10.998 86.495 2896 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.41 % Allowed : 19.45 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1540 helix: 0.04 (0.89), residues: 28 sheet: 0.15 (0.21), residues: 584 loop : -0.68 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 150 TYR 0.014 0.002 TYR D 121 PHE 0.016 0.002 PHE A 410 TRP 0.016 0.002 TRP C 178 HIS 0.003 0.001 HIS B 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (13004) covalent geometry : angle 0.67093 / 0.34 (17644) SS BOND : bond 0.00328 / 0.21 ( 36) SS BOND : angle 1.08457 / 0.73 ( 72) hydrogen bonds : bond 0.03925 / 2.71 ( 367) hydrogen bonds : angle 6.75934 / 4.58 ( 1026) link_ALPHA1-2 : bond 0.01517 / 0.78 ( 4) link_ALPHA1-2 : angle 2.39348 / 1.28 ( 12) link_ALPHA1-3 : bond 0.00413 / 0.23 ( 8) link_ALPHA1-3 : angle 4.61027 / 2.62 ( 24) link_ALPHA1-6 : bond 0.00474 / 0.24 ( 4) link_ALPHA1-6 : angle 1.39605 / 0.75 ( 12) link_BETA1-4 : bond 0.01030 / 0.64 ( 20) link_BETA1-4 : angle 3.18052 / 2.05 ( 60) link_NAG-ASN : bond 0.00394 / 0.24 ( 24) link_NAG-ASN : angle 2.85862 / 2.02 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3864.73 seconds wall clock time: 67 minutes 7.19 seconds (4027.19 seconds total)